Detection and treatment of propionibacterium acnes bacteria related diseases

Abstract

The present invention relates to a method for treating or preventing a disease associated with a Propionibacterium acnes bacterium in a subject, said method comprising modulating, in particular reducing, the ratio of the amount of a newly identified class of Propionibacterium acnes bacterium, referred to as type alpha, to the amount of a newly identified class of Propionibacterium acnes bacterium, referred to as type #, in said subject, alpha type classes effectively define acne-related strains, and # type classes define non-acne-related strains.

Description

Technical Field

[0001] This invention relates to Propionibacterium acnes for use in treating subjects. C. acnes Bacterial-related diseases, particularly acne treatments for subjects, especially methods for treating acne vulgaris. Background Technology

[0002] Propionibacterium acnes is a major commensal bacterium in the skin microbiome, representing the most abundant bacteria in hair follicles. While it plays an important role in maintaining skin health, it is also associated with a variety of diseases and infections, including acne vulgaris (Brüggemann et al. (2021) Front Microbiol. 12:673845) or progressive macular hypopigmentation (McDowell et al. (2021) J. Eur. Acad. Dermatol. Venereol. 35:338-344).

[0003] Acne vulgaris is a chronic inflammatory condition of the hair follicles, and Propionibacterium acnes has been described as one of its causative factors. In fact, previous studies have shown that (i) the efficacy of antimicrobial treatments is associated with a reduction in Propionibacterium acnes burden (Lessin et al. (2020) Skin Microbiome Handbook: From Basic Research to Product Development, edited by Nava Dayan, pp. 289-302); (ii) isotretinoin (the most effective drug available to date for treating acne) leads to a reduction in Propionibacterium acnes burden (Oprica et al. (2007) Acta Derm Venerol 87:246-254; Nolan et al. (2023) Exp. Dermatol. 32:955-964; McCoy et al. (2019) JInvest. Dermatol. 139:732-735; Kelhälä et al. (2017) Exp. Dermatol. 27:30-36); (iii) Antibiotic ineffectiveness is associated with the presence of antibiotic-resistant strains of Propionibacterium acnes (Simonart et al. (2005) British J. Dermatol. 153:395-403); (iv) Propionibacterium acnes triggers acne-like inflammation in different in vitro models (Laclaverie et al. (2021) Exp. Dermatol. 30:347-357) and in vivo models (Kolar et al. (2019) JCIInsight 4(5):e124687); and (v) patients with acne vulgaris have antibodies against Propionibacterium acnes (Wang et al. (2018) J. Invest. Dermatol. 138:2355-2364; Huang et al. (2021) Front. Microbiol. 12:709562).

[0004] Since Propionibacterium acnes also plays an important role in maintaining skin health, it is crucial to identify those Propionibacterium acnes types involved in inflammatory conditions (such as acne vulgaris) and to differentiate them from those types associated with non-inflammatory conditions.

[0005] Different studies have attempted to achieve this identification, but with limited success. In 2013, Fitz-Gibbon et al. compared the skin microbiome at both the strain and genomic levels of *Propionibacterium acnes* between acne patients and healthy individuals. They showed significant enrichment of specific *Propionibacterium acnes* ribosomal types (i.e., RT4, RT5, RT8, and RT10 ribosomal types) in acne patients and significant enrichment of another specific *Propionibacterium acnes* ribosomal type (i.e., RT6 ribosomal type) in healthy subjects (Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152-2160). However, not all acne patients showed a clear presence of *Propionibacterium acnes* bacteria belonging to acne-associated ribosomal types. Therefore, the distinction between different *Propionibacterium acnes* ribosomal types is not a reliable method for identifying acne-associated *Propionibacterium acnes* bacteria.

[0006] Based on whole-genome sequencing of *Propionibacterium acnes* clones belonging to different ribosomal subtypes, Fitz-Gibbon et al. also demonstrated that three loci (designated by the authors as loci 1, 2, and 3) are specific for the ribosomal subtypes RT4 and RT5, which are enriched in acne patients (Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152-2160). However, the presence of these loci cannot specifically identify acne-associated strains because *Propionibacterium acnes* strains belonging to the RT8 ribosomal subtype (which are enriched in acne patients) are not enriched in these three loci, and *Propionibacterium acnes* strains belonging to the RT1 ribosomal subtype (which are enriched in both acne patients and healthy subjects) can carry loci 1, 2, and 3.

[0007] Subsequently, metagenomic profiling of acne-associated follicular plugs in the same laboratory was performed, showing that RT4, RT5, and RT8 ribosomal typing was more abundant and prevalent in acne patients, while RT2 and RT6 ribosomal typing was more abundant and prevalent in healthy subjects, with enrichment of specific genes contained in previously identified loci 1, 2, and 3 (Barnard et al. (2016) Scientific Reports 6:39491). However, most acne metagenomic samples did not carry loci 1, 2, and 3, and conversely, some healthy metagenomic samples carried loci 1 or 3. This confirms that ribosomal typing and loci 1, 2, and 3 are not suitable for effective identification of acne-associated strains.

[0008] Other different typing methods have been used to attempt to distinguish acne-associated and non-acne-associated strains, including multi-locus sequence typing (MLST), single-locus sequence typing (SLST), the Belfast protocol using 7 target genes, multiplex landing PCR, the Aarhus protocol using 9 target genes, typing based on MALDI-TOF MS, and MLVA typing using 13 VNTR polymorphisms. However, the types defined by these methods are inconsistent when compared with each other, and none of them can clearly and effectively identify acne-associated strains (Mayslich et al. (2021) Microorganisms 9:203).

[0009] Therefore, there is an urgent need for tools that can clearly and effectively identify acne-associated strains, enabling specific targeting of these strains while keeping non-acne-associated strains alive and healthy.

[0010] Several studies have reported that acne-associated strains produce higher levels of certain porphyrins (primarily coprophyrin III) (Johnson et al. (2016) mSphere 1(1):e00023-15; Barnard et al. (2020) mSphere 5:e00793-19). Porphyrins are considered relevant because, when extracted from acne-associated strains, they show activation of inflammasomes, providing an explanation for the role of Propionibacterium acnes in inflammation (Spittaels et al. (2021) iScience 24:102575). Therefore, using differences in porphyrin production could be one way to distinguish acne-associated strains from non-acne-associated strains.

[0011] Enzymes involved in the porphyrin pathway are encoded by eight hem genes at a conserved locus among Propionibacterium acnes strains, and are shown in... Figure 5 In addition, Huiying Li's team reported the presence of a putative repressor from the deoR family (also known as glpR) near this locus in non-acne-associated strains (Johnson et al. (2016) mSphere 1(1):e00023-15; Barnard et al. (2020) mSphere 5:e00793-19), and therefore speculated that the deoR gene may be of interest in the diagnosis and / or treatment of acne vulgaris (WO2017 / 136738). However, as the authors emphasize, "due to the discovery deoR They expressed it in both high- and low-level porphyrin-producing strains, [and] attempted to determine... deoRAre there differences in the gene sequences that could explain the variations in regulation and porphyrin production among strains? (...) [However, they] did not identify any single nucleotide polymorphisms (SNPs) uniquely shared by strains from clades IB-3 and IC that could potentially explain the increased porphyrin production in these lineages (see Barnard et al. (2020) mSphere 5:e00793-19).

[0012] Therefore, there remains an urgent need for tools that can robustly and effectively identify acne-associated strains, enabling specific targeting of these strains while keeping non-acne-associated strains alive and healthy.

[0013] This invention fulfills this need. Summary of the Invention

[0014] This invention stems from an accidental discovery by the inventors that a set of 218 SNPs at the hem locus (containing genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) enabled the classification of known Propionibacterium acnes strain diversity into two groups, referred to herein as α-type and β-type. Importantly, unlike the deoR gene, this new typing is strictly correlated with the published porphyrin production levels, where α-type contains all Propionibacterium acnes strains that produce large amounts of porphyrin, while β-type contains all Propionibacterium acnes strains that produce small amounts of porphyrin or none at all. Furthermore, after developing a method for estimating the relative abundance of α- and β-type Propionibacterium acnes strains in shotgun metagenomic sequencing data and applying it to a publicly available dataset related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491), the inventors demonstrated that α-type Propionibacterium acnes strains form a significantly larger proportion of Propionibacterium acnes populations in patients with acne vulgaris compared to healthy subjects.

[0015] The present invention thus relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising adjusting, in particular reducing, the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

[0016] The present invention also relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising specifically reducing the amount of Propionibacterium acnes type α bacteria in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0017] The present invention also relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising genetically modifying the DNA sequence of Propionibacterium acnes type α in the subject to produce at least one change, preferably at least one change in the hem locus of the Propionibacterium acnes type α. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0018] The present invention also relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising increasing the amount of Propionibacterium acnes type β in the subject. Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes. Alpha-type Propionibacterium acnes is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0019] The present invention further relates to compositions for treating or preventing Propionibacterium acnes-related diseases in subjects, said compositions comprising a therapeutic or preventative agent that induces, preferably, a reduction in the ratio of α-type Propionibacterium acnes bacteria to β-type Propionibacterium acnes bacteria in said subjects. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

[0020] The present invention also relates to compositions for treating or preventing Propionibacterium acnes-related diseases in subjects, said compositions comprising a therapeutic or preventative agent that specifically reduces the amount of Propionibacterium acnes type α bacteria in said subjects. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0021] The present invention also relates to compositions for treating or preventing Propionibacterium acnes-related diseases in subjects, the compositions comprising a therapeutic or preventative agent that genetically modifies the DNA sequence of Propionibacterium acnes type α in the subject to produce at least one change, preferably at least one change in the hem locus of the Propionibacterium acnes type α. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0022] The present invention further relates to compositions for treating or preventing Propionibacterium acnes-related diseases in subjects, said compositions comprising a therapeutic or preventative agent that increases the amount of Propionibacterium acnes type β in said subjects. Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes. Alpha-type Propionibacterium acnes is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0023] The present invention also relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising specifically reducing the expression of at least one hem locus protein in Propionibacterium acnes type α in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0024] The present invention also relates to compositions for treating or preventing Propionibacterium acnes-related diseases in subjects, the compositions comprising a therapeutic or preventative agent that genetically modifies the DNA sequence of Propionibacterium acnes type α in the subject to produce at least one change, preferably at least one change in the hem locus of Propionibacterium acnes type α, to specifically reduce the expression of at least one hem locus protein in Propionibacterium acnes type α in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0025] Another object of the present invention relates to a pharmaceutical composition comprising a bacteriophage, a recombinant bacteriophage, a packaged phage particle, a plasmid, a vesicle containing DNA or RNA, an extracellular vesicle, bacteria, or engineered bacteria encoding a programmable nuclease or gene-editing enzyme or system specifically targeting *Propionibacterium acnes* bacteria. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

[0026] Another object of the present invention relates to a method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, the method comprising the steps of: a) Determine the presence and / or quantity of Propionibacterium acnes type α in the sample, wherein the Propionibacterium acnes type α is a Propionibacterium acnes bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1. and b) Based on the presence and / or amount determined in step a), determine whether the subject is at risk of developing acne, particularly acne vulgaris.

[0027] Another object of the present invention relates to a method for diagnosing acne, particularly acne vulgaris, in a subject, the method comprising the following steps: a) Determine the presence and / or quantity of Propionibacterium acnes type α in the sample, wherein the Propionibacterium acnes type α is a Propionibacterium acnes bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the positions are defined with reference to the sequence SEQ ID NO: 10. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1, and b) Diagnose the subject’s acne, particularly acne vulgaris, based on the presence and / or amount determined in step a). Detailed Implementation

[0028] Propionibacterium acnes type α and Propionibacterium acnes type β Propionibacterium acnes ( Cutibacterium acnes (Previously) Propionibacterium acnes *Actinomyces* is a Gram-positive, rod-shaped, aerobic bacterium, first isolated from the skin in 1897. It belongs to the order Actinomycetes (…). Actinomycetales ), belongs to the Propionibacterium family ( Propionibacteriaceae It is part of the genus Propionibacterium ( ) and belongs to the genus Propionibacter Cutibacterium Propionibacterium acnes is one of the most common and abundant bacteria on human skin, found both on the skin's surface (stratum corneum) and in hair follicles. Inside the hair follicle, it comes into direct contact with a diverse range of living cells, such as keratinocytes, stem cells, sebaceous cells, and immune cells, unlike its contact with dead keratinocytes in the stratum corneum. Propionibacterium acnes is a symbiotic bacterium, but it is also associated with several skin conditions, such as acne vulgaris or progressive hypopigmentation.

[0029] Propionibacterium acnes strains were previously classified into two main types (I and II) based on their cell wall carbohydrate content and serum agglutinin reactivity (Johnson et al. (1982) J Bacteriol. 109(3):1047-66). Subsequently, based on... RecA and tlyGenes and the use of QUBPa1 and QUBPa2 antibodies were used to identify these subclusters (McDowell et al. (2005) J Clin Microbiol. 43(1):326-334). Subsequently, additional phylogenetic types (type III) corresponding to strains with filamentous appendages were added to the classification (McDowell et al. (2008) J Medical Microbiol. 57:218-224). Multi-locus sequence typing (MLST) methods were also developed to improve typing resolution. The Belfast scheme based on 7 target genes distinguished type I into clades IA1, IA2, IB, and IC (McDowell et al. (2011) Microbiology157:1990-2003), while the Aarhus scheme based on 9 target genes distinguished type I into clades I-1a, I-1b, and I-2 (Lomholt et al. (2010) PLoS ONE 5(8):e12277). Then, SLST and whole-genome sequencing (WGS) technologies were used to develop new methods for classifying Propionibacterium acnes strains into SLST types (Scholz et al. (2014) PLoS ONE 9(8):e104199).

[0030] Mass spectrometry-based methods have also been used to characterize Propionibacterium acnes strains, and in the MALDI-MS prototype method, when associated with spectral analysis of ribosomal subunit proteins, it makes it possible to distinguish all the aforementioned phylogenetic types (Teramoto et al. (2019) Proc. Jpn. Acad. Ser. B 95:612-623).

[0031] Based on 16S rRNA gene analysis, Propionibacterium acnes strains were also classified into the ribosomal typing defined and cited in Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152-2160.

[0032] However, as Mayslich et al. have emphasized (Mayslich et al. (2021) Microorganisms 9:303), there is an urgent need for standardization among all the above nomenclatures, and as highlighted above, none of them enables a robust and effective distinction between acne-related strains and non-acne-related strains.

[0033] The inventors of this invention identified a set of 218 SNPs in the hem locus (containing genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY), which enables the classification of known Propionibacterium acnes strain diversity into two groups, referred to herein as α-type and β-type. Importantly, unlike the deoR gene, this new typing is strictly correlated with the published porphyrin production levels, where α-type contains all Propionibacterium acnes strains that produce large amounts of porphyrin, while β-type contains all Propionibacterium acnes strains that produce small amounts of porphyrin or none at all. Furthermore, after developing a method for estimating the relative abundance of α- and β-type Propionibacterium acnes strains in shotgun metagenomic sequencing data and applying it to a publicly available dataset related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491), the inventors demonstrated that α-type Propionibacterium acnes strains form a significantly larger proportion of Propionibacterium acnes populations in patients with acne vulgaris compared to healthy subjects.

[0034] The inventors thereby identified *Propionibacterium acnes* alpha type as *Propionibacterium acnes* bacteria in which at least 90% of the marker positions defined in Table 1 below have a nucleotide variation defined as “α variant”, wherein the positions are defined relative to the reference gene sequence SEQ ID NO: 3 for the hemA gene, relative to SEQ ID NO: 4 for the hemB gene, relative to SEQ ID NO: 5 for the hemC gene, relative to SEQ ID NO: 6 for the hemD gene, relative to SEQ ID NO: 7 for the hemE gene, relative to SEQ ID NO: 8 for the hemH gene, relative to SEQ ID NO: 9 for the hemL gene, and relative to SEQ ID NO: 10 for the hemY gene.

[0035] The values ​​indicated in the column titled "Reference Position (Based on 0)" are 0-based, meaning the first nucleotide in the gene sequence is indexed as 0. As will be readily understood by those skilled in the art, positions can alternatively be defined in a "1-based" manner, meaning the first nucleotide in the gene sequence is indexed as 1. In this case, all "0-based" defined positions would be incremented by 1. For example, the "0-based" defined position T173 in the hemA gene is the same as the "1-based" defined position T174 in the hemA gene. The values ​​indicated in the column titled "Reference Position (Based on 1)" are 1-based. In this document, unless otherwise specified, the values ​​of reference positions are 0-based.

[0036] Table 1: A set of reference locations for α / β types of the hem locus In the context of this invention, *Propionibacterium acnes* alpha-type is preferably a *Propionibacterium acnes* bacterium containing at least 90%, particularly at least 90.5%, at least 91%, at least 91.5%, at least 92%, at least 92.5%, at least 93%, at least 93.5%, at least 94%, at least 94.5%, at least 95%, at least 95.5%, at least 96%, at least 96.5%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5% or 100% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0037] Alternatively, the α-type Propionibacterium acnes bacteria may be Propionibacterium acnes bacteria containing at least 197, at least 198, at least 199, at least 200, at least 201, at least 202, at least 203, at least 204, at least 205, at least 206, at least 207, at least 208, at least 209, at least 210, at least 211, at least 212, at least 213, at least 214, at least 215, at least 216, at least 217 or all of the α-nucleotide variations as defined in Table 1.

[0038] Alternatively, using the "based on 1" definition, *Propionibacterium acnes* bacteria can be *Propionibacterium acnes* bacteria containing at least 90%, particularly at least 90.5%, at least 91%, at least 91.5%, at least 92%, at least 92.5%, at least 93%, at least 93.5%, at least 94%, at least 94.5%, at least 95%, at least 95.5%, at least 96%, at least 96.5%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, or 100% of the following nucleotide variations at the hem locus: - In the hemA gene: T174, A480, T507, A615, T630, C672, T972, A990, T1086, and T1095, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C143, A156, A177, A184, C225, C246, G249, T282, G312, C315, T347, C375, G378, C453, T627, C684, A694, A721, C739, C795, A921, T945, T993, G1023, and T1032, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G78, A97, C150, A234, T237, T256, A258, A261, C318, A348, T426, T438, A465, A487, A488, C489, A525, A546, A591, T606, A645, A666, C711, C714, A738, A771, A777, T786, T803, G831, C843, T846, G856, C894, A897, C898, G903, G909, A942, and A948, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T12, T42, T51, A151, T156, G160, G177, T258, C267, T279, G324, A325, T363, T368, T375, G388, A399, A400, T408, G423, G426, G433, A447, A460, T465, G596, T618, T644, A645, and C681, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T242, T477, A531, T705, A729, G768, T835, A868, A873, A883, and A958, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T12, T24, A49, T90, C189, G339, T465, T471, G537, T549, T609, G627, T633, T642, T672, T675, C684, C690, A741, G746, G788, A798, T894, A899, T1035, T1040, T1047, C1072, G1096, C1110, T1154, T1359, G1497, C1512, C1528, G1533, T1599, T1713, A1851, G1902, A1927, C1932, and C1998, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T108, C198, T230, A243, C311, A339, A375, T390, G393, T443, C468, G471, C483, G519, and C642, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A90, A237, A355, C384, C393, A396, T399, T466, T475, C522, T539, C567, A594, A768, T783, G864, G921, T928, A933, G936, C980, G990, C1020, T1056, G1092, T1137, G1144, G1153, T1167, T1173, A1177, T1185, C1200, C1206, G1269, G1279, T1296, T1319, A1337, G1344, C1347, G1356, T1360, and C1396, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0039] In this paper, "hem locus" refers to the locus included in the porphyrin biosynthesis locus of Propionibacterium acnes and containing eight hem genes (i.e., hemA, hemB, hemC, hemD, hemE, hemH, hemL and hemY genes).

[0040] Alternatively or further, in the context of this invention, *Propionibacterium acnes* type α is defined as a bacterium whose nucleic acid sequence at the hem locus (which comprises genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) shares at least 97% identity with sequence SEQ ID NO: 1, particularly at least 97.1%, at least 97.2%, at least 97.3%, at least 97.4%, at least 97.5%, at least 97.6%, at least 97.7%, at least 97.8%, at least 97.9%, at least 98%, at least 98.1%, at least 98.2%, at least 98.3%, at least 98.4%, and at least 98.5%. Propionibacterium acnes bacteria with at least 98.6% identity, at least 98.7% identity, at least 98.8% identity, at least 98.9% identity, at least 99% identity, at least 99.1% identity, at least 99.2% identity, at least 99.3% identity, at least 99.4% identity, at least 99.5% identity, at least 99.6% identity, at least 99.7% identity, at least 99.8% identity, at least 99.9% identity, or 100% identity.

[0041] Preferably, the α-type Propionibacterium acnes is Propionibacterium acnes. (i) It contains at least 90%, particularly at least 90.5%, at least 91%, at least 91.5%, at least 92%, at least 92.5%, at least 93%, at least 93.5%, at least 94%, at least 94.5%, at least 95%, at least 95.5%, at least 96%, at least 96.5%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5% or 100% of the α-nucleotide variations as defined in Table 1, or it contains at least 197, at least 198, at least 199, at least 200, at least 201, at least 202, at least 203, at least 204, at least 205, at least 206, at least 207, at least 208, at least 209, at least 210, at least 211, at least 212, at least 213, at least 214, at least 215, at least 216, at least 217 or all of the α-nucleotide variations as defined in Table 1, and (ii) The nucleic acid sequence of the hem locus has at least 97% identity with sequence SEQ ID NO: 1, particularly at least 97.1%, at least 97.2%, at least 97.3%, at least 97.4%, at least 97.5%, at least 97.6%, at least 97.7%, at least 97.8%, at least 97.9%, at least 98%, at least 98.1%, at least 98.2%, at least 98.3%, at least 98.4%, and at least 98.5% identity, at least 98.6% identity, at least 98.7% identity, at least 98.8% identity, at least 98.9% identity, at least 99% identity, at least 99.1% identity, at least 99.2% identity, at least 99.3% identity, at least 99.4% identity, at least 99.5% identity, at least 99.6% identity, at least 99.7% identity, at least 99.8% identity, at least 99.9% identity, or 100% identity.

[0042] In the context of this invention, β-type Propionibacterium acnes is a Propionibacterium acnes bacterium that is not α-type Propionibacterium acnes as defined above.

[0043] Preferably, the *Propionibacterium acnes* bacterium contains at least 90%, particularly at least 90.5%, at least 91%, at least 91.5%, at least 92%, at least 92.5%, at least 93%, at least 93.5%, at least 94%, at least 94.5%, at least 95%, at least 95.5%, at least 96%, at least 96.5%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, or 100% of the following nucleotide variations at the hem locus: - In the hemA gene: G173, G479, C506, G614, G629, A671, C971, G989, C1085, and C1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: T142, G155, G176, G183, T224, T245, A248, C281, A311, T314, C346, T374, T377, T452, C626, G683, G693, G720, T738, T794, C920, G944, C992, C1022, and C1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: A77, G96, G149, G233, C236, C255, G257, C260, T317, G347, C425, C437, G464, G486, G487, T488, G524, G545, G590, C605, G644, G665, T710, G713, G737, G770, G776, A785, C802, A830, T842, C845, A855, G893, T896, T897, A902, T908, G941, and G947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: C11, C41, C50, G150, C155, A159, T176, C257, T266, C278, C323, G324, C362, C367, C374, A387, G398, G399, C407, A422, A425, A432, G446, G459, C464, A595, C617, A643, G644, and T680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: C241, C476, G530, C704, G728, C767, A834, G867, G872, C882, and G957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: C11, C23, G48, C89, T188, A338, C464, C470, A536, C548, C608, A626, C632, C641, C671, C674, T683, T689, T740, A745, A787, G797, C893, T898, C1034, C1039, C1046, G1071, A1095, T1109, C1153, C1358, C1496, T1511, T1527, A1532, C1598, C1712, G1850, C1901, G1926, T1931, and T1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: C107, T197, A229, G242, A310, G338, G374, C389, T392, C442, T467, A470, T482, T518, and G641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: G89, G236, G354, T383, T392, G395, C398, C465, C474, T521, C538, T566, C593, C767, A782, A863, A920, A927, G932, A935, A979, C989, G1019, C1055, A1091, C1136, A1143, T1152, C1166, G1172, G1176, C1184, T1199, T1205, A1268, A1278, C1295, C1318, G1336, A1343, T1346, C1355, G1359, and G1395, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0044] Alternatively, using the "based on 1" definition, *Propionibacterium acnes* bacteria can be those containing at least 90%, particularly at least 90.5%, at least 91%, at least 91.5%, at least 92%, at least 92.5%, at least 93%, at least 93.5%, at least 94%, at least 94.5%, at least 95%, at least 95.5%, at least 96%, at least 96.5%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, or 100% of the following nucleotide variations at the hem locus: - In the hemA gene: G174, G480, C507, G615, G630, A672, C972, G990, C1086, and C1095, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: T143, G156, G177, G184, T225, T246, A249, C282, A312, T315, C347, T375, T378, T453, C627, G684, G694, G721, T739, T795, C921, G945, C993, C1023, and C1032, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: A78, G97, G150, G234, C237, C256, G258, C261, T318, G348, C426, C438, G465, G487, G488, T489, G525, G546, G591, C606, G645, G666, T711, G714, G738, G771, G777, A786, C803, A831, T843, C846, A856, G894, T897, T898, A903, T909, G942, and G948, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: C12, C42, C51, G151, C156, A160, T177, C258, T267, C279, C324, G325, C363, C368, C375, A388, G399, G400, C408, A423, A426, A433, G447, G460, C465, A596, C618, A644, G645, and T681, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: C242, C477, G531, C705, G729, C768, A835, G868, G873, C883, and G958, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: C12, C24, G49, C90, T189, A339, C465, C471, A537, C549, C609, A627, C633, C642, C672, C675, T684, T690, T741, A746, A788, G798, C894, T899, C1035, C1040, C1047, G1072, A1096, T1110, C1154, C1359, C1497, T1512, T1528, A1533, C1599, C1713, G1851, C1902, G1927, T1932, and T1998, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: C108, T198, A230, G243, A311, G339, G375, C390, T393, C443, T468, A471, T483, T519, and G642, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: G90, G237, G355, T384, T393, G396, C399, C466, C475, T522, C539, T567, C594, C768, A783, A864, A921, A928, G933, A936, A980, C990, G1020, C1056, A1092, C1137, A1144, T1153, C1167, G1173, G1177, C1185, T1200, T1206, A1269, A1279, C1296, C1319, G1337, A1344, T1347, C1356, G1360, and G1396, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0045] Alternatively, the β-type Propionibacterium acnes bacteria may be Propionibacterium acnes bacteria containing at least 197, at least 198, at least 199, at least 200, at least 201, at least 202, at least 203, at least 204, at least 205, at least 206, at least 207, at least 208, at least 209, at least 210, at least 211, at least 212, at least 213, at least 214, at least 215, at least 216, at least 217 or all of the β-nucleotide variations as defined in Table 1.

[0046] Alternatively or additionally, the bacteria *Propionibacterium acnes* type β-form preferably have a nucleic acid sequence of the hem locus (which contains genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) that shares at least 97% identity with sequence SEQ ID NO: 2, particularly at least 97.1%, at least 97.2%, at least 97.3%, at least 97.4%, at least 97.5%, at least 97.6%, at least 97.7%, at least 97.8%, at least 97.9%, at least 98%, at least 98.1%, at least 98.2%, at least 98.3%, at least 98.4%, and at least 98.5%. Propionibacterium acnes bacteria with at least 98.6% identity, at least 98.7% identity, at least 98.8% identity, at least 98.9% identity, at least 99% identity, at least 99.1% identity, at least 99.2% identity, at least 99.3% identity, at least 99.4% identity, at least 99.5% identity, at least 99.6% identity, at least 99.7% identity, at least 99.8% identity, at least 99.9% identity, or 100% identity.

[0047] Preferably, the β-type Propionibacterium acnes bacteria is Propionibacterium acnes. (i) It contains at least 90%, particularly at least 90.5%, at least 91%, at least 91.5%, at least 92%, at least 92.5%, at least 93%, at least 93.5%, at least 94%, at least 94.5%, at least 95%, at least 95.5%, at least 96%, at least 96.5%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5% or 100% of the β-nucleotide variations as defined in Table 1, or it contains at least 197, at least 198, at least 199, at least 200, at least 201, at least 202, at least 203, at least 204, at least 205, at least 206, at least 207, at least 208, at least 209, at least 210, at least 211, at least 212, at least 213, at least 214, at least 215, at least 216, at least 217 or all of the β-nucleotide variations as defined in Table 1, and (ii) The nucleic acid sequence of the hem locus has at least 97% identity with sequence SEQ ID NO: 2, particularly at least 97.1%, at least 97.2%, at least 97.3%, at least 97.4%, at least 97.5%, at least 97.6%, at least 97.7%, at least 97.8%, at least 97.9%, at least 98%, at least 98.1%, at least 98.2%, at least 98.3%, at least 98.4%, and at least 98.5% identity, at least 98.6% identity, at least 98.7% identity, at least 98.8% identity, at least 98.9% identity, at least 99% identity, at least 99.1% identity, at least 99.2% identity, at least 99.3% identity, at least 99.4% identity, at least 99.5% identity, at least 99.6% identity, at least 99.7% identity, at least 99.8% identity, at least 99.9% identity, or 100% identity.

[0048] As used herein, the “percentage of identity” between two sequences refers to the percentage of identical nucleotides or amino acids between the sequences obtained through the best alignment of the two sequences to be compared. As used herein, “best alignment” or “optimal alignment” means that the determined percentage of identity (see below) is the highest among the alignments. Sequence comparisons between two sequences are typically performed by comparing these sequences that have previously been aligned according to the best alignment; this comparison is performed on the comparison segments to identify and compare locally similar regions. Besides manual methods, optimal sequence alignment can be achieved using the global homology algorithm developed by Smith and Waterman (Smith and Waterman (1981) Ad. App. Math. 2:482), the local homology algorithm developed by Needleman and Wunsch (Needleman and Wunsch (1970) J. Mol. Biol 48:443), the similarity method developed by Pearson and Lipman (Pearson and Lipman (1988) Proc. Natl. Acd. Sci. USA 85:2444), computer software utilizing such algorithms (GAP, BESTFIT, BLAST P, BLAST N, FASTA, TFASTA, etc.), and the MUSCLE multiple alignment algorithm (Edgar (2004) Nucleic Acids Research 32:1792). For optimal local alignment, the Needleman-Wunsch algorithm is preferred. The identity percentage between two sequences is determined by comparing the two best-aligned sequences (sequences may contain additions or deletions relative to a reference sequence to obtain the best alignment between the two sequences). The identity percentage can be calculated by determining the number of identical positions between the two sequences, dividing that number by the total number of positions compared, and multiplying the result by 100 to obtain the identity percentage between the two sequences. Preferably, for the purposes of this document, the identity percentage value refers to the value generated using the pairwise sequence alignment program EMBOSSNeedle, which uses the Needleman-Wunsch algorithm to generate the best global alignment of the two sequences, where all search parameters are set to default values, i.e., score matrix = BLOSUM62 for protein sequences and DNAfull for DNA sequences, void open = 10, void extension = 0.5, terminal void penalty = false, terminal void open = 10, and terminal void extension = 0.5.

[0049] Methods for treating or preventing Propionibacterium acnes-related diseases This invention relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising adjusting the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in the subject. in Alpha-type Propionibacterium acnes is as defined in the section "Alpha-type Propionibacterium acnes and Beta-type Propionibacterium acnes" above, and The β-type Propionibacterium acnes bacteria are as defined in the section "α-type Propionibacterium acnes and β-type Propionibacterium acnes" above.

[0050] The present invention also relates to compositions for treating or preventing Propionibacterium acnes-related diseases in subjects, said compositions comprising a therapeutic or preventative agent that induces and regulates the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in said subjects. in Alpha-type Propionibacterium acnes is as defined in the section "Alpha-type Propionibacterium acnes and Beta-type Propionibacterium acnes" above, and The β-type Propionibacterium acnes bacteria are as defined in the section "α-type Propionibacterium acnes and β-type Propionibacterium acnes" above.

[0051] The present invention also relates to the use of therapeutic or preventive agents that induce and regulate the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in the manufacture of medicaments for the treatment or prevention of diseases related to Propionibacterium acnes bacteria. in Alpha-type Propionibacterium acnes is as defined in the section "Alpha-type Propionibacterium acnes and Beta-type Propionibacterium acnes" above, and The β-type Propionibacterium acnes bacteria are as defined in the section "α-type Propionibacterium acnes and β-type Propionibacterium acnes" above.

[0052] "Propionibacterium acnes-associated diseases" in this article refer to diseases caused by Propionibacterium acnes, particularly skin diseases, or diseases associated with the presence of Propionibacterium acnes, or diseases in which Propionibacterium acnes plays a negative role.

[0053] Examples of Propionibacterium acnes-related diseases include, but are not limited to, acne (such as acne vulgaris, acne paradoxica, acne conglobata, or systemic acne), keratitis, synovitis, acne pustulosis, hypertrophic osteitis (SAPHO) syndrome, endocarditis, medical implant biofilm infection, artificial joint infection, surgical wound infection, vascular graft infection, anaerobic arthritis, cardiovascular device-related infection (such as prosthetic valve endocarditis), intraocular implant infection, breast implant disease, sciatica, conjunctivitis, shunt-related and / or spinal hardware (spinal) infections. Central nervous system infections (CNS), shunt-related CNS infections, sarcoidosis, endophthalmitis, osteomyelitis, allergic alveolitis, rheumatoid arthritis, infectious arthritis, chronic juvenile arthritis, chronic destructive oligoarthritis, degenerative disc disease, dental infections, ulcerative colitis with high fever, brain abscess, subdural empyema, peritonitis, periodontitis, root canal infection, chronic sinusitis, folliculitis, corneal ulcer, prostatitis, chronic prostatitis, primary biliary cirrhosis, hidradenitis suppurativa, pulmonary vasculitis, atherosclerosis, prostate cancer, progressive macular hypopigmentation, eczema, psoriasis, seborrheic dermatitis, rosacea, lichen sclerosus, lichen planus, nodular prurigo, and chronic simple lichen.

[0054] In one particular implementation, the *Propionibacterium acnes* bacterial-associated disease is a *Propionibacterium acnes* bacterial-associated skin disease. Examples of *Propionibacterium acnes* bacterial-associated skin diseases include, but are not limited to, acne (such as acne vulgaris, acne paradoxica, acne conglobata, or systemic acne), surgical skin wound infections, folliculitis, eczema, psoriasis, seborrheic dermatitis, erythematous acne, lichen sclerosus, lichen planus, nodular prurigo, and chronic simple lichen simplex.

[0055] In one particular implementation, the *Propionibacterium acnes* bacterial-associated disease is a *Propionibacterium acnes* bacterial-associated inflammatory disease. Examples of *Propionibacterium acnes* bacterial-associated inflammatory diseases are well known to those skilled in the art and include, but are not limited to, acne (such as acne vulgaris, acne paradoxica, acne conglobata, or systemic acne), sarcoidosis, SAPHO syndrome, eczema, psoriasis, seborrheic dermatitis, erythematous acne, lichen sclerosus, lichen planus, nodular prurigo, and chronic simple lichen simplex.

[0056] Therefore, in a preferred embodiment, the Propionibacterium acnes-related diseases are selected from acne (such as acne vulgaris, acne paradoxica, acne conglobata, or systemic acne), sarcoidosis, SAPHO syndrome, eczema, psoriasis, seborrheic dermatitis, erythematous acne, lichen sclerosus, lichen planus, nodular prurigo, and chronic simple lichen.

[0057] In a more preferred embodiment, the Propionibacterium acnes bacterial-associated disease is acne, more particularly acne vulgaris.

[0058] As used in the context of this invention, acne vulgaris is a chronic inflammatory condition of the pilosebaceous unit. It affects almost everyone at some point in their lives, with 15 to 20% experiencing moderate to severe forms of acne. Acne can be classified as mild, moderate, or severe. Mild acne typically corresponds to the presence of fewer than 20 comedones and / or fewer than 15 inflammatory lesions and / or a total lesion count strictly below 30. Moderate acne typically corresponds to the presence of 20 to 100 comedones and / or 15 to 50 inflammatory lesions and / or a total lesion count of 30 to 125. Severe acne typically corresponds to the presence of more than 5 pseudocysts and / or more than 100 comedones and / or more than 50 inflammatory lesions.

[0059] In one particular implementation, the Propionibacterium acnes bacterial-associated disease is severe acne.

[0060] As used herein, the terms “treatment”, “treating,” etc., refer to achieving a desired pharmacological or physiological effect. This effect can be therapeutic in relation to a partial or complete cure of a disease or condition, or a symptom of a disease or condition, or an adverse effect attributable to a disease or condition. As used herein, “treatment” includes suppressing a disease, condition, or symptom, i.e., preventing its development; and alleviating a disease, condition, or symptom, i.e., causing the disease, condition, or symptom to subside.

[0061] When applied to acne, the term "treatment" includes, for example, reducing the number of acne lesions, sebum production, follicular keratinization, comedones, bacterial colonization of hair follicles, proliferation of Propionibacterium acnes, and / or inflammation. It further encompasses, for example, reducing the severity of the disease, such as reducing severe acne to moderate or mild acne, or moderate acne to mild acne.

[0062] As used herein, the terms “prevention,” “preventing,” etc., encompass preventing or reducing the likelihood or severity of disease onset. This includes preventative treatment for those at increased risk of developing such diseases. An increased risk indicates a higher-than-average risk that a subject will develop the disease, which can be determined, for example, through family history, testing for genes that predispose to developing the disease, or antibiotic treatment.

[0063] When applied to acne, the term "prevention" encompasses, for example, the fact of avoiding reaching a given acne severity state, such as avoiding severe acne, moderate acne, or mild acne.

[0064] In one particular embodiment of the invention, treatment and / or prevention of Propionibacterium acnes-related diseases are achieved by adjusting the ratio of the amount of Propionibacterium acnes type 1 as defined in the "Propionibacterium acnes type 1 and Propionibacterium acnes type 2" section above to the amount of Propionibacterium acnes type 2 as defined in the "Propionibacterium acnes type 1 and Propionibacterium acnes type 2" section above.

[0065] In this document, “amount” refers to a relative amount (e.g., relative to the entire bacterial population of a subject, particularly the dermal bacterial population, or relative to the entire Propionibacterium acnes population of a subject, particularly the dermal Propionibacterium acnes population) or an absolute amount (or concentration), which can be determined by any suitable technique known to those skilled in the art. Examples of techniques suitable for determining the amount of a given bacterial type include direct cell counting, indirect cell counting, PCR (including real-time and quantitative PCR), and shotgun metagenomic sequencing.

[0066] "Adjustment ratio" in this document refers to the increase or decrease in the ratio after the implementation of the method and / or the application of the treatment or prophylaxis, compared to the ratio before the implementation of the method and / or the application of the treatment or prophylaxis.

[0067] In one particular implementation, the adjustment of the ratio is statistically significant.

[0068] In a preferred embodiment, treatment and / or prevention of Propionibacterium acnes-related diseases, particularly Propionibacterium acnes-related inflammatory diseases, are achieved by reducing the ratio of the amount of Propionibacterium acnes type α as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β" section above to the amount of Propionibacterium acnes type β as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β" section above.

[0069] "Reduction in rate" in this document refers to the reduction in the rate after implementation of the method and / or application of the treatment or prophylaxis, compared to the rate before implementation of the method and / or application of the treatment or prophylaxis.

[0070] Preferably, the reduction in the ratio is statistically significant.

[0071] In one particular implementation, the aforementioned adjustment of the ratio, preferably a reduction, was observed after the first implementation of the method and / or one day after the first application of the therapeutic or preventive agent, particularly after the first implementation of the method and / or two, three, four, five, six, seven days, two weeks, three weeks, one month, two months, three months, four months, five months, six months, or one year after the first application of the therapeutic or preventive agent.

[0072] In one particular implementation, the adjustment of the ratio is preferably reduced to 1 day after the first implementation of the method and / or after the first application of the therapeutic or preventive agent (not necessarily at the same level), particularly for 2, 3, 4, 5, 6, 7 days, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year after the first implementation of the method and / or after the first application of the therapeutic or preventive agent.

[0073] In one particular implementation, the adjustment of the ratio is preferably reduced and maintained (not necessarily at the same level) throughout the entire period of implementation and / or application of the therapeutic or preventative agent.

[0074] Preferably, the ratio is the ratio of the amount of Propionibacterium acnes bacteria on the subject's skin as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β" section above to the amount of Propionibacterium acnes bacteria on the subject's skin as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β" section above.

[0075] According to the present invention, skin refers to the skin of the arms (especially the hands), legs (especially the feet), armpits, neck, chest, back, scalp, and / or face. In a preferred embodiment, the skin is the skin of the face, neck, chest, and / or back. In a more preferred embodiment, the skin is the skin of the face.

[0076] Specifically reduces the amount of Propionibacterium acnes type 1 bacteria. In one particular embodiment, the treatment or prevention method of the present invention includes specifically reducing, in particular on the skin of a subject, the amount of Propionibacterium alpha-acne as defined in the “Propionibacterium alpha-acne and Propionibacterium beta-acne” section above.

[0077] This invention therefore relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising specifically reducing the amount of Propionibacterium acnes type α bacteria in the subject, wherein Propionibacterium acnes type α bacteria are as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β bacteria" section above. It also relates to a composition for treating or preventing Propionibacterium acnes-related diseases in a subject, the composition comprising a therapeutic or preventive agent that specifically reduces the amount of Propionibacterium acnes type α bacteria in the subject, wherein Propionibacterium acnes type α bacteria are as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β bacteria" section above. Further, it relates to the use of a therapeutic or preventive agent that specifically reduces the amount of Propionibacterium acnes type α bacteria in a subject in the manufacture of a medicament for treating or preventing Propionibacterium acnes-related diseases, wherein Propionibacterium acnes type α bacteria are as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β bacteria" section above.

[0078] As used herein, the term “quantity” has the same meaning as disclosed in the “Methods for treating or preventing diseases associated with Propionibacterium acnes” section above.

[0079] "Specific reduction in the amount of Propionibacterium acnes type α" herein means, in the subject, particularly on the subject's skin, that the amount of Propionibacterium acnes type other than α, particularly Propionibacterium acnes type β, is not significantly reduced, and / or that the amount of other bacterial species is not significantly reduced in the subject, particularly on the subject's skin. Preferably, "specific reduction in the amount of Propionibacterium acnes type α" herein means, in the subject, particularly on the subject's skin, that the amount of Propionibacterium acnes type other than α, particularly Propionibacterium acnes type β, is not significantly reduced.

[0080] "Reduction in amount" in this document refers to a reduction in amount after the implementation of the method and / or after the application of the treatment or preventive agent, compared to the amount before the implementation of the method and / or the application of the treatment or preventive agent.

[0081] Preferably, the reduction in quantity is statistically significant.

[0082] In one particular implementation, the reduction in amount was observed one day after the first administration of the method and / or one day after the first application of the therapeutic or preventive agent, particularly two, three, four, five, six, seven days, two weeks, three weeks, or one month after the first administration of the method and / or the first application of the therapeutic or preventive agent.

[0083] In one particular implementation, the reduction in amount is maintained (not necessarily at the same level) for 1 day after the first implementation of the method and / or after the first application of the therapeutic or preventive agent, particularly for 2, 3, 4, 5, 6, 7 days, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or 1 year after the first implementation of the method and / or after the first application of the therapeutic or preventive agent.

[0084] In one particular implementation, the reduction in amount is maintained (not necessarily at the same level) throughout the entire period of implementing the method and / or applying the therapeutic or preventative agent.

[0085] In one particular embodiment, the treatment or prevention method of the present invention includes, in particular, the specific killing or inhibition of the growth of *Propionibacterium acnes* bacteria as defined in the above section “Alpha-type and Beta-type” on a subject’s skin.

[0086] This invention therefore relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising specifically killing or inhibiting the growth of *Propionibacterium acnes* type α bacteria in the subject, wherein *Propionibacterium acnes* type α bacteria are as defined in the "Propionibacterium acnes type α and *Propionibacterium acnes type β" section above. It also relates to compositions for treating or preventing *Propionibacterium acnes*-related diseases in a subject, the compositions comprising a therapeutic or preventive agent that specifically kills or inhibits the growth of *Propionibacterium acnes* type α bacteria in the subject, wherein *Propionibacterium acnes type α bacteria are as defined in the "Propionibacterium acnes type α and *Propionibacterium acnes type β" section above. Further, it relates to the use of a therapeutic or preventive agent that specifically kills or inhibits the growth of *Propionibacterium acnes type α bacteria in the manufacture of a medicament for treating or preventing *Propionibacterium acnes*-related diseases, wherein *Propionibacterium acnes type α bacteria are as defined in the "Propionibacterium acnes type α and *Propionibacterium acnes type β" section above.

[0087] In one particular implementation, the *Propionibacterium acnes* bacteria are killed at a level corresponding to a reduction of at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%, preferably at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%, compared to an untreated population or to the *Propionibacterium acnes* bacterial population in the subject before the implementation of the method and / or application of the therapeutic or preventative agent.

[0088] In a preferred embodiment, the *Propionibacterium acnes* bacteria are killed at a level corresponding to a reduction of at least 0.1 log, at least 0.2 log, at least 0.5 log, at least 1 log, preferably at least 2 log, more preferably at least 3 log, at least 4 log, or at least 5 log in the *Propionibacterium acnes* bacterial population of the subject before the implementation of the method and / or application of the therapeutic or preventative agent, compared to an untreated population or to the *Propionibacterium acnes* bacterial population of the subject before the implementation of the method and / or application of the therapeutic or preventative agent.

[0089] As used in this article, the term "log" refers to the common logarithm, which is the logarithm to base 10 (also expressed as log). 10 ).

[0090] "Specific killing of Propionibacterium acnes type α" herein means that other types of Propionibacterium acnes bacteria present in the subject, particularly on the subject's skin, besides type α, especially type β, and / or other bacterial species are not significantly killed, particularly at a level lower than that of Propionibacterium acnes type α by at least 1 log, at least 2 log, at least 3 log, or at least 4 log. Preferably, "specific killing of Propionibacterium acnes type α" herein means that other types of Propionibacterium acnes bacteria present in the subject, particularly on the subject's skin, besides type α, especially type β, are not significantly killed, particularly at a level lower than that of Propionibacterium acnes type α by at least 1 log, at least 2 log, at least 3 log, or at least 4 log. In some specific embodiments, "specific killing of Propionibacterium acnes type α" herein refers to the killing of Propionibacterium acnes bacteria of a type other than α, particularly Propionibacterium acnes type β, and / or other bacterial species, preferably Propionibacterium acnes type β, present in the subject, particularly on the subject's skin, and / or on the skin of the subject, in accordance with the method and / or application of the therapeutic or prophylactic agent. The killing of Propionibacterium acnes bacteria of a type other than α, particularly Propionibacterium acnes type β, and / or other bacterial species, preferably Propionibacterium acnes type β, is defined as a reduction of less than 20%, preferably less than 10%, in the subject's propionibacterium acnes bacteria population compared to an untreated population or compared to the population of Propionibacterium acnes bacteria of a type other than α, particularly Propionibacterium acnes type β, and / or other bacterial species, preferably Propionibacterium acnes type β, in the subject's skin, in accordance with the method and / or application of the therapeutic or prophylactic agent.

[0091] In one particular embodiment, the growth of the *Propionibacterium acnes* bacteria is inhibited to a level corresponding to a reduction of at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%, preferably at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%, compared to an untreated population or to the *Propionibacterium acnes* bacterial population in the subject prior to the implementation of the method and / or application of a therapeutic or preventative agent.

[0092] In a preferred embodiment, the growth of *Propionibacterium acnes* bacteria is inhibited at a level corresponding to a reduction of at least 0.1 log, at least 0.2 log, at least 0.5 log, at least 1 log, preferably at least 2 log, more preferably at least 3 log, at least 4 log, or at least 5 log compared to the untreated population or to the *Propionibacterium acnes* bacterial population in the subject before the implementation of the method and / or application of the therapeutic or preventative agent.

[0093] "Specific inhibition of the growth of Propionibacterium acnes type α" herein means that the growth of Propionibacterium acnes bacteria other than type α, particularly type β, and / or other bacterial species present in the subject, especially on the subject's skin, is not significantly inhibited, particularly at a level at least 1 log, at least 2 log, at least 3 log, or at least 4 log lower than that of Propionibacterium acnes type α. Preferably, "specific inhibition of the growth of Propionibacterium acnes type α" herein means that the growth of Propionibacterium acnes bacteria other than type α, particularly type β, present in the subject, particularly on the subject's skin, is not significantly inhibited, particularly at a level at least 1 log, at least 2 log, at least 3 log, or at least 4 log lower than that of Propionibacterium acnes type α. In some specific embodiments, “specific inhibition of the growth of Propionibacterium acnes type α” herein refers to the presence of another type of Propionibacterium acnes bacteria besides type α, particularly type β, and / or other bacterial species present in the subject, particularly on the subject’s skin, preferably type β growth of Propionibacterium acnes bacteria, corresponding to a reduction of less than 20%, preferably less than 10%, of the growth of Propionibacterium acnes bacteria compared to an untreated population or compared to the population of other types of Propionibacterium acnes bacteria besides type α, particularly type β, and / or other bacterial species, preferably type β, in the subject, particularly on the subject’s skin, before the implementation of the method and / or application of the therapeutic or prophylactic agent.

[0094] In one particular embodiment, the treatment or prevention method of the present invention includes administering to the subject a therapeutic or preventative amount of an antibacterial agent, bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria specifically targeting the α-Propionibacterium acnes bacteria as defined in the “α-Propionibacterium acnes and β-Propionibacterium acnes” section above.

[0095] Similarly, in specific embodiments of the use of the composition according to the invention or the therapeutic or preventative agent according to the invention, the therapeutic or preventative agent is an antibacterial agent, a bacteriophage, a recombinant bacteriophage, a packaged phage particle, a plasmid, a vesicle containing DNA or RNA, an extracellular vesicle, a bacterium, or engineered bacteria that specifically targets the *Propionibacterium acnes* bacteria as defined in the "Propionibacterium acnes type α and *Propionibacterium acnes type β" section above.

[0096] As used in this article, the term "therapeutic effective amount" refers to an amount of active agent that is non-toxic but sufficient to provide the desired therapeutic effect.

[0097] As used in this article, the term "preventive effective amount" refers to an amount of active agent that is non-toxic but sufficient to provide the desired preventive effect.

[0098] "Targeting the α-type Propionibacterium acnes bacteria" in this document means that the therapeutic or preventive agent can recognize, preferably specifically recognize, the α-type Propionibacterium acnes bacteria, and / or exert its activity against the α-type Propionibacterium acnes bacteria, preferably specifically exerting its activity.

[0099] "Specifically targeting the α-type Propionibacterium acnes" herein means that the therapeutic or preventative agent recognizes the α-type Propionibacterium acnes and / or exerts its activity against the α-type Propionibacterium acnes, but does not significantly recognize or exert its activity against other types of Propionibacterium acnes present in the subject, particularly on the subject's skin, other than the α-type, particularly the β-type Propionibacterium acnes, and / or other bacterial species, and / or exerts its activity against other types of Propionibacterium acnes present in the subject, particularly on the subject's skin, other than the α-type, particularly the β-type Propionibacterium acnes, and / or other bacterial species. Preferably, "specifically targeting the α-type Propionibacterium acnes" herein means that the therapeutic or preventative agent recognizes the α-type Propionibacterium acnes and / or exerts its activity against the α-type Propionibacterium acnes, but does not significantly recognize other types of Propionibacterium acnes present in the subject, particularly on the subject's skin, especially β-type Propionibacterium acnes and / or exerts its activity against other types of Propionibacterium acnes present in the subject, particularly on the subject's skin, especially β-type Propionibacterium acnes.

[0100] "Antibacterial agent" herein refers to a compound that inhibits or prevents bacterial growth, kills bacteria, or reduces the number of bacteria. The antimicrobial agent can typically be a small molecule, protein, peptide, or polypeptide, or a nucleic acid such as DNA or RNA. Examples of antimicrobial agents include antibiotics, bacteriocins, and endolysins. Thus, in a particular embodiment, the antimicrobial agent is an antibiotic, bacteriocin, and / or endolysin that specifically targets *Propionibacterium acnes* bacteria as defined in the "Propionibacterium acnes type α and *Propionibacterium acnes type β" section above.

[0101] In this paper, "bacteriocin" refers to a protein toxin produced by bacteria to kill or inhibit the growth of other bacteria. Bacteriocins are classified in several ways, including by producing strain, common resistance mechanism, and killing mechanism. Such bacteriocins from Gram-negative bacteria (e.g., microcin, coliform bacteriocins, and tailocin) and from Gram-positive bacteria (e.g., Group I, II, III, or IV bacteriocins) have been described.

[0102] In the context of this invention, the bacteriocin can be a wild-type bacteriocin or an engineered bacteriocin, particularly a bacteriocin mutant, variant, or chimeric form, which typically includes modifications and / or alterations to the amino acid sequence. Such alterations and / or modifications can include mutations (such as deletions, insertions and additions, substitutions, or combinations thereof) and / or chemical changes (e.g., biotinylation, acetylation, PEGylation, chemical changes to amino, thiol, or carboxyl groups) of amino acid residues. Such modified bacteriocins typically exhibit the cleavage activity of wild-type bacteriocins. However, the activity can be the same as, higher than, or lower than that of wild-type bacteriocins. The activity can be about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, or about 200% or even higher than the activity of wild-type bacteriocins. Activity can be measured by those skilled in the art using assays known in the art, such as plate lysis assays or liquid lysis assays, as described, for example, in Briers et al. (2007) J. Biochem. Biophys Methods 70:531-533 or Donovan et al. (2006) FEMS Microbiol Lett. 265:133-139. Alternatively, such modified bacteriocins can exhibit different lytic activities compared to wild-type bacteriocins, such as lytic activities with different specificities compared to wild-type bacteriocins.

[0103] In this article, "endolysin" or "lysozyme" refers to the enzymes that bacteriophages use at the end of their replication cycle to degrade the peptidoglycan of the bacterial host from within, leading to cell lysis and the release of progeny virions. These are typically β(1,4)-glycosylationases (lysozymes), transglycosylases, amidases, or endopeptidases.

[0104] In the context of this invention, the endolysin can be a wild-type endolysin or an engineered endolysin, particularly an endolysin mutant, variant, or chimeric form, which typically involves modifications and / or alterations to the amino acid sequence. Such modifications and / or alterations can include mutations (such as deletions, insertions and additions, substitutions, or combinations thereof) and / or chemical changes (e.g., biotinylation, acetylation, PEGylation, chemical changes to amino, SH, or carboxyl groups). Such modified endolysins typically exhibit the cleavage activity of wild-type endolysins. However, the activity can be the same as, higher than, or lower than that of wild-type endolysins. The activity can be about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, or about 200% or even higher than the activity of wild-type endolysins. Activity can be measured by those skilled in the art using assays known in the art, such as plate cleavage assays or liquid cleavage assays, as described, for example, in Briers et al. (2007) J. Biochem. Biophys Methods 70:531-533 or Donovan et al. (2006) FEMS Microbiol Lett. 265:133-139. Alternatively, such modified endosomalins can exhibit different cleavage activities compared to wild-type endosomalins, such as having different specific cleavage activities compared to wild-type endosomalins.

[0105] In this article, "phage" or "bacteriophage" refers to a bacterial virus. Phages are obligate intracellular parasites that multiply within bacteria by assimilating some or all of the host's biosynthetic mechanisms. Phages can exist inside bacteria as prophages whose genome is integrated into the bacterial chromosome or as phage-plasmids whose genome is part of an extrachromosomal plasmid (such phage-plasmids are disclosed, for example, in Ravin et al. (1999) Molecular Microbiology 34(5):980–994). Phages contain nucleic acids (i.e., a genome) and proteins and can be encapsulated by a lipid membrane. Depending on the phage, the nucleic acid genome can be DNA or RNA and can exist in a circular or linear form. The size of a phage genome varies depending on the phage. The simplest phages have genomes of only a few thousand nucleotides, while more complex phages can contain more than 100,000 nucleotides in their genomes, and in rare cases, more than 1,000,000 nucleotides. The number and amount of individual types of proteins in a bacteriophage particle will vary depending on the bacteriophage.

[0106] In the context of this invention, the terms "recombinant" and "engineered" are used interchangeably. "Recombinant" herein refers to nucleic acids, proteins, or microorganisms containing genetic material derived from a variety of different sources and / or obtained using molecular biology and / or synthetic biology tools, or nucleic acids, proteins, or microorganisms encoded by genetic material derived from a variety of different sources and / or obtained using molecular biology and / or synthetic biology tools. Therefore, in the context of this invention, "recombinant" nucleic acids, proteins, or microorganisms are not wild-type nucleic acids, proteins, or microorganisms.

[0107] As used herein, “recombinant phage” refers to a phage as defined above that has been modified at the protein and / or nucleic acid level. Therefore, in the context of this invention, “recombinant phage” is not a wild-type phage or a phage obtained through natural evolution, but rather a phage that has been actively modified, for example, using molecular biology and / or synthetic biology tools.

[0108] As used herein, the terms "phage particle" or "phage" are equivalent and refer to a vector derived from both a plasmid and a bacteriophage genome. Phage particles typically contain a bacteriophage packaging site and an optional origin of replication (ori), particularly a bacterial and / or bacteriophage origin of replication. In one embodiment, the phage particle does not contain a functional bacterial origin of replication and therefore cannot replicate spontaneously once injected into bacteria. Alternatively, the phage particle may contain a plasmid origin of replication, particularly a bacterial and / or bacteriophage origin of replication.

[0109] As used herein, the term "packaged phage particle" refers to a phage particle encapsulated in a phage scaffold, phage-derived delivery particle, or capsid. Specifically, it refers to a phage scaffold, phage delivery particle, or capsid lacking a phage genome. Packaged phage particles can be generated using helper phage strategies known to those skilled in the art. Helper phages typically contain all genes encoding structural and functional proteins essential for the phage particle to be encapsulated according to the invention.

[0110] As used herein, the term "plasmid" refers to a circular nucleic acid molecule capable of autonomous replication within a host cell. The plasmid may be a conjugating plasmid. In one particular embodiment, the plasmid is a recombinant plasmid.

[0111] As used herein, the term "vesicle containing DNA or RNA" refers to an artificial delivery medium that encapsulates at least one nucleic acid molecule (which may be DNA, RNA, or a mixture thereof) within a shell-enclosed nucleus. The DNA- or RNA-containing vesicle can be chemically based vesicles, particularly polymer-based vesicles (such as polymeric vesicles), or nonionic surfactant-based vesicles (such as liposomes), lipid-based vesicles (such as liposomes), protein- or peptide-based vesicles, or nanoparticle-based vesicles.

[0112] As used herein, the term "extracellular vesicle" or "cell-derived nanovesicle" refers to nanoscale structures in particulate form released or secreted from cells that encapsulate biomolecules (such as proteins, nucleic acid molecules, lipids, or organelles) within a lipid layer of the cell membrane, typically identical to the cell membrane of the cell from which the biomolecule is derived. Examples of extracellular vesicles include microvesicles, exosomes, oncosomes, and apoptotic bodies. Extracellular vesicles typically have an average diameter of 30 nm to 1 μm, preferably 100 nm to 1 μm. Extracellular vesicles can be isolated from naturally occurring extracellular vesicles (e.g., by differential centrifugation ending with ultrafiltration, density gradient / buffered centrifugation, and immunoaffinity-based capture) or obtained by artificial methods (e.g., by extrusion processes in which cells pass through microfluidic channels, multi-stage filtration processes, etc.).

[0113] The bacteria used in the context of this invention may be wild-type bacteria, such as wild-type bacteria that are naturally produced by, for example, an antimicrobial agent as defined above that specifically targets *Propionibacterium acnes* α-type bacteria, or a bacteriophage as defined above that specifically targets *Propionibacterium acnes* α-type bacteria, or wild-type bacteria that are naturally capable of specifically targeting *Propionibacterium acnes* α-type bacteria as defined in the "Propionibacterium acnes α-type and *Propionibacterium acnes β-type" section above. Alternatively, the bacteria used in the context of this invention may be engineered (also called recombinant bacteria), for example, bacteria engineered to produce an antimicrobial agent as defined above that specifically targets *Propionibacterium acnes* α-type bacteria, or to produce a bacteriophage or engineered bacteriophage as defined above that specifically targets *Propionibacterium acnes* α-type bacteria, or bacteria containing bacteriophage particles or plasmids as defined above that specifically target *Propionibacterium acnes* α-type bacteria.

[0114] As used herein, “engineered bacteria” refers to bacteria that have been modified at the protein and / or nucleic acid level. Therefore, in the context of this invention, “engineered bacteria” is not wild-type bacteria or bacteria obtained through natural evolution, but rather bacteria that have been actively modified, for example, using molecular biology and / or synthetic biology tools.

[0115] In one particular embodiment, the treatment or prevention method of the present invention includes administering to the subject a therapeutic or preventative amount of a phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria as defined above, specifically targeting the α-Propionibacterium acnes bacteria as defined in the “α-Propionibacterium acnes and β-Propionibacterium acnes” section above.

[0116] Similarly, in specific embodiments of the use of the composition according to the invention or the therapeutic or preventative agent according to the invention, the therapeutic or preventative agent is a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria as defined above, specifically targeting the *Propionibacterium acnes* bacteria as defined in the "Propionibacterium acnes type α and *Propionibacterium acnes type β" section above.

[0117] In a preferred embodiment, the bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encodes a programmable nuclease (or contains a nucleic acid encoding the programmable nuclease) designed to specifically target the *Propionibacterium acnes* bacteria.

[0118] "Programmable nuclease" in this document refers to an enzyme designed to recognize and cleave specific nucleic acid sequences. Programmable nucleases are well known to those skilled in the art and include CRISPR-Cas systems (including CRISPR-Cas nucleases), TALENs and their variants, zinc finger nucleases (ZFNs) and their variants, a wide range of native, evolved or engineered nuclease or recombinase variants, and any combinations and hybrids thereof.

[0119] Therefore, in one particular embodiment, the programmable nuclease is selected from CRISPR-Cas nucleases, TALEN and its variants, ZFN and its variants, a wide range of natural, evolved or engineered nuclease or recombinase variants, and any combination and hybrid thereof.

[0120] As used herein, the term "TALEN" or "transcription activator-like effector nuclease" refers to a recombinant protein containing a transcription activator-like effector (TALE) binding domain and a nuclease domain. The transcription activator-like effector (TALE) binding domain refers to a protein containing a "repetitive region" (also called a "repetitive domain") containing multiple highly conserved 33-34 amino acid sequences (referred to as "repetitive modules" and "repeat modules"), with the last repeat module at the C-terminus being partially or half-length (approximately 20 amino acids). The combination of repeat modules within the repeat region binds to specific nucleotide sequences in the target DNA and / or RNA sequences, such that the TALEN is modified within or adjacent to the specific nucleotide sequence in the cell or its progeny.

[0121] As used herein, the term “zinc finger nuclease” or “ZFN” refers to a chimeric protein containing a zinc finger DNA-binding domain fused to a nuclease domain derived from an endonuclease or exonuclease.

[0122] As used herein, the term "macronuclease" refers to an endonuclease that binds to double-stranded DNA at a recognition sequence of more than 12 base pairs. Naturally occurring macronucleases can be monomeric (e.g., I-Scel) or dimeric (e.g., I-Crel). As used herein, the term macronuclease can be used to refer to monomeric macronucleases, dimer macronucleases, or monomers that associate to form dimer macronucleases. Because macronucleases have a large recognition site, this site typically occurs only once in any given genome.

[0123] As used herein, the term “recombinase” refers to a DNA-modifying enzyme (i.e., an enzyme capable of DNA recombination) that binds to, cleaves, exchanges strands with, and rejoins DNA at its respective recombination sites.

[0124] The “CRISPR-Cas system” refers to clusters of regularly spaced short palindromic repeats and their associated CRISPR (Cas) proteins. These systems comprise a variety of RNA-guided prokaryotic adaptive immune systems used by these organisms to defend against foreign parasitic nucleic acids.

[0125] The CRISPR-Cas system contains two distinct components: i) a nuclease, in this case a CRISPR-associated nuclease (Cas or “CRISPR-associated protein”) and ii) a guide RNA. Depending on the type of CRISPR-Cas system, the guide RNA can be in the form of a chimeric RNA, consisting of a combination of CRISPR (crRNA) bacterial RNA and tracrRNA (trans-activating RNA CRISPR) (Jinek et al. (2012) Science 337(6096):816-21). The guide RNA combines the target specificity of the crRNA, corresponding to the “spacer sequence” that acts as a guide for the Cas protein, and the conformational properties of the tracrRNA within a single transcript. When the guide RNA and the Cas protein are co-expressed in the cell, the target genomic sequence can be permanently interrupted (and result in the disappearance of the target sequence and surrounding sequences and / or cell death, depending on location) or modified. Modification can be guided by a repair matrix.

[0126] Depending on the mechanism of nuclease action, CRISPR-Cas systems include two main categories: - Class 1 consists of multi-subunit effector complexes and includes types I, III, and IV; - Class 2 consists of a single-unit effector module (such as Cas9 nuclease) and includes type II (II-A, II-B, II-C, II-C variants), type V (VA, VB, VC, VD, VE, V-U1, V-U2, V-U3, V-U4, V-U5) and type VI (VI-A, VI-B1, VI-B2, VI-C, VI-D).

[0127] In one particular embodiment, the programmable nuclease is a CRISPR-Cas nuclease (also referred to herein as a Cas nuclease or CRISPR enzyme). Various CRISPR enzymes can be used in the context of this invention. In some embodiments, the CRISPR enzyme is a type II, type II-A, or type II-B CRISPR enzyme. In another embodiment, the CRISPR enzyme is a type I or type III CRISPR enzyme. In some embodiments, the CRISPR enzyme catalyzes DNA cleavage. In still other embodiments, the CRISPR enzyme catalyzes RNA cleavage.

[0128] Non-limiting examples of Cas proteins that are part of a multi-subunit effector or a single-unit effector include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Cas11 (SS), Cas12a (Cpf1), Cas12b (C2c1), Cas12c (C2c3), Cas12d (CasY), Cas12e (CasX), C2c4, C2c8, C2c5, C2c10, C2c9, Cas13a (C2c2), and Cas13b. (C2c6), Cas13c(C2c7), Cas13d, Csa5, Csc1, Csc2, Cse1, Cse2, Csy1, Csy2, Csy3, Csf1, Csf2, Cs f3, Csf4, Csm1, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csn2, Csb1, Csb2, Cs b3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx13, Csx1, Csx15, SdCpf1, CmtCpf1, TsCpf1, CmaCpf1, PcCpf1, ErCpf1, FbCpf1, UbcCpf1, AsCpf1, LbCpf1, Mad4, Mad7, Cms1, their homologs, their orthologs, their variants, or modified forms thereof. In some embodiments, the CRISPR enzyme cleaves both strands of the target nucleic acid at a site adjacent to the protospacer motif (PAM).

[0129] In one particular implementation, the CRISPR enzyme is any Cas9 protein, such as any naturally occurring bacterial Cas9 and any variants, homologs, or orthologs thereof.

[0130] "Cas9" refers to the protein Cas9 (also known as Csn1 or Csx12) or its functional protein, peptide, or polypeptide fragment, that is, the protein capable of interacting with guide RNA and exerting enzymatic activity (nuclease) that enables it to perform double-strand cleavage of DNA from a target genome. "Cas9" can thus also refer to a modified protein, for example, truncated to remove domains that are not essential for the protein's intended function, particularly domains that are not essential for interaction with gRNA.

[0131] As used in the context of this invention, the sequence encoding Cas9 (the complete protein or a fragment thereof) can be obtained from any known Cas9 protein (Fonfara et al. (2014) Nucleic Acids Res. 42(4):2577-90; Koonin et al. (2017) Curr Opin Microbiol. 37:67-78). Examples of Cas9 proteins that can be used in this invention include, but are not limited to, Cas9 proteins of Streptococcus pyogenes (SpCas9), Streptococcus thermophilus (St1Cas9, St3Cas9), Streptococcus mutans, Staphylococcus aureus (SaCas9), Campylobacter jejuni (CjCas9), Francisella neonicotinoides (FnCas9), and Neisseria meningitidis (NmCas9).

[0132] In one particular implementation, the CRISPR enzyme is dCas9.

[0133] The sequence encoding Cpf1 (Cas12a) (the whole protein or a fragment thereof) as used in the context of this invention can be obtained from any known Cpf1 (Cas12a) protein (Koonin et al. (2017) Curr Opin Microbiol. 37:67-78). Examples of Cpf1 (Cas12a) proteins that can be used in this invention include, but are not limited to, Cpf1 (Cas12a) proteins of *C.* spp., *C.* spp., and *C.* spp. *Franciscus*.

[0134] The sequence encoding Cas13a (the whole protein or a fragment thereof) as used in the context of this invention can be obtained from any known Cas13a (C2c2) protein (Abudayyeh et al. (2017) Nature 550(7675):280-284). Examples of Cas13a (C2c2) proteins that can be used in this invention include, but are not limited to, the LwaCas13a (C2c2) protein from *Lithotriton waseri*.

[0135] The sequence encoding Cas13d (the whole protein or a fragment thereof) as used in the context of this invention can be obtained from any known Cas13d protein (Yan et al. (2018) Mol Cell. 70(2):327-339.e5.). Examples of Cas13d proteins that can be used in this invention include, but are not limited to, Cas13d proteins of indolent eubacteria and Ruminococcus spp.

[0136] The sequence encoding Mad4 (the whole protein or a fragment thereof) as used in the context of this invention is disclosed in international application WO2018 / 236548.

[0137] The sequence encoding Mad7 (the whole protein or a fragment thereof) as used in the context of this invention is disclosed in international application WO2018 / 236548.

[0138] The sequence encoding Cms1 (the whole protein or a fragment thereof) as used in the context of this invention is disclosed in International Patent Application WO2017 / 141173.

[0139] In one implementation, the CRISPR enzyme may be linked to a guide RNA or a single guide RNA (sgRNA).

[0140] Therefore, in a preferred embodiment, the phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria are further encoded with guide RNA specifically targeting the Propionibacterium acnes type bacterium.

[0141] As used herein, the term "guide RNA" refers to crRNA (also known as CRISPR RNA), or a combination of crRNA and trRNA (also known as tracrRNA). crRNA and trRNA can be associated as a single RNA molecule (single guide RNA, sgRNA) or in two separate RNA molecules (dual guide RNA, dgRNA). trRNA can be a naturally occurring sequence or a trRNA sequence modified or mutated compared to a naturally occurring sequence. For clarity, as used herein and unless otherwise specifically stated, the term "guide RNA" can refer to an RNA molecule (containing A, C, G, and U nucleotides) or a DNA molecule (containing A, C, G, and T nucleotides) encoding such an RNA molecule, or its complementary sequence. As is well known to those skilled in the art, a "guide RNA" in a CRISPR-Cas system is used to detect target nucleic acids and is responsible for recognizing a portion of the sequence possessed by the target nucleic acid. The guide RNA contains a sequence for recognizing a portion of the sequence carried by the target nucleic acid and is responsible for the target nucleic acid detection specificity in the CRISPR-Cas system. Guide RNAs are typically designed to match the Cas protein administered with them. Methods for designing and producing guide RNAs are well known.

[0142] In one particular implementation, the guide RNA is designed to specifically target bacterial-specific sequences, genes, or loci of Propionibacterium acnes type 1.

[0143] In one particular implementation, the guide RNA is designed to specifically target the hem locus of the Propionibacterium acnes type α bacteria.

[0144] In a more preferred embodiment, the guide RNA is designed to specifically target at least one nucleotide variation in the hem locus associated with *Propionibacterium acnes* as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type β" section above. Preferably, the guide RNA is selected to have at least one mismatch between *Propionibacterium acnes* type α and *Propionibacterium acnes type β*, preferably two mismatches and / or mismatches at the PAM site.

[0145] Therefore, in a more specific embodiment, the guide RNA is designed to specifically target at least one of the following nucleotide variations in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0146] Preferably, the phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encode multiple (at least 2, 3, 4, 5, or more) guide RNAs that specifically target multiple (at least 2, 3, 4, 5, or more) nucleotide variations in the hem locus associated with Propionibacterium acnes as defined in the “Propionibacterium acnes type α and Propionibacterium acnes type β” section above.

[0147] In one particular embodiment, the phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria contains a sequence encoding a guide RNA selected from SEQ ID NO: 13 to 16.

[0148] Genetically modified DNA sequences in Propionibacterium acnes type 1 bacteria In one particular embodiment, the treatment or prevention method of the present invention includes genetically modifying the DNA sequence of *Propionibacterium acnes* bacteria as defined in the above section “Propionibacterium acnes type α and Propionibacterium acnes type β” on the skin of the subject, to produce at least one change in the *Propionibacterium acnes* bacteria, preferably in the hem locus of the *Propionibacterium acnes* bacteria.

[0149] Similarly, in a particular embodiment of the use of the composition according to the invention or the therapeutic or preventative agent according to the invention, the therapeutic or preventative agent induces genetic modification of the DNA sequence in the subject, particularly on the skin of the subject, of the α-propionibacterium acnes bacteria as defined in the above section "α-propionibacterium acnes and β-propionibacterium acnes bacteria", to produce at least one change in the α-propionibacterium acnes bacteria, preferably in the hem locus of the α-propionibacterium acnes bacteria.

[0150] The present invention therefore relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising genetically modifying a DNA sequence in *Propionibacterium acnes* bacteria, particularly on the skin of the subject, to produce at least one change in the *Propionibacterium acnes* bacteria, preferably in the *hem* locus of the *Propionibacterium acnes* bacteria. It also relates to a composition for treating or preventing *Propionibacterium acnes*-related diseases in a subject, the composition comprising a therapeutic or preventative agent that genetically modifies a DNA sequence in *Propionibacterium acnes* bacteria, particularly on the skin of the subject, to produce at least one change in the *Propionibacterium acnes* bacteria, preferably in the *hem* locus of the *Propionibacterium acnes* bacteria. Further relating to the use of therapeutic or preventive agents in the manufacture of medicaments for treating or preventing diseases associated with Propionibacterium acnes bacteria, wherein the therapeutic or preventive agent genetically modifies the DNA sequence of Propionibacterium acnes type 1 bacteria on the subject, particularly on the skin of the subject, to produce at least one change in the Propionibacterium acnes type 1 bacteria, preferably in the hem locus of the Propionibacterium acnes type 1 bacteria.

[0151] "Genetically modified DNA sequence" or "genetic modification of DNA sequence" herein refers to the modification of at least one nucleotide of a DNA sequence. The modification may be a substitution of at least one nucleotide, an insertion of at least one nucleotide, a deletion of at least one nucleotide, or a modification of the nucleobase of at least one nucleotide (such as methylation).

[0152] In the context of this invention, the genetic modification preferably occurs at the hem locus of the α-propionibacterium acnes bacteria; in other words, the genetic modification preferably produces at least one change at the hem locus of the α-propionibacterium acnes bacteria.

[0153] In one particular embodiment, the genetic modification preferably produces at least one change in at least one of the following nucleotide variations in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: Defined by 8, - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, where the positions are defined by reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0154] In one particular embodiment, the genetic modification produces at least one change in at least one nucleotide variation in the hem locus associated with Propionibacterium acnes type 1, to a nucleotide variation in the hem locus associated with Propionibacterium acnes type 2, as defined in the “Propionibacterium acnes type 1 and Propionibacterium acnes type 2” section.

[0155] Therefore, in one particular embodiment, the genetic modification produces at least one, more particularly at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 218 or all of the following variations: - In the hemA gene: T173G, A479G, T506C, A614G, T629G, C671A, T971C, A989G, T1085C, and T1094C, where the positions are defined with reference to sequence SEQ ID NO: 3. - In the hemB gene: C142T, A155G, A176G, A183G, C224T, C245T, G248A, T281C, G311A, C314T, T346C, C374T, G377T, C452T, T626C, C683G, A693G, A720G, C738T, C794T, A920C, T944G, T992C, G1022C, and T1031C, where the positions are defined with reference to sequence SEQ ID NO: 4. - In the hemC gene: G77A, A96G, C149G, A233G, T236C, T255C, A257G, A260C, C317T, A347G, T425C, T437C, A464G, A486G, A487G, C488T, A524G, A545G, A590G, T605C, A6 44G, A665G, C710T, C713G, A737G, A770G, A776G, T785A, T802C, G830A, C842T, T845C, G855A, C893G, A896T, C897T, G902A, G908T, A941G, and A947G, where the positions are defined with reference to sequence SEQ ID NO: 5. - In the hemD gene: T11C, T41C, T50C, A150G, T155C, G159A, G176T, T257C, C266T, T278C, G323C, A324G, T362C, T367C, T374C, G387A, A398G, A399G, T407C, G422A, G425A, G432A, A446G, A459G, T464C, G595A, T617C, T643A, A644G, and C680T, where the positions are defined with reference to sequence SEQ ID NO: 6. - In the hemE gene: T241C, T476C, A530G, T704C, A728G, G767C, T834A, A867G, A872G, A882C, and A957G, where the positions are defined with reference to sequence SEQ ID NO: 7. - In the hemH gene: T11C, T23C, A48G, T89C, C188T, G338A, T464C, T470C, G536A, T548C, T608C, G626A, T632C, T641C, T671C, T674C, C683T, C689T, A740T, G745A, G787A, A797G, T893C, A89 The sequences 8T, T1034C, T1039C, T1046C, C1071G, G1095A, C1109T, T1153C, T1358C, G1496C, C1511T, C1527T, G1532A, T1598C, T1712C, A1850G, G1901C, A1926G, C1931T, and C1997T, where the positions are defined with reference to the sequence SEQ ID NO: 8, are listed below. - In the hemL gene: T107C, C197T, T229A, A242G, C310A, A338G, A374G, T389C, G392T, T442C, C467T, G470A, C482T, G518T, and C641G, where the positions are defined with reference to sequence SEQ ID NO: 9, and - In the hemY gene: A89G, A236G, A354G, C383T, C392T, A395G, T398C, T465C, T474C, C521T, T538C, C566T, A593C, A767C, T782A, G863A, G920A, T927A, A932G, G935A, C979A, G989C, C1019G, T1055 C, G1091A, T1136C, G1143A, G1152T, T1166C, T1172G, A1176G, T1184C, C1199T, C1205T, G1268A, G1278A, T1295C, T1318C, A1336G, G1343A, C1346T, G1355C, T1359G, and C1395G, where the position is defined with reference to the sequence SEQ ID NO: 10.

[0156] Genetic modifications can be point mutations, deletions, insertions, or any combination thereof. Preferably, the genetic modification is a point modification.

[0157] Genetic modifications are preferably used to eliminate, reduce, or increase gene expression. Genetic modifications can occur in the translated or untranslated regions of a gene. They can also occur in the promoter region of a gene or in any other region involved in gene regulation.

[0158] In one particular embodiment, the genetic modification eliminates and / or reduces the expression of one or more genes (i.e., hemA, hemB, hemC, hemD, hemE, hemH, hemL, and / or hemY genes) at the hem locus, preferably in *Propionibacterium acnes* type α. In a more particular embodiment, the genetic modification eliminates or reduces porphyrin production in *Propionibacterium acnes* bacteria, particularly *Propionibacterium acnes* type α.

[0159] In some embodiments, the genetic modification results in the alteration of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 100, 200, and 500 amino acids to different amino acids. In some embodiments, the genetic modification introduces a stop codon. In some embodiments, the genetic modification is performed outside the protein-coding sequence, within RNA, or within a regulatory sequence. In some embodiments, the genetic modification introduces one or more rare codons, thereby affecting, preferably reducing, protein expression. In some embodiments, the start codon is modified, thereby altering or eliminating the normal start codon.

[0160] In one particular embodiment, the genetic modification results in the modified *Propionibacterium acnes* bacteria no longer belonging to the group of *Propionibacterium acnes* bacteria as defined in the "Alpha-type and Beta-type" section above. In a preferred embodiment, the genetic modification results in the modified *Propionibacterium acnes* bacteria becoming *Propionibacterium acnes* bacteria as defined in the "Alpha-type and Beta-type" section above.

[0161] A therapeutic or preventative agent that genetically modifies the DNA sequence of *Propionibacterium acnes* to produce at least one change in the *Propionibacterium acnes* bacteria, preferably in the *hem* locus of the *Propionibacterium acnes* bacteria, may be a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding a gene-editing enzyme or system that targets the *hem* locus in the *Propionibacterium acnes* bacteria, particularly at least one nucleotide variation as defined above.

[0162] In one particular embodiment, the treatment or prevention method of the present invention includes administering to the subject a therapeutic or preventative amount of a phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding the hem locus targeting the Propionibacterium acnes type 1 bacteria, particularly at least one gene-editing enzyme or system with a nucleotide variation as defined above.

[0163] Similarly, in a particular embodiment of the use of the composition according to the invention or the therapeutic or preventative agent according to the invention, the therapeutic or preventative agent is a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding the hem locus in the *Propionibacterium acnes* bacteria that targets and genetically modifies, in particular, at least one gene-editing enzyme or system with a nucleotide variation as defined above.

[0164] As used in this article, the term "gene editing" refers to a type of genetic engineering that involves inserting, deleting, modifying, or replacing DNA in the genome of a living organism.

[0165] In this article, "gene editing system" refers to the combination of components required to perform gene editing on the genome in a cell. The various components of the system, such as peptides and gRNAs, can exist independently of each other or in any combination thereof.

[0166] In this document, "gene-editing enzyme" refers to an enzyme that enables gene editing of the genome within a cell. The gene-editing enzyme is typically part of a gene-editing system as defined above and is used in conjunction with another component of the system.

[0167] In one particular implementation, the gene-editing enzyme or system is a base-editing enzyme or system.

[0168] Base editing (BE) refers to the ability of a specific nucleotide base pair on a DNA or RNA molecule to be replaced by another nucleotide base pair. In base editing technology, there is no DNA exchange; instead, an enzymatic reaction converts one nucleotide into another, resulting in a mismatch at the dsDNA level, which is subsequently corrected by cellular mechanisms.

[0169] In some implementations, the base editing system comprises one or more of the following enzymes and systems: Cytosine base editors (CBEs) and adenosine base editors (ABEs), such as Rees and Liu (2018). Nat Rev Genet As described in 19:770–788.

[0170] Examples of DNA base editors include: - Cytosine base editor (CBE), which converts C:G to T:A (Komor et al. (2016) Nature 533:420-4); - Adenine base editor (ABE), which converts A:T to G:C (Gaudelli et al. (2017) Nature 551(7681):464-471); - Cytosine-guanine base editor (CGBE), which converts C:G to G:C (Chen et al. (2020) Precise and programmable C:G to G:C base editing in genomic DNA. Biorxiv; Kurt et al. (2020) CRISPRC-to-G base editors for inducing targeted DNA transversions in human cells. Nature Biotechnology); - Cytosine adenine base editor (CABE), which converts C:G to A:T (Zhao et al. (2020) Newbase editors change C to A in bacteria and C to G in mammalian cells. Nature Biotechnology); - Adenine-cytosine base editor (ACBE), which converts A:T to C:G (WO2020181180); - Adenine-thymine base editor (ATBE), which converts A:T to T:A (WO2020181202); - Thymine adenine base editor (TABE), which converts T:A to A:T (WO2020181193; WO2020181178; WO2020181195).

[0171] Base editors differ in their base-modifying enzymes. CBE depends on ssDNA cytidine deaminases, including: APOBEC1, rAPOBEC1, APOBEC1 mutants or evolved forms (evoAPOBEC1) and APOBEC homologs (APOBEC3A (eA3A), Anc689), cytidine deaminase 1 (CDA1), evoCDA1, FERNY, and evoFERNY.

[0172] ABE depends on the deoxyadenosine deaminase activity of the tandem fusion TadA-TadA*, where TadA* is an evolutionary form of TadA (an E. coli tRNA adenosine deaminase capable of converting adenosine to inosine on ssDNA). TadA* includes TadA-8a-e and TadA-7.10.

[0173] In addition to base-modifying enzymes, the base editor was also modified to improve editing efficiency, accuracy, and modularity: - Add one or two uracil DNA glycosylation inhibitor domains (UGIs) to prevent the base excision repair mechanism from resuming base editing; - Add Mu-GAM to reduce insertion / deletion rates by inhibiting the non-homologous end junction (NHEJ) mechanism in cells; - Use the nicking enzyme activity Cas9 (nCas9 D10A), which promotes repair of the non-edited strand by creating nicks on it and thus promotes the fixation of edited bases; - Use mutants (e.g., Cas12a) from different organisms, with different PAM motifs, different fidelity, or different families.

[0174] Non-limiting examples of DNA-based editing proteins include BE1, BE2, BE3, BE4, BE4-GAM, HF-BE3, Sniper-BE3, Target-AID, Target-AID-NG, ABE, EE-BE3, YE1-BE3, YE2-BE3, YEE-BE3, BE-PLUS, SaBE3, SaBE4, SaBE4-GAM, Sa(KKH)-BE3, VQR-BE3, VRER-BE3, EQR-BE3, xBE3, Cas12a-BE, Ea3A-BE3, A3A-BE3, TAM, CRISPR-X, and ABE7. .9, ABE7.10, ABE7.10*, xABE, ABESa, VQR-ABE, VRER-ABE, Sa(KKH)-ABE, ABE8e, SpRY-ABE, SpRY-CBE, SpG-CBE4, SpG-ABE, SpRY-CBE4, SpCas9-N G-ABE, SpCas9-NG-CBE4, enAsBE1.1, enAsBE1.2, enAsBE1.3, enAsBE1.4, AsBE1.1, AsBE1.4, CRISPR-Abest, CRISPR-Cbest, eA3A-BE3, AncBE4.

[0175] The cytosine-guanine base editor (CGBE) consists of a nicking enzyme, CRISPR, fused with the following: - Cytosine deaminase (rAPOBEC) and base excision repair proteins (e.g., rXRCC1) (Chen et al. Precise and programmable C:G to G:C base editing in genomic DNA. Biorxiv (2020); Chen et al. (2021) Nature Communications 12:1384); - Rat APOBEC1 variant (R33A) protein and E. coli-derived uracil DNA N-glycosylation enzyme (eUNG) (Kurt et al. (2020) CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nature Biotechnology).

[0176] The cytosine-adenine base editor (CABE) consists of a Cas9 nicking enzyme, a cytidine deaminase (e.g., AID), and a uracil-DNA glycosylase (Ung) (Zhao et al. (2020) New base editors change C to A inbacteria and C to G in mammalian cells. Nature Biotechnology).

[0177] ACBE includes nucleic acid programmable DNA-binding proteins and adenine oxidase (WO2020181180).

[0178] ATBE consists of a Cas9 nickase and one or more adenosine deaminase or oxidase domains (WO2020181202).

[0179] TABE consists of Cas9 nickase and adenosine methyltransferase, thymidine alkyltransferase or adenosine deaminase domains (WO2020181193; WO2020181178; WO2020181195).

[0180] Base editor molecules can also consist of two or more editor enzymes listed above fused to the Cas protein (e.g., a combination of ABE and CBE). These biomolecules are named dual-deaminase editors and enable the editing of two different bases (Grunewald et al. (2020) A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing, Nature Biotechnology; Li et al. (2020) Targeted, random mutagenesis of plant genes with dual cytosine and adeninebase editors, Nature Biotechnology).

[0181] In one particular embodiment, the base editing enzyme is a fusion protein comprising a Cas9 (e.g., Cas9 nickase) domain and a deaminase domain. In some embodiments, the base editing enzyme comprises Cas9 and a cytosine deaminase, such as an APOBEC enzyme, or an adenosine deaminase, such as an ADAT enzyme, as disclosed in U.S. Patent Publication 2015 / 0166980. In one embodiment, the deaminase is an ACF1 / ASE deaminase. In various embodiments, the APOBEC enzyme is selected from APOBEC1 deaminase, APOBEC2 deaminase, APOBEC3A deaminase, APOBEC3B deaminase, APOBEC3C deaminase, APOBEC3D deaminase, APOBEC3F deaminase, APOBEC3G deaminase, and APOBEC3H deaminase. In various embodiments, the base editing enzyme comprises a Cas9 domain, a cytosine deaminase domain, and a uracil glycosylation inhibitor (UGI) domain. In one embodiment, the deaminase is an adenosine deaminase that deaminates adenosine in DNA, such as that disclosed in U.S. Patent 10,113,163. In some embodiments, the base editing system further comprises a base repair inhibitor, such as a nuclease-inactivating inosine-specific nuclease (dISN), such as that disclosed in U.S. Patent 10,113,163.

[0182] In one particular implementation, the base editing system includes a cytosine base editor (CBE) and / or an adenosine base editor (ABE) as defined above.

[0183] In another specific implementation, the gene-editing enzyme or system is a guide editing enzyme or system.

[0184] Guided editing (PE) enables the introduction of insertions, deletions (indels), and multiple base-base transitions. Guided editing typically relies on the ability of a reverse transcriptase (RT) fused to a Cas nickase variant to convert an RNA sequence brought by the guide RNA (pegRNA) into DNA at a nick site created by the Cas protein. The DNA flap generated by this process may or may not be included in the targeted DNA sequence.

[0185] As described by Anzalone et al. (2019) Nature 576:149–157, the guide editor typically consists of an nCas9 fused with reverse transcriptase and used in combination with a guide editing RNA (pegRNA; which includes a template region for reverse transcription).

[0186] Guided editing systems typically include: - Cas nickase variants such as Cas9-H840A fused with reverse transcriptase domains such as M-MLV RT or its mutant forms (M-MLV RT(D200N), M-MLV RT(D200N / L603W), M-MLV RT(D200N / L603W / T330P / T306K / W313F), and - Guide RNA for editing (pegRNA).

[0187] To facilitate editing, the guided editing system may include the expression of an additional sgRNA that ideally targets the Cas nickase activity to the unedited DNA strand only after the edited strand has been integrated into the flop (resolution). This is achieved by designing the sgRNA to anneal to the edited strand but not to the original strand.

[0188] Non-restricted instances of the guided editing system include PE1, PE1-M1, PE1-M2, PE1-M3, PE1-M6, PE1-M15, PE1-M3inv, PE2, PE3, and PE3b.

[0189] In various implementations, the guided editing system comprises a fusion protein containing a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a guide RNA (pegRNA) that both specifies the target site and encodes the desired edit, as described, for example, in (2019) Nature 576:149–157.

[0190] Other suitable gene editing systems or enzymes include: - Cas9 Retron precISe Parallel Editing via homologY (“CRISPEY”), which is a retrotranscripton RNA fused with sgRNA and expressed along with Cas9 and at least a retrotranscripton protein including reverse transcriptase (Sharon et al. (2018) Cell 175:544-557.e16).

[0191] - SCRIBE strategy: A reverse transcriptase system co-expressed with recombinases that promote single-stranded DNA recombination, also known as single-stranded annealing proteins (SSAPs) (Farzadfard and Lu (2014) Science 346:1256272). Such recombinases include, but are not limited to, phage recombinases such as λred, recET, Sak, Sak4, and SSAP, as described in Wannier et al., Improved bacterial recombineering by parallelized protein discovery. Biorxiv 2020.01.14.906594 (2020) doi:10.1101 / 2020.01.14.906594.

[0192] - The targetron system based on type II introns, described in Karberg et al., Nat Biotechnol (2001) 19:1162–7, has been adapted to many bacterial species.

[0193] Other reverse transcriptase-based gene targeting methods, such as those described in Simon et al. (2019) Nucleic Acids Res 47:11007–11019.

[0194] - based on IS1111 and IS110 Members of the Insertion Sequence (IS) family use a bridging system with non-coding RNAs (ncRNAs) having two distinct binding loops that recognize the IS DNA donor and its genomic insertion target site, respectively. By bridging the donor and target DNA molecules via direct base-pairing interactions, bispecific bridging RNAs promote DNA recombination via IS recombinases (Durrant et al. Nature. 2024 Jun;630(8018):984-993; Siddiquee et al. NatCommun 15,5235 (2024)).

[0195] In one particular implementation, the gene editing system or enzyme is a base editor or bootstrap editor as defined above.

[0196] The present invention also relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising specifically reducing the expression of at least one hem locus protein in α-type Propionibacterium acnes bacteria in the subject, wherein α-type Propionibacterium acnes bacteria are Propionibacterium acnes bacteria as defined in the “α-type Propionibacterium acnes bacteria and β-type Propionibacterium acnes bacteria” section above.

[0197] It also relates to compositions for treating or preventing bacterial diseases associated with Propionibacterium acnes in subjects, the compositions comprising a therapeutic or preventative agent that genetically modifies the DNA sequence of Propionibacterium acnes type α in the subject to produce at least one change, preferably producing at least one change in the hem locus of Propionibacterium acnes type α, to specifically reduce the expression of at least one hem locus protein in Propionibacterium acnes type α in the subject, and wherein Propionibacterium acnes type α is Propionibacterium acnes as defined in the “Propionibacterium acnes type α and Propionibacterium acnes type β” section above.

[0198] Further relating to the use of therapeutic or preventive agents in the manufacture of medicaments for treating or preventing Propionibacterium acnes-related diseases in a subject, wherein the therapeutic or preventive agent genetically modifies the DNA sequence of Propionibacterium acnes type α in the subject to produce at least one change, preferably producing at least one change in the hem locus of the Propionibacterium acnes type α, to specifically reduce the expression of at least one hem locus protein in the Propionibacterium acnes type α in the subject, and wherein the Propionibacterium acnes type α is the Propionibacterium acnes bacteria as defined in the "Propionibacterium acnes type α and Propionibacterium acnes type" section above.

[0199] Therapeutic or preventative agents can be defined as above.

[0200] In one particular implementation, a therapeutic or preventative agent that specifically reduces the expression of at least one hem locus protein in *Propionibacterium acnes* bacteria in a subject by genetically modifying the DNA sequence of the bacteria is a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding the hem locus targeting the *Propionibacterium acnes* bacteria, particularly at least one gene-editing enzyme or system with a nucleotide variation as defined above.

[0201] In one particular embodiment, the treatment or prevention method of the present invention includes administering to the subject a therapeutic or preventatively effective amount of a therapeutic or preventative agent, said therapeutic or preventative agent specifically reducing the expression of at least one hem locus protein in the subject by genetically modifying the DNA sequence of *Propionibacterium acnes* bacteria in the subject. Preferably, said therapeutic or preventative agent is a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding a gene-editing enzyme or system that targets said hem locus, particularly at least one nucleotide variant as defined above.

[0202] Genetic modifications can be as defined above and can be performed as described above.

[0203] In one particular implementation, genetic modification eliminates and / or reduces the expression of one or more genes (i.e., hemA, hemB, hemC, hemD, hemE, hemH, hemL and / or hemY genes) at the hem locus in Propionibacterium acnes type α.

[0204] In a more specific implementation, genetic modification eliminates or reduces porphyrin production by Propionibacterium acnes type α.

[0205] "Specific reduction of expression of at least one hem locus protein in Propionibacterium acnes type α" in this document means that, in the subject, particularly on the skin of the subject, the expression of at least one hem locus protein (i.e., hemA, hemB, hemC, hemD, hemE, hemH, HemL and / or hemY protein) of another type of Propionibacterium acnes bacteria other than type α, particularly type β, and / or other bacterial species is not significantly reduced. Preferably, in the subject, particularly on the skin of the subject, the expression of at least one hem locus protein of another type of Propionibacterium acnes bacteria other than type α, particularly type β, is not significantly reduced. Preferably, compared with an untreated population or with a population of Propionibacterium acnes bacteria of a type other than α, particularly Propionibacterium acnes, and / or other bacterial species in the subject prior to implementation of the method and / or application of the therapeutic or preventative agent, the expression of at least one hem locus protein of the type other than α, particularly Propionibacterium acnes, and / or other bacterial species is reduced by less than 20%, preferably less than 10%.

[0206] Genetic modifications that induce a decrease in the expression of at least one hem locus protein may or may not affect the ratio of the amount of *Propionibacterium acnes* type α to *Propionibacterium acnes* type β. That is, the genetic modification may or may not result in the modified *Propionibacterium acnes* bacteria no longer belonging to the group of *Propionibacterium acnes* type α as defined in the "*Propionibacterium acnes* type α and *Propionibacterium acnes* type β" section above. In some specific embodiments, the ratio of the amount of *Propionibacterium acnes* type α to *Propionibacterium acnes* type β is unaffected by the genetic modification.

[0207] Increase the amount of Propionibacterium acnes type bacterium. In one particular embodiment, the treatment or prevention method of the present invention includes increasing the amount of Propionibacterium acnes as defined in the above section "Propionibacterium acnes type α and Propionibacterium acnes type β" in the subject, particularly on the skin of the subject.

[0208] This invention therefore relates to a method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising increasing the amount of Propionibacterium acnes type β bacteria in the subject, particularly on the subject's skin. It also relates to a composition for treating or preventing Propionibacterium acnes-related diseases in a subject, the composition comprising a therapeutic or preventive agent that increases the amount of Propionibacterium acnes type β bacteria in the subject, particularly on the subject's skin. Further, it relates to the use of a therapeutic or preventive agent that increases the amount of Propionibacterium acnes type β bacteria in a subject, particularly on the subject's skin, in the manufacture of a medicament for treating or preventing Propionibacterium acnes-related diseases in the subject.

[0209] As used herein, the term “quantity” has the same meaning as disclosed in the “Methods for treating or preventing diseases associated with Propionibacterium acnes” section above.

[0210] In one particular implementation, the amount of Propionibacterium acnes, as defined in the “Alpha-type and Beta-type” section above, is specifically increased in the subject, particularly on the subject’s skin.

[0211] "Specifically increased amount of Propionibacterium acnes type β" in this document means that, in the subject, particularly on the subject's skin, the amount of Propionibacterium acnes type other than β, particularly Propionibacterium acnes type α, was not significantly increased, and / or the amount of other bacterial species was not significantly increased in the subject, particularly on the subject's skin.

[0212] In this paper, "increase in quantity" refers to the increase in quantity after implementing the method compared to the quantity before or without the implementation of the method.

[0213] In one particular implementation, the increase in quantity is a statistically significant increase.

[0214] In one particular implementation, an increase in the amount was observed one day after the first implementation of the method, particularly two, three, four, five, six, seven days, two weeks, three weeks, or one month after the first implementation of the method.

[0215] In one particular implementation, the increase in quantity is maintained (not necessarily at the same level) for 1 day after the first implementation of the method, particularly for 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months or 1 year after the first implementation of the method.

[0216] In one particular implementation, the increase in the amount is maintained (not necessarily at the same level) throughout the entire time period of the implementation method.

[0217] In one particular embodiment, the treatment or prevention method of the present invention includes, in particular, applying Propionibacterium acnes as defined in the above section “Alpha-type Propionibacterium acnes and Beta-type Propionibacterium acnes” to the subject, especially to the skin of the subject.

[0218] Specifically, therapeutics or preventative agents that increase the amount of β-propionibacterium acnes bacteria can be bacteriophages, recombinant bacteriophages, packaged phage particles, plasmids, vesicles containing DNA or RNA, extracellular vesicles, bacteria, or engineered bacteria that encode a hem locus targeting α-propionibacterium acnes bacteria, particularly a gene-editing enzyme or system for α-nucleotide variants as defined in Table 1, to produce changes in said α-propionibacterium acnes bacteria that result in the modified α-propionibacterium acnes bacteria becoming β-propionibacterium acnes bacteria.

[0219] Subjects, protocol and administration The subjects according to the invention are animals, preferably mammals, and even more preferably humans. However, the term "subject" can also refer to non-human animals, especially mammals.

[0220] The human subject according to the invention can be a newborn, child, infant, adolescent, or adult of any age. In one particular embodiment, the human subject is an adolescent.

[0221] In one preferred embodiment, the subject has been diagnosed with acne, particularly acne vulgaris, or is at risk of developing acne, particularly acne vulgaris. In one preferred embodiment, the subject has been diagnosed with acne, particularly acne vulgaris, using the diagnostic methods disclosed in the "Risk and Diagnosis of Acne Development" section below. In one preferred embodiment, the subject has been identified as being at risk of developing acne, particularly acne vulgaris, using the methods disclosed in the "Risk and Diagnosis of Acne Development" section below.

[0222] In one particular implementation, the subject had never received any treatment prior to the treatment or prevention method of the present invention.

[0223] In one particular implementation, prior to the treatment or prevention method of the present invention, the subject has received at least one line of treatment, preferably multiple lines of treatment.

[0224] Preferably, the treatment is applied regularly, preferably between daily and monthly, more preferably between daily and bi-weekly, even more preferably between daily and weekly, and even more preferably daily. In one particular embodiment, the treatment is applied several times a day, preferably twice a day.

[0225] The duration of treatment according to the invention is preferably from 1 day to 1 year, more preferably from 1 week to 6 months, even more preferably from 2 weeks to 3 months, and even more preferably from 3 weeks to 2 months. In one particular embodiment, the duration of treatment is about 1 month. Alternatively, treatment can continue as long as the disease persists.

[0226] The form, route of administration, and dosage of the pharmaceutical composition according to the invention can be adjusted by those skilled in the art according to the type and severity of the disease and the patient or subject, particularly their age, weight, sex, and general physical condition.

[0227] In particular, the amount of therapeutic or preventative agent to be administered must be determined using standard procedures known to those skilled in the art. The patient's or subject's physiological data (e.g., age, body size, and weight) and route of administration must be considered to determine an appropriate dosage for administering an effective amount of treatment or prevention to the patient or subject.

[0228] For example, for each application, the total amount of the phage, engineered phage, or packaged phage particles according to the invention typically contains 10 4 Up to 10 15 A delivery medium.

[0229] In the context of this invention, the preferred method of application is local application.

[0230] The treatment or prevention methods of the present invention are envisioned to be used in combination with other standard treatments. For example, in some embodiments, the treatment or prevention methods of the present invention are performed before, after, or simultaneously with the application of additional therapeutic agents or the implementation of additional treatment or prevention methods. In some embodiments, the additional therapeutic agent may be a topical antibiotic. Non-limiting examples of topical antibiotics include clindamycin, deoxytetracycline, erythromycin, and tetracycline. In some embodiments, the additional therapeutic agent may be an oral antibiotic. Non-limiting examples of oral antibiotics include erythromycin; or tetracycline, such as deoxytetracycline or minocycline. Other additional therapeutic agents may include anti-inflammatory agents, antioxidants, acids, or combinations thereof.

[0231] In some embodiments, the additional treatment or prevention method is phototherapy. In some embodiments, the additional treatment or prevention method is laser therapy. In some embodiments, the additional treatment or prevention method includes treating the subject with blue light. In some embodiments, the additional treatment or prevention method includes treating the subject with red light. In some embodiments, the additional treatment or prevention method includes treating the subject with a targeted laser device. In some embodiments, the additional treatment or prevention method includes treating the subject with a laser targeting porphyrins.

[0232] Other treatments and combinations of other treatments or preventative measures, as disclosed above, may also be used.

[0233] Pharmaceutical Composition The present invention also relates to pharmaceutical compositions comprising: bacteriophages, recombinant bacteriophages, packaged phage particles, plasmids, vesicles containing DNA or RNA, extracellular vesicles, bacteria, or engineered bacteria as defined in the above section “Specifically reducing the amount of Propionibacterium acnes”, which encode a programmable nuclease as defined in the above section “Specifically reducing the amount of Propionibacterium acnes”, or a gene-editing enzyme or system as defined in the above section “Genetically modifying the DNA sequence in Propionibacterium acnes”, wherein the Propionibacterium acnes bacteria are as defined in the above section “Propionibacterium acnes and Propionibacterium beta”.

[0234] In one particular embodiment, the pharmaceutical composition further comprises a pharmaceutically acceptable mediator.

[0235] "Pharmaceutically acceptable mediator" in this document refers to a pharmaceutical ingredient known to be suitable for use in the preparation of pharmaceutical compositions to be administered to patients in need. Such ingredients are safe and non-sensitizing under the conditions of use.

[0236] Pharmaceutically acceptable mediators are known to those skilled in the art and include common excipients, diluents, or carriers.

[0237] In one particular embodiment, the pharmaceutical composition further comprises at least one pharmaceutically acceptable excipient and / or adjuvant.

[0238] "Pharmaceutical-acceptable excipients" in this document refer to non-pharmaceutical-active additives used in the manufacture of pharmaceutical compositions that enable the pharmaceutically active ingredient to be formulated into a pharmaceutical composition or galenine formulation, which provides the necessary bioavailability of the drug to a patient after administration of the pharmaceutical composition. The excipients are preferably compatible with the other components of the composition and do not produce adverse effects, allergic reactions, or other undesirable reactions when administered to humans or animals.

[0239] "Pharmaceutical-acceptable adjuvants" in this document refer to non-toxic, biologically tolerable, and otherwise biologically suitable substances added to a pharmaceutical composition to enhance the effect of excipients or therapeutic active ingredients.

[0240] In one particular embodiment, the pharmaceutical composition further comprises additional therapeutically active agents.

[0241] "Additional therapeutic agents" in this document refers to any chemical, biochemical, organic, or inorganic compound, composition, element, or substance that is generally designated for or can be used to treat diseases, symptoms, or functional disorders of biological or biomaterials, and is distinct from the therapeutic or preventative agents defined in the sections "Methods for treating or preventing diseases related to Propionibacterium acnes", "Specifically reducing the amount of Propionibacterium acnes type 1", "Genetically modifying the DNA sequence in Propionibacterium acnes type 1" and / or "Increasing the amount of Propionibacterium acnes type 2" above.

[0242] The additional therapeutic agents may be selected from nonsteroidal anti-inflammatory drugs (NSAIDs) analgesics; opioid agonist analgesics; salicylates analgesics; H1-blocking antihistamines; H2-blocking antihistamines; anti-infective agents; anti-anaerobic anti-infective agents; antifungal antibiotics; macrolide antibiotics; miscellaneous β-lactam antibiotics; penicillin antibiotics; quinolone antibiotics; tetracycline antibiotics; antituberculosis and antimycobacterial antibiotics; anti-antigenic animal antibiotics; antimalarial anti-antigenic animal antibiotics; antiretroviral antibiotics; antiviral anti-infective agents; alkylated antitumor agents; nitrosourea alkylated antitumor agents; antimetabolite antitumor agents; pyrimidine analogue antimetabolites. Oncology agents; Hormonal antitumor drugs; Natural antitumor drugs; Antibiotic natural antitumor drugs; Vinca alkaloid natural antitumor drugs; Autonomic nervous system agents; Anticholinergic autonomic nervous system agents; Antimuscarinic anticholinergic autonomic nervous system agents; Ergot alkaloid autonomic nervous system agents; Cholinergic agonists parasympathomimetic drugs; Cholinesterase inhibitors parasympathomimetic drugs; Alpha blockers sympathetic blockers; Beta blockers sympathetic blockers; Adrenergic agonists sympathomimetic drugs; Cardiovascular drugs; Beta blockers antianginal drugs; Calcium channel blockers antianginal drugs; Nitrate antianginal drugs; Cardiac glycosides antiarrhythmic drugs; Class I antiarrhythmic drugs; Class II antiarrhythmic drugs; Class III antiarrhythmic drugs; Class IV antiarrhythmic drugs; Alpha blockers Discontinuation antihypertensive drugs; angiotensin-converting enzyme inhibitors (ACE inhibitors) antihypertensive drugs; beta-blockers antihypertensive drugs; calcium channel blockers antihypertensive drugs; centrally acting adrenergic antihypertensive drugs; diuretics antihypertensive drugs; peripheral vasodilators antihypertensive drugs; antilipidemic drugs; bile acid sequestrants antilipidemic drugs; HMG-CoA reductase inhibitors antilipidemic drugs; positive inotropic agents; cardiac glycosides positive inotropic agents; thrombolytic agents or enzymes; dermatological medications; corticosteroid anti-inflammatory drugs for dermatological conditions; topical antifungal agents; topical antiviral agents; topical antitumor agents; electrolyte and nephrological medications; loop diuretics; potassium-sparing diuretics; thiazide diuretics; uricosuric agents; enzymes, such as ribonuclease and deoxyribonuclease; immunosuppressants; antiemetics. Drugs; salicylates; gastrointestinal anti-inflammatory drugs; gastric acid pump inhibitors; anti-ulcer drugs; H2 blockers; digestive aids; prokinetic agents; opioid agonists; intravenous anesthetics; hematopoietic and anti-anemic agents; coagulants; anticoagulants; growth receptor inhibitors; abortifacients; antidiabetic drugs; oral contraceptives; progestin contraceptives; estrogens; fertility factors; parathyroid agents; pituitary hormones; progesterone; thyroid hormones; immunobiological agents; immunoglobulins; amide local anesthetics; ester local anesthetics; musculoskeletal corticosteroids; musculoskeletal anti-inflammatory immunosuppressants; musculoskeletal nonsteroidal anti-inflammatory drugs (NSAIDs); skeletal muscle relaxants; neuromuscular blockade reversal agents; skeletal muscle relaxants; neurological drugs; anticonvulsants; barbiturates.Benzodiazepine anticonvulsants; anti-Parkinson's disease drugs; anti-vertigo drugs; opioid agonists; opioid antagonists; beta-blockers for glaucoma; miotics for glaucoma; ophthalmic aminoglycoside anti-infectives; ophthalmic quinolone anti-infectives; ophthalmic corticosteroid anti-inflammatory drugs; ophthalmic nonsteroidal anti-inflammatory drugs (NSAIDs); antipsychotics; benzodiazepine anxiolytics, sedatives, and hypnotics; psychostimulants; antitussives; bronchodilators; adrenergic agonists for bronchodilators; respiratory corticosteroid anti-inflammatory drugs; antidotes; heavy metal antagonists / chelators; substance abuse deterrents; substance abuse withdrawal drugs; minerals such as iron, calcium, and magnesium; vitamin B compounds such as cyanocobalamin (vitamin B12) and niacin (vitamin B3); Vitamin C compounds; vitamin D compounds, such as calcitriol; vitamins A, E, and vitamin E compounds; antihemorrhagic agents; anthelmintic and anti-infective agents; sclerosing agents; anabolic agents; antacids; antiasthmatics; anticholinergics and antilipidemics; antidiarrheals; antimanic agents; antinausea agents; weight-loss drugs; antipyretics and analgesics; antispasmodics; antithrombotics; antiuric agents; antitussives; appetite suppressants; cerebral vasodilators; coronary vasodilators; decongestants; diagnostic drugs; erythropoiesis agents; expectorants; gastrointestinal sedatives; hyperglycemic agents; hypoglycemic agents; ion exchange resins; laxatives; mucolytics; neuromuscular drugs; peripheral vasodilators; psychotropic drugs, stimulants; thyroid drugs and antithyroid drugs; and uterine relaxants.

[0243] In one particular embodiment, the pharmaceutical composition may further comprise a skin care agent.

[0244] In this article, "skin care agent" refers to any agent that has one or more beneficial effects on the care and / or hygiene of the skin. Skin care agents may be selected from antioxidants, free radical scavengers, skin protectants, skin conditioning agents, skin soothing agents, exfoliants, emollients, softeners, and moisturizers.

[0245] In this document, "skin conditioning agents" refers to agents that can maintain the skin in good condition. Examples of skin conditioning agents include urea, guanidine, aloe vera, glycolic acid and glycolates (such as ammonium and alkyl quaternary ammonium), lactic acid and lactates (such as sodium lactate, ammonium lactate and alkyl quaternary ammonium lactate), polyhydroxy alcohols (such as sorbitol, glycerin, glycerol, tocopherol, propylene glycol, butylene glycol, hexanediol, polyethylene glycol), carbohydrates (such as alkoxylated glucose, starch, starch derivatives), glycerin, pyrrolidone carboxylic acid (PCA), lactamide monoethanolamine, acetamide monoethanolamine, volatile silicone oils, non-volatile silicone oils, sunflower seed oil, phospholipids, white willow (willow tree) bark extract, soybean seed extract, and mixtures thereof.

[0246] Examples of skin soothing agents include bisabolol.

[0247] As used in this article, "skin protectant" is a pharmaceutical agent that protects the skin from chemical and / or physical irritants such as UV light, including sunscreens, anti-wrinkle agents, and anti-skin atrophy agents.

[0248] Examples of UV masking agents include 2-ethylhexyl p-methoxycinnamate, 2-ethylhexyl N,N-dimethyl-p-aminobenzoate, p-aminobenzoic acid, 2-phenylbenzimidazole-5-sulfonic acid, octocrylene, oxybenzone, and homosalicylate. salicylate), octyl salicylate, 4,4'-methoxy-tert-butyldibenzoylmethane, 4-isopropyldibenzoylmethane, 3-benzylidene camphor, 3-(4-methylbenzylidene)camphor, anthranilic benzoate, ultrafine titanium dioxide, zinc oxide, iron oxide, silicon dioxide, 4-N,N-(2-ethylhexyl)methylaminobenzoate of 2,4-dihydroxybenzophenone, 4-N,N-(2-ethylhexyl)methylaminobenzoate of 4-hydroxy-4-(2-hydroxyethoxy)benzophenone, and 4-N,N-(2-ethylhexyl)methylaminobenzoate of 4-(2-hydroxyethoxy)dibenzoylmethane.

[0249] Examples of anti-wrinkle and anti-skin atrophy agents include retinoic acid and its derivatives, retinol, retinyl esters, salicylic acid and its derivatives, sulfur-containing D and L amino acids other than cysteine, α-hydroxy acids (such as glycolic acid and lactic acid), phytic acid, lipoic acid and lysophosphatidic acid.

[0250] Examples of antioxidants and / or free radical scavengers include ascorbic acid, salts of ascorbic acid such as ascorbyl palmitate and sodium ascorbate, ascorbyl glucosamine, vitamin E (i.e., tocopherol such as α-tocopherol), derivatives of vitamin E (e.g., tocopheryl acetate), retinoids such as retinoic acid, retinol, trans-retinol, cis-retinol, mixtures of trans-retinol and cis-retinol, 3-dehydroretinol, and derivatives of vitamin A (e.g., retinyl acetate, retinal, and retinyl palmitate, also known as tetinyl palmitate). palmitate), lipoic acid, sodium citrate, sodium sulfite, lycopene, anthocyanins, bioflavonoids (e.g., hesperidin, naringin, rutin and quercetin), superoxide dismutase, glutathione peroxidase, butylated hydroxytoluene (BHT), butylated hydroxyanisole (BHA), indole-3-methanol, pycnogenol, melatonin, sulforaphane, pregnenolone, lipoic acid and 4-hydroxy-5-methyl-3[2H]-furanone.

[0251] Examples of exfoliants include hydroxycarboxylic acids such as α-hydroxy acids or β-hydroxy acids, keto acids, and hydroxybenzoic acid.

[0252] Examples of emollients include lactic acid and other hydroxy acids and their salts, glycerin, propylene glycol, butylene glycol, sodium PCA, sodium hyaluronate, Carbowax 200, Carbowax 400 and Carbowax 800.

[0253] Examples of softeners or humectants include panthenol, cetyl palmitate, glycerin (glycerol), PPG-15 stearyl ether, lanolin alcohol, lanolin, lanolin derivatives, cholesterol, petrolatum, isostearyl neopentanoate, octyl stearate, mineral oil, isocetyl stearate, myristyl myristate, octyl dodecyl alcohol, 2-ethylhexyl palmitate (octyl palmitate), polydimethylsiloxane, phenyl polytrimethylsiloxane, cyclodimethylsiloxane, and C benzoate. 12 -C 15 Alkyl esters, polydimethylsiloxane alcohol, propylene glycol, cocoa seed oil, ceramides (e.g., ceramide 2 or ceramide 3), hydroxypropyl bispalmitamide MEA, hydroxypropyl bislauramide MBA, hydroxypropyl bisisostearylamide MEA, 1,3-bis(N-2-(hydroxyethyl)stearoylamino)-2-hydroxypropane, bis(hydroxyethyl)tocopherol succinylaminohydroxypropane, urea, aloe vera, allantoin, glycyrrhetinic acid, safflower oil, oleyl alcohol, oleic acid, stearic acid, dioctanoate / didecanoate, diethyl sebacate, isostearyl alcohol, pentylene glycol, isononyl isononanoate, and 1,3-bis(N-2-(hydroxyethyl)palmitoylamino)-2-hydroxypropane.

[0254] The pharmaceutical compositions of the present invention can be formulated in any suitable form known to those skilled in the art.

[0255] In one particular embodiment, the composition is in the form of: an aqueous, hydroalcoholic, or oily solution; a solution or dispersion in the form of a toner or serum; an emulsion (particularly an emulsion of liquid or semi-liquid consistency of the emulsion type, which is typically obtained by dispersing a fat phase in an aqueous phase (O / W) or vice versa (W / O)); or a suspension or emulsion of a soft semi-solid or solid consistency of the cream type; a cream; an aqueous or anhydrous gel; a microemulsion; a nanoemulsion; microcapsules; microparticles; ionic and / or nonionic vesicle dispersions; rods; aerosol sprays; pump sprays; or foams. In one particular embodiment, the composition is in the form of an emulsion, microemulsion, or nanoemulsion.

[0256] The pharmaceutical compositions of the present invention may be in any form known to those skilled in the art, depending generally on their route of administration.

[0257] For oral administration, the pharmaceutical composition may be in the form of tablets, capsules, sugar-coated pills, syrups, suspensions, solutions, powders, granules, emulsions, suspensions of microspheres or nanospheres providing controlled release, or lipid or polymer vesicles.

[0258] For parenteral administration, the pharmaceutical composition may be in the form of a solution or suspension for infusion or injection.

[0259] For topical application, the pharmaceutical composition may be in the form of ointment, cream, emulsion, ointment, powder, medicated swabs, solution, gel, spray, lotion, or suspension. It may also be in the form of a suspension, lipid or polymer vesicle, polymer patch, or hydrogel providing controlled release of microspheres or nanospheres. Such formulations for topical application may be in anhydrous, aqueous, or emulsion form.

[0260] Preferably, the pharmaceutical composition of the present invention is used for local application.

[0261] The pharmaceutical compositions according to the invention can be prepared by mixing essential and optional ingredients (if desired).

[0262] The methods and means of mixing the above-mentioned essential and optional components are not limited. Any conventional methods and means can be used to mix the above-mentioned essential and optional components to prepare the formulation according to the invention.

[0263] Risks and diagnosis of acne development The present invention also relates to a method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, the method comprising the steps of: a) Determine the presence and / or quantity of *Propionibacterium acnes* type α in samples, particularly skin samples, from the subject, wherein *Propionibacterium acnes* type α is as defined in the “Propionibacterium acnes type α and *Propionibacterium acnes type β” section above, and b) Based on the presence and / or amount determined in step a), determine whether the subject is at risk of developing acne, particularly acne vulgaris.

[0264] The present invention also relates to a method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, the method comprising the steps of: a) Determine the presence and / or quantity of *Propionibacterium acnes* bacterium in samples, particularly skin samples, from the subject, wherein *Propionibacterium acnes* bacterium is as defined in the “Alpha- and Beta-type Propionibacterium acnes” section above, and b) Based on the presence and / or amount determined in step a), determine whether the subject is at risk of developing acne, particularly acne vulgaris.

[0265] The present invention also relates to a method for diagnosing acne, particularly acne vulgaris, in a subject, the method comprising the following steps: a) Determine the presence and / or quantity of *Propionibacterium acnes* type α in samples, particularly skin samples, from the subject, wherein *Propionibacterium acnes* type α is as defined in the “Propionibacterium acnes type α and *Propionibacterium acnes type β” section above, and b) Diagnose the subject’s acne, particularly acne vulgaris, based on the presence and / or amount determined in step a).

[0266] The present invention also relates to a method for diagnosing acne, particularly acne vulgaris, in a subject, the method comprising the following steps: a) Determine the presence and / or quantity of *Propionibacterium acnes* bacterium in samples, particularly skin samples, from the subject, wherein *Propionibacterium acnes* bacterium is as defined in the “Alpha- and Beta-type Propionibacterium acnes” section above, and b) Diagnose the subject’s acne, particularly acne vulgaris, based on the presence and / or amount determined in step a).

[0267] As used herein, the term “quantity” has the same meaning as disclosed in the “Methods for treating or preventing diseases associated with Propionibacterium acnes” section above.

[0268] In a preferred embodiment of the method, the amount of Propionibacterium acnes type α or Propionibacterium acnes type β is the relative abundance of Propionibacterium acnes type α or Propionibacterium acnes type β.

[0269] As used herein, the term "presence" means that the amount of *Propionibacterium acnes* type α or *Propionibacterium acnes* bacteria in the sample is within the detectable range of the techniques used to detect the bacteria, and more particularly, to detect *Propionibacterium acnes* type α or *Propionibacterium acnes* type β. In other words, when it is determined that *Propionibacterium acnes* type α or *Propionibacterium acnes* bacteria are not present in the sample, this means that they are below the detection threshold of the techniques used for that determination step.

[0270] Preferably, the sample is a skin sample.

[0271] Skin samples can be any sample taken from the subject's skin. Skin samples can be obtained by any means known in the art, including but not limited to wiping the skin with a tool capable of collecting skin cells (e.g., a cotton swab (Q-tip) or cotton swab), placing adhesive or tape on the skin surface and removing the adhesive or tape, thereby creating a skin sample on the adhesive or tape, or by biopsy (e.g., scraping biopsy, drilling biopsy, excisional biopsy, disc biopsy, or open biopsy). As those skilled in the art will understand, skin samples need to be obtained by any means that enables the collection of bacteria present on the subject's skin (preferably in the subject's hair follicles). Therefore, skin samples contain at least a portion of the skin microbiome.

[0272] In some implementations, the skin sample further includes epithelial cells, epidermal cells, dermal cells, hair / skin follicles, adipose tissue (i.e., subcutaneous fat), and / or connective tissue.

[0273] As highlighted above and in the following examples, the inventors demonstrate that a set of 218 SNPs at the hem locus (containing genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) can classify the known diversity of *Propionibacterium acnes* strains into two groups, referred to herein as α-type and β-type. Importantly, this novel typing correlates with publicly available porphyrin production levels more precisely than the deoR gene. Furthermore, after developing a method for estimating the relative abundance of α-type and β-type *Propionibacterium acnes* strains in shotgun metagenomic sequencing data and applying it to publicly available datasets related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491), the inventors demonstrate that α-type *Propionibacterium acnes* strains are significantly more abundant in patients with acne vulgaris than in healthy subjects.

[0274] Therefore, in the method of the present invention for determining whether a subject is at risk of developing acne, particularly acne vulgaris, the subject is identified as being at risk of developing acne, particularly acne vulgaris, when (i) it is determined that *Propionibacterium acnes* type α is present in the sample and / or when the amount of *Propionibacterium acnes* type α, particularly its relative abundance (e.g., relative to the subject's entire bacterial population, particularly the dermal bacterial population, or relative to the subject's entire *Propionibacterium acnes* population, particularly the dermal *Propionibacterium acnes* population) is higher than a reference value, or (ii) it is determined that *Propionibacterium acnes* type β is present in the sample and / or when the amount of *Propionibacterium acnes* type β, particularly its relative abundance (e.g., relative to the subject's entire bacterial population, particularly the dermal bacterial population, or relative to the subject's entire *Propionibacterium acnes* population, particularly the dermal *Propionibacterium acnes* population) is lower than a reference value. Similarly, in the diagnostic method of the present invention, a subject is diagnosed with acne, particularly acne vulgaris, when (i) it is determined that *Propionibacterium acnes* type α is present in the sample and / or when the amount of *Propionibacterium acnes* type α, particularly its relative abundance (e.g., relative to the subject's entire bacterial population, particularly the dermal bacterial population, or relative to the subject's entire *Propionibacterium acnes* population, particularly the dermal *Propionibacterium acnes* population) is higher than a reference value, or (ii) it is determined that *Propionibacterium acnes* type β is present in the sample and / or when the amount of *Propionibacterium acnes* type β, particularly its relative abundance (e.g., relative to the subject's entire bacterial population, particularly the dermal bacterial population, or relative to the subject's entire *Propionibacterium acnes* population, particularly the dermal *Propionibacterium acnes* population) is lower than a reference value.

[0275] In one particular implementation, the reference values ​​are the amounts of Propionibacterium alpha-acne and Propionibacterium β-acne in corresponding samples, particularly skin samples, from healthy subjects, especially their relative abundance (e.g., relative to the subject’s entire bacterial population, particularly the skin bacterial population, or relative to the subject’s entire Propionibacterium acne population, particularly the dermal Propionibacterium acne population).

[0276] “Healthy subject” in this document means a subject who does not have acne, especially acne vulgaris, and preferably does not have any Propionibacterium acnes-related diseases, especially skin diseases, and / or inflammatory diseases and / or skin diseases, and more preferably does not further show any signs of skin discomfort, such as signs associated with sensitive skin, sensitized skin, fragile skin or weakened skin, or any uncomfortable and unsightly manifestations of sensitized, fragile and / or weakened skin.

[0277] “Sensitive skin” in this context refers to skin that is inherently intolerant to aggressive factors, particularly environmental factors (such as pollutants), climatic factors (wind, cold, heat), emotional factors (especially stress), and / or chemical factors (heavy metals, detergents, compounds contained in cosmetic compositions such as fragrances, preservatives, alcohols, pH, AHAs, or dermatological treatments such as retinoic acid) and / or aggressive conditions, including sweating and mechanical abrasion such as waxing, shaving, friction, and even water, especially hard water. Unlike allergic skin, sensitive skin is not pathological. However, it can respond to aggressive factors and / or conditions through unsightly and / or uncomfortable skin manifestations such as tingling, hot or warm sensations, tension, tingling, tightness, and redness. Thus, the characteristics of “sensitive skin” can be assessed by the subject themselves with subjective skin sensations or by a dermatologist with objective skin reactions.

[0278] "Sensitive skin" in this article refers to skin and / or mucous membranes that have temporarily become sensitive as defined above, and is therefore not pathological in itself.

[0279] "Vulnerable skin" and / or "weakened skin" (i.e., skin that has temporarily become vulnerable) refers to skin with weakened barrier function in this article. This can be related to an individual's condition; for example, older adults and infants have more vulnerable skin. This condition can be caused by chemical or physical abrasion (e.g., abrasion, friction).

[0280] The discomfort and unsightly appearance of sensitized, fragile, and / or weakened skin are the same as those of sensitive skin, and these appearances and / or skin conditions are not considered to be related to the prevention and / or treatment of pathology.

[0281] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains.

[0282] It is important to note that, as used herein, unless the context clearly indicates otherwise, the singular forms “a,” “an,” and “the / that” include plural indicators. Thus, for example, reference to “a cell” includes multiple such cells (e.g., a population of such cells). Similarly, reference to “a nucleic acid” includes one or more such nucleic acids.

[0283] Although the invention has been described in conjunction with its specific embodiments, many alternatives, modifications, and variations will be apparent to those skilled in the art. Therefore, it is intended to cover all such alternatives, modifications, and variations falling within the spirit and broad scope of the appended claims.

[0284] All publications, patents, and patent applications mentioned in this specification are incorporated herein by reference in their entirety, to the extent that such individual publications, patents, or patent applications are specifically and individually cited and incorporated herein. Furthermore, any reference or designation of any reference in this application should not be construed as an admission that such reference is prior art to the invention. The use of section headings should not be construed as necessarily limiting.

[0285] The following examples are provided to illustrate various embodiments of the present invention and are not intended to limit the invention in any way.

[0286] Sequence details Brief description of the attached diagram Figure 1 Phylogenetic tree of the annotated SLST cluster and the hem loci classified by α / β typing as disclosed in this paper.

[0287] Figure 2: Published porphyrin production levels and their designated α / β types and the presence (deoR+) or absence (deoR-) of deoR repressors. Figure 2A Adapted from Barnard et al. (2020) mSphere 5:e00793-19 Figure 1 ; Figure 2B Adapted from Johnson et al. (2016) mSphere1(1):e00023-15 Figure 1 ; Figure 2C : Adapted from Figure S4 of Johnson et al. (2016) mSphere 1(1):e00023-15.

[0288] Figure 3 Extraction of the glpR / deoR reference DNA sequence by alignment with the common glpR / deoR DNA sequence of most strains in the SLST D cluster. Insertion of a poly-G into the SLST D variant DNA sequence resulted in a frameshift and the generation of an early stop codon at position 105, while the glpR / DeoR reference protein was 310 AA long.

[0289] Figure 4 The difference in the ratio of Propionibacterium acnes type α populations in the skin metagenomics of healthy skin and patients with acne vulgaris.

[0290] Figure 5The hem locus is conserved in Propionibacterium acnes strains and contains eight hem genes: hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY. Representatives from each SLST cluster are shown.

[0291] Figure 6: Specific nuclease-mediated killing of α-type Propionibacterium acnes strains. A) Specific nuclease-mediated killing of Propionibacterium acnes phylogenetics and α-strains relative to β-strains. Four diluted populations of Propionibacterium acnes strains (one α-strain: SLST A5; three β-strains: SLST D1, D2, K9) were transduced with phages packaged in three different ways. Each phage package contained a DNA payload carrying a chloramphenicol cassette, a nuclease (SEQ ID NO: 11) expression cassette, and non-targeting gRNA (SEQ ID NO: 12, black bar), or gRNA targeting strains A5, D1, and D2 (SEQ ID NO: 13, gray bar), or HemB gRNA targeting only strain SLST A5 (SEQ ID NO: 14, white bar). Y-axis: Colony-forming units (cfu) per μL of phage packaged on a BHI+3 μg / mL chloramphenicol plate. B) Specific nuclease-mediated killing of α-strains of Propionibacterium acnes relative to β-strains. Six different packaged phage particles were used to transduce each diluted population of four Propionibacterium acnes strains (three α-type strains: 2×SLST A1, SLST A5; and one β-type strain: SLST K9). Each phage particle contained a DNA payload carrying a chloramphenicol cassette, a nuclease (SEQ ID NO: 11) expression cassette, and a non-targeting gRNA (SEQ ID NO: 12) or a set of hem gRNAs targeting the three α-type strains at different locations on the hem locus: HemB_1 gRNA targeting HemB α nucleotide variant A155 (SEQ ID NO: 14); HemL_2 gRNA targeting HemL α nucleotide variants C389 and T392 (SEQ ID No: 15); and HemY_2 gRNA targeting HemY α nucleotide variants T1199 and T1205 (SEQ ID No: 16). Y-axis: colony-forming units per μL of phage particle packaged on a BHI+3 μg / mL chloramphenicol plate.

[0292] Example Example 1 Heme molecules (which are porphyrin rings complexed with iron) are enzymatic cofactors and an essential iron source for the survival of bacterial pathogens (Choby et al. (2016) J. Mol. Biol. 428:3408-3428). *Propionibacterium acnes* (… Cutibacterium acnes(Hereinafter referred to as Propionibacterium acnes) C. acnes Propionibacterium acnes is one of the most abundant bacteria inhabiting human skin (Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152-2160; Oh et al. (2014) Nature 515-59-64). It is also known to be involved in acne vulgaris, an inflammatory skin disease affecting the vast majority of adolescents and young adults (Bhate et al. (2013) British Journal of Dermatology 168:474-485). Propionibacterium acnes has been shown to produce porphyrins that trigger inflammation (Schaller et al. (2005) British J Dermatol. 153:66-71; Spitaels et al. (2021) iScience 24:102575). Interestingly, different porphyrin production levels were observed in Propionibacterium acnes strains from different lineages (Johnson et al. (2016) mSphere 1:e00023-15; Barnard et al. (2020) mSphere 5:e00793-19), and the presence of a putative repressor gene from the deoR family had previously been speculated to be the cause of low porphyrin production levels (Johnson et al. (2016) mSphere 1:e00023-15). However, this explanation is incomplete, as high porphyrin production levels have also been observed in some strains that encode deoR in their genomes (Barnard et al. (2020) mSphere 5:e00793-19). Furthermore, while strain lineage generally indicates low / high porphyrin production, exceptions have been described in the literature (Johnson et al. (2016) mSphere 1:e00023-15).

[0293] Key enzymes involved in the porphyrin biosynthesis pathway in Propionibacterium acnes are encoded by eight genes (hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY). These gene clusters are located at a conserved locus (hereinafter referred to as the hem locus) across all strains of Propionibacterium acnes.

[0294] The inventors discovered that a set of 218 SNPs at the hem locus can classify the known diversity of *Propionibacterium acnes* strains into two groups: α and β. While the inventors can definitively assign types from classic *Propionibacterium acnes* typing schemes (SLST, recA) to α or β, based on core genome phylogeny, α and β types are not monologous (i.e., overall similarity of the strain genome cannot predict whether a strain is α or β). Importantly, the α / β typing is strictly correlated with the presence / absence of publicly known porphyrin production levels; α-type strains are high-yielding strains, while β-type strains are low-yielding strains.

[0295] Furthermore, the inventors developed a method for estimating the relative abundance of α- and β-type Propionibacterium acnes strains in shotgun metagenomic sequencing data and applied it to a publicly available dataset related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491). They found that α-type strains formed a significantly larger proportion of Propionibacterium acnes populations in patients with acne vulgaris than in healthy volunteers. Therefore, therapeutic approaches that specifically kill α-type Propionibacterium acnes strains, specifically inhibit the growth of α-type Propionibacterium acnes strains, or inactivate porphyrins in α-type Propionibacterium acnes strains have the potential to prevent and / or treat acne vulgaris.

[0296] Genome assemblies of 475 Propionibacterium acnes strains were obtained by sequencing via Eligo Bioscience or downloaded from public libraries. For each assembly, single locus sequence type (SLST) was predicted using computed PCR amplification and sequence alignment with primers and reference sequences described by Scholz et al. (Scholz et al. (2014) PloS ONE9:e104199). Pan-genome analysis of the entire collection was also performed using roary (Page et al. (2015) Bioinformatics 31:3691-3693) and panX (Ding et al. (2018) Nucleic Acids Res. 46:e5), and a phylogenetic tree based on the core genome was constructed using RaxML (Stamatakis (2014) Bioinformatics 30:1312-1313). Based on the branch length of the core genome phylogenetic tree, the inventors defined a coarser typing scheme, SLST clusters, which include groupings of SLST types that begin with the same letter (e.g., SLST cluster A includes SLST A1, A2, etc.).

[0297] Genes from the hem locus were extracted from all available assemblies, and phylogenetic trees were constructed based on their tandem amino acid sequences using IQ-TREE (Minh et al. (2020) Mol. Biol. Evol. 37:1530-1534), an edge-equal partitioning model (Chernomor et al. (2016) Syst. Biol. 65:997-1008), and a modified Dayhoff matrix substitution model (Kosiol et al. (2005) Mol Biol Evol 22:193–199). The obtained trees ( Figure 1 In the study, the inventors observed two distinct groups that did not match the phylogenetic structure of the core genome—one containing SLST clusters A, B, C, E, F, G, and H (designated α type), and the other containing SLST clusters D, K, and L (designated β type). Importantly, no SLST clusters were separated between the two types.

[0298] To obtain the set of marker SNPs for these types, the inventors calculated multiple sequence alignments of each gene with MUSCLE (Edgar (2004) Nucleic Acids Res 32:1792-1797) at the nucleotide level and identified positions that distinguished α-type and β-type, while being conserved in more than 90% of the genome from each type. This procedure identified 218 marker positions (see Table 1 above). Based on these results, the inventors defined α-type (and β-type) as strains possessing α-characteristic (or β-characteristic) nucleotide variations at at least 90% of the stated positions.

[0299] Analysis of publicly available porphyrin levels Available scientific literature was searched to obtain reported porphyrin production levels in *Propionibacterium acnes* strains. Data from two articles (Johnson et al. (2016) mSphere 1:e00023-15; Barnard et al. (2020) mSphere 5:e00793-19) were summarized, and the strains used were genotyped using available genome sequences and the SLST protocol. In cases where genome sequences were unavailable, SLST clusters were inferred from the authors' reported lineages.

[0300] Based on the SLST cluster, strains were designated as α- or β-type. The inventors observed that strains classified as high- or low-porphyrin-producing strains precisely corresponded to α- and β-type strains, respectively (Figure 2), providing a more reliable explanation of production levels than the presence of the deoR repressor. Furthermore, through multiple sequence alignment of the deoR gene, the inventors discovered that strains in the SLST cluster D carried a poly-G insertion in this gene, which in most cases resulted in transposed reading frames and nonsense mutations, including HL025PA1 (…). Figure 3 Therefore, the deoR in the SLST cluster D is not expected to be functional and cannot explain the measured low porphyrin production. Thus, the inventors believe that the SNPs in Table 1 above are biomarkers for high porphyrin production (α-type). Conversely, β-type is associated with low porphyrin production.

[0301] Metagenomic analysis Metagenomic shotgun sequencing data (including follicular plug samples from 42 patients with acne vulgaris and 40 healthy volunteers) from Barnard et al. (2016) Scientific Reports 6:39491 were obtained from the NCBI dbGaP resource (accession number phs001655). Raw reads were preprocessed using fastp (Chen et al. (2018) Bioinformatics 34:i884-i890) and aligned with the human reference genome and PhiX genome using bowtie2 (Langmead et al. (2012) Nature Methods 9:357-359). Reads aligned to the host or PhiX genome were removed, and those that passed QC were mapped to the reference hem locus using bwa mem (Li (2013) arXiv:1303.3997), retaining only correctly matched mappings for downstream analysis.

[0302] Because the locus is always a single copy in the available Propionibacterium acnes genome and does not have close orthologs in other species (in Cutibacterium modestum The closest one in the dataset has 86% identity at the nucleotide level, so the inventors did not include other reference sequences in the alignment database. However, to validate their method, they also used Kraken2 (Wood et al. (2019) Genome Biology 20:257) to remove reads assigned to species other than Propionibacterium acnes from the dataset, and no differences were observed in our results.

[0303] For each of the 218 distinguishing positions, scores for α and β variants were calculated from alignment stacking. The overall relative abundance of each type within the *Propionibacterium acnes* population was calculated using the median frequency of its characteristic SNPs at the 218 positions. α variants were found to be significantly more abundant in patients with acne vulgaris than in healthy controls (p < 0.0112; Mann-Whitney U test). Figure 4 ).

[0304] Example 2 Specific nuclease-mediated killing of Propionibacterium acnes phylogenetic and α strains relative to β strains This embodiment demonstrates nuclease-mediated specific killing of *Propionibacterium acnes* serotypes and α strains relative to β strains. Nucleases can be programmed to target and kill specific serotypes (serotypes IA1 and II in this embodiment), encompassing both α and β strains as defined in the "α-type and β-type *Propionibacterium acnes* bacteria" section above. Figure 6A Similarly, nucleases can be programmed to target and kill only the α strain while keeping the β strain intact. Figure 6B ).

[0305] Four strains of Propionibacterium acnes (one α-type strain: SLST A5; three β-type strains: SLST D1, D2, and K9) were anaerobically grown overnight at 37°C and diluted to an OD600 of 0.05 the next day. Strains SLST A5, SLST D1, and SLST D2 belonged to phylogenetic IA1. SLST K9 belonged to phylogenetic II. Each diluted population of Propionibacterium acnes was transduced with three different packaged phages, each phage packaged with a DNA payload carrying a chloramphenicol cassette, a Mad4 nuclease (SEQ ID NO: 11) expression cassette, and a non-targeting gRNA (SEQ ID NO: 12), or targeting phylogenetic IA1 (i.e., gRNA of strains A5, D1, and D2 (SEQ ID NO: 13)), or targeting the hemB α nucleotide variant A155 and thus targeting only the HemB gRNA (HemB_1 gRNA) (SEQ ID NO: 14) of α-type Propionibacterium acnes strains (such as strain SLSTA5). After transduction, the transduced cells were serially diluted and plated on plates with 3 μg / mL solutions. -1 Chloramphenicol was placed on BHI agar and incubated in an anaerobic chamber at 37°C.

[0306] like Figure 6A As shown, phage particles packaged with HemB_1 gRNA programmed to target the hemB α nucleotide variant A155 selectively reduced the number of α-type strains (SLST A5) by more than 4 logs, without affecting the growth of any β-type strains (SLST D1, D2, and K9). As expected, phage particles packaged with IA1 gRNA selectively reduced the colony counts from strains SLST A5, D1, and D2 to 1 / 10. 4 At the same time, it does not affect the number of colonies from strain SLST K9.

[0307] Specific nuclease-mediated killing of Propionibacterium acnes α strains relative to β strains Four strains of Propionibacterium acnes (three α-type strains: 2×SLST A1, SLST A5; and one β-type strain: SLST K9) were anaerobically grown overnight at 37°C and diluted to an OD600 of 0.05 the next day. Each diluted Propionibacterium acnes population was transduced with six different packaged phages. Each phage package contained a DNA payload carrying a chloramphenicol cassette, a Mad4 nuclease (SEQ ID NO: 11) expression cassette, and a non-targeting gRNA (SEQ ID NO: 12) or a set of Hem gRNAs targeting the three α-type strains at different locations on the hem locus: HemB_1 gRNA (SEQ ID NO: 14) targeting the HemB α nucleotide variant A155; HemL_2 gRNA (SEQ ID No: 15) targeting the HemL α nucleotide variants C389 and T392; and HemY_2 gRNA (SEQ ID No: 16) targeting the HemY α nucleotide variants T1199 and T1205. After transduction, the transduced cells were serially diluted and plated on plates with 3 μg / mL solutions. -1 Chloramphenicol was loaded onto BHI agar. The plates were incubated at 37°C in an anaerobic chamber.

[0308] like Figure 6B As shown, phage particles packaged with Hem gRNA programmed to target α-nucleotide variations selectively reduced the number of three α-type strains by more than 99.9% without affecting the number of colonies from β-type strains.

Claims

1. A method for treating or preventing Propionibacterium acnes-related diseases in a subject, the method comprising adjusting, in particular reducing, the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

2. The method of claim 1, wherein the ratio is the ratio of the amount of Propionibacterium acnes type α bacteria on the subject's skin to the amount of Propionibacterium acnes type β bacteria on the skin.

3. The method according to claim 1 or 2, wherein the method comprises specifically reducing the amount of Propionibacterium acnes type α bacteria in the subject, particularly on the skin of the subject.

4. The method of claim 3, wherein the method comprises specifically killing or inhibiting the growth of Propionibacterium acnes type α bacteria, particularly on the skin of the subject.

5. The method of claim 4, wherein the method comprises administering to the subject a therapeutically or preventively effective amount of an antibacterial agent, a bacteriophage, a recombinant bacteriophage, a packaged phage particle, a plasmid, a vesicle containing DNA or RNA, an extracellular vesicle, a bacterium, or engineered bacteria specifically targeting the Propionibacterium acnes type α bacteria.

6. The method of claim 5, wherein the method comprises administering to the subject a therapeutically or preventively effective amount of a phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria specifically targeting the Propionibacterium acnes type α bacteria.

7. The method of claim 6, wherein the bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encodes a programmable nuclease designed to specifically target the α-type Propionibacterium acnes bacteria.

8. The method of claim 7, wherein the programmable nuclease is selected from CRISPR-Cas nucleases, TALENs and their variants, zinc finger nucleases (ZFNs) and their variants, a wide range of natural, evolved or engineered nuclease or recombinase variants, and any combination and hybrid thereof.

9. The method of claim 8, wherein the programmable nuclease is a CRISPR-Cas nuclease.

10. The method of claim 9, wherein the phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria further encodes a guide RNA designed to specifically target the Propionibacterium acnes type α bacteria.

11. The method of claim 10, wherein the guide RNA is designed to specifically target the hem locus of the α-type Propionibacterium acnes, and particularly, the guide RNA is selected from SEQ ID No: 13-16.

12. The method according to any one of claims 5 to 11, wherein the application is a local application.

13. The method of claim 3, wherein the method comprises genetically modifying the DNA sequence of *Propionibacterium acnes* bacteria, particularly on the skin of the subject, to produce at least one change in the *hem* locus of *Propionibacterium acnes* bacteria.

14. The method of claim 13, wherein the method comprises administering to the subject a therapeutically or preventively effective amount of a phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding a gene-editing enzyme or system targeting the hem locus in the Propionibacterium acnes type 1 bacteria.

15. The method according to claim 13 or 14, wherein the genetic modification is a dot modification.

16. The method of claim 14, wherein the gene-editing enzyme is a base editor or a bootstrap editor.

17. The method according to any one of claims 14 to 16, wherein the application is a local application.

18. The method of claim 1 or 2, wherein the method comprises increasing the amount of Propionibacterium β-acne bacteria in the subject, particularly on the skin of the subject.

19. The method according to any one of claims 1 to 18, wherein the Propionibacterium acnes bacterial-associated disease is a Propionibacterium acnes bacterial-associated inflammatory disease.

20. The method according to any one of claims 1 to 19, wherein the Propionibacterium acnes bacterial-associated disease is acne, particularly acne vulgaris.

21. A method for treating or preventing Propionibacterium acnes-related disease in a subject, the method comprising specifically reducing the expression of at least one hem locus protein in Propionibacterium acnes type α in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) wherein the nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

22. The method of claim 21, wherein the method comprises administering to the subject a therapeutic or preventative amount of a therapeutic or preventative agent, the therapeutic or preventative agent specifically reducing the expression of at least one hem locus protein in the subject by genetically modifying the DNA sequence of *Propionibacterium acnes* bacteria in the subject, preferably the agent being a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding a gene-editing enzyme or system targeting the hem locus.

23. A composition for treating or preventing Propionibacterium acnes-related diseases in a subject, the composition comprising a therapeutic or preventive agent that induces a reduction in the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

24. The composition used according to claim 23, wherein the therapeutic or preventative agent is an antibacterial agent, a bacteriophage, a recombinant bacteriophage, a packaged phage particle, a plasmid, a vesicle containing DNA or RNA, an extracellular vesicle, a bacterium, or engineered bacteria that specifically targets the α-proteobacterium acnes bacteria.

25. The composition used according to claim 24, wherein the therapeutic or preventative agent is a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding a programmable nuclease designed to specifically target the α-type Propionibacterium acnes bacteria.

26. The composition used according to claim 25, wherein the programmable nuclease is selected from CRISPR-Cas nucleases, TALENs and their variants, zinc finger nucleases (ZFNs) and their variants, a wide range of natural, evolved or engineered nuclease or recombinase variants, and any combination and hybrid thereof.

27. The composition used according to claim 26, wherein the programmable nuclease is a CRISPR-Cas nuclease.

28. The composition used according to claim 27, wherein the phage, recombinant phage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacterium, or engineered bacteria further encodes a guide RNA designed to specifically target the Propionibacterium acnes type α bacteria.

29. The composition for use according to claim 28, wherein the guide RNA is designed to specifically target the hem locus of the α-type Propionibacterium acnes, and particularly, the guide RNA is selected from SEQ ID No: 13-16.

30. The composition used according to claim 23, wherein the therapeutic or preventative agent is a bacteriophage, recombinant bacteriophage, packaged phage particle, plasmid, vesicle containing DNA or RNA, extracellular vesicle, bacteria, or engineered bacteria encoding a gene-editing enzyme or system that targets and genetically modifies the hem locus in the α-proteobacterium acnes bacteria.

31. The composition used according to claim 30, wherein the genetic modification is a dot modification.

32. The composition used according to claim 30 or 31, wherein the gene editing enzyme is a base editor or a guide editor.

33. The composition used according to any one of claims 23 to 32, wherein the Propionibacterium acnes bacterial-associated disease is a Propionibacterium acnes bacterial-associated inflammatory disease.

34. The composition used according to any one of claims 23 to 33, wherein the Propionibacterium acnes bacterial-associated disease is acne, particularly acne vulgaris.

35. The composition used according to any one of claims 23 to 34, wherein the composition is for topical application.

36. A composition for treating or preventing Propionibacterium acnes-related diseases in a subject, the composition comprising a therapeutic or preventative agent, said therapeutic or preventative agent specifically reducing the expression of at least one hem locus protein in the Propionibacterium acnes bacterium in the subject by genetically modifying the DNA sequence of the bacteria in the subject to produce at least one change, preferably producing at least one change in the hem locus of the bacteria in the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

37. A pharmaceutical composition comprising a bacteriophage, a recombinant bacteriophage, a packaged phage particle, a plasmid, a vesicle containing DNA or RNA, an extracellular vesicle, bacteria, or engineered bacteria encoding a programmable nuclease or gene-editing enzyme or system specifically targeting *Propionibacterium acnes*. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO:

1.

38. A method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, said method comprising the following steps: a) Determine the presence and / or quantity of Propionibacterium acnes type α in the samples, particularly skin samples, of the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with sequence SEQ ID NO: 1, and b) Based on the presence and / or amount determined in step a), determine whether the subject is at risk of developing acne, particularly acne vulgaris.

39. A method for diagnosing acne, particularly acne vulgaris, in a subject, said method comprising the following steps: a) Determine the presence and / or quantity of Propionibacterium acnes type α in the samples, particularly skin samples, of the subject. Among them, Propionibacterium acnes type α is a bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, where the positions are defined with reference to sequence SEQ ID NO:

5. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with sequence SEQ ID NO: 1, and b) Based on the presence and / or amount determined in step a), diagnose the subject's acne, particularly acne vulgaris.

40. A method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, the method comprising the steps of: a) Determine the presence and / or quantity of Propionibacterium β-acne in the subjects' samples, particularly skin samples. Among them, Propionibacterium β-formis is a Propionibacterium acnes bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: G173, G479, C506, G614, G629, A671, C971, G989, C1085, and C1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: T142, G155, G176, G183, T224, T245, A248, C281, A311, T314, C346, T374, T377, T452, C626, G683, G693, G720, T738, T794, C920, G944, C992, C1022, and C1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: A77, G96, G149, G233, C236, C255, G257, C260, T317, G347, C425, C437, G464, G486, G487, T488, G524, G545, G590, C605, G644, G665, T710, G713, G737, G770, G776, A785, C802, A830, T842, C845, A855, G893, T896, T897, A902, T908, G941, and G947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: C11, C41, C50, G150, C155, A159, T176, C257, T266, C278, C323, G324, C362, C367, C374, A387, G398, G399, C407, A422, A425, A432, G446, G459, C464, A595, C617, A643, G644, and T680, wherein the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: C241, C476, G530, C704, G728, C767, A834, G867, G872, C882, and G957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: C11, C23, G48, C89, T188, A338, C464, C470, A536, C548, C608, A626, C632, C641, C671, C674, T683, T689, T740, A745, A787, G797, C893, T898, C1034, C1039, C1046, G1071, A1095, T1109, C1153, C1358, C1496, T1511, T1527, A1532, C1598, C1712, G1850, C1901, G1926, T1931, and T1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: C107, T197, A229, G242, A310, G338, G374, C389, T392, C442, T467, A470, T482, T518, and G641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: G89, G236, G354, T383, T392, G395, C398, C465, C474, T521, C538, T566, C593, C767, A782, A863, A920, A927, G932, A935, A979, C989, G1019, C1055, A1091, C1136, A1143, T1152, C1166, G1172, G1176, C1184, T1199, T1205, A1268, A1278, C1295, C1318, G1336, A1343, T1346, C1355, G1359, and G1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with sequence SEQ ID NO: 2, and b) Based on the presence and / or amount determined in step a), determine whether the subject is at risk of developing acne, particularly acne vulgaris.

41. A method for diagnosing acne, particularly acne vulgaris, in a subject, said method comprising the following steps: a) Determine the presence and / or quantity of Propionibacterium β-acne in the subjects' samples, particularly skin samples. Among them, Propionibacterium β-formis is a Propionibacterium acnes bacterium that (i) contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: G173, G479, C506, G614, G629, A671, C971, G989, C1085, and C1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: T142, G155, G176, G183, T224, T245, A248, C281, A311, T314, C346, T374, T377, T452, C626, G683, G693, G720, T738, T794, C920, G944, C992, C1022, and C1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: A77, G96, G149, G233, C236, C255, G257, C260, T317, G347, C425, C437, G464, G486, G487, T488, G524, G545, G590, C605, G644, G665, T710, G713, G737, G770, G776, A785, C802, A830, T842, C845, A855, G893, T896, T897, A902, T908, G941, and G947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: C11, C41, C50, G150, C155, A159, T176, C257, T266, C278, C323, G324, C362, C367, C374, A387, G398, G399, C407, A422, A425, A432, G446, G459, C464, A595, C617, A643, G644, and T680, wherein the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: C241, C476, G530, C704, G728, C767, A834, G867, G872, C882, and G957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: C11, C23, G48, C89, T188, A338, C464, C470, A536, C548, C608, A626, C632, C641, C671, C674, T683, T689, T740, A745, A787, G797, C893, T898, C1034, C1039, C1046, G1071, A1095, T1109, C1153, C1358, C1496, T1511, T1527, A1532, C1598, C1712, G1850, C1901, G1926, T1931, and T1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: C107, T197, A229, G242, A310, G338, G374, C389, T392, C442, T467, A470, T482, T518, and G641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: G89, G236, G354, T383, T392, G395, C398, C465, C474, T521, C538, T566, C593, C767, A782, A863, A920, A927, G932, A935, A979, C989, G1019, C1055, A1091, C1136, A1143, T1152, C1166, G1172, G1176, C1184, T1199, T1205, A1268, A1278, C1295, C1318, G1336, A1343, T1346, C1355, G1359, and G1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with sequence SEQ ID NO: 2, and b) Based on the presence and / or amount determined in step a), diagnose the subject's acne, particularly acne vulgaris.

42. Use of a therapeutic or preventive agent in the manufacture of a medicament for treating or preventing a Propionibacterium acnes-related disease in a subject, wherein the therapeutic or preventive agent induces a reduction in the ratio of the amount of α-type Propionibacterium acnes to the amount of β-type Propionibacterium acnes in the subject. Among them, Propionibacterium acnes type α is a type of Propionibacterium acnes. (i) It contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) The nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1; and Among them, β-type Propionibacterium acnes is a type of Propionibacterium acnes that is not α-type Propionibacterium acnes.

43. Use of a therapeutic or preventive agent in the manufacture of a medicament for treating or preventing a Propionibacterium acnes-related disease in a subject, wherein the therapeutic or preventive agent genetically modifies the DNA sequence of Propionibacterium acnes type α in the subject to produce at least one change, preferably producing at least one change in the hem locus of the Propionibacterium acnes type α, to specifically reduce the expression of at least one hem locus protein in the Propionibacterium acnes type α in the subject, and Among them, Propionibacterium acnes type α is a type of Propionibacterium acnes. (i) It contains at least 90% of the following nucleotide variations at the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085, and T1094, where the positions are defined with reference to sequence SEQ ID NO: 3, and the first nucleotide in said sequence is indexed as 0. - In the hemB gene: C142, A155, A176, A183, C224, C245, G248, T281, G311, C314, T346, C374, G377, C452, T626, C683, A693, A720, C738, C794, A920, T944, T992, G1022, and T1031, where the positions are defined with reference to sequence SEQ ID NO: 4, and the first nucleotide in said sequence is indexed as 0. - In the hemC gene: G77, A96, C149, A233, T236, T255, A257, A260, C317, A347, T425, T437, A464, A486, A487, C488, A524, A545, A590, T605, A644, A665, C710, C713, A737, A770, A776, T785, T802, G830, C842, T845, G855, C893, A896, C897, G902, G908, A941, and A947, wherein the positions are defined with reference to sequence SEQ ID NO: 5, and the first nucleotide in said sequence is indexed as 0. - In the hemD gene: T11, T41, T50, A150, T155, G159, G176, T257, C266, T278, G323, A324, T362, T367, T374, G387, A398, A399, T407, G422, G425, G432, A446, A459, T464, G595, T617, T643, A644, and C680, where the positions are defined with reference to sequence SEQ ID NO: 6, and the first nucleotide in said sequence is indexed as 0. - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882, and A957, where the positions are defined with reference to sequence SEQ ID NO: 7, and the first nucleotide in said sequence is indexed as 0. - In the hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931, and C1997, where the positions refer to the sequence SEQ ID NO: The sequence is defined as 8, and the first nucleotide in the sequence is indexed as 0. - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518, and C641, wherein the positions are defined by reference to sequence SEQ ID NO: 9, and the first nucleotide in said sequence is indexed as 0. - In the hemY gene: A89, A236, A354, C383, C392, A395, T398, T465, T474, C521, T538, C566, A593, A767, T782, G863, G920, T927, A932, G935, C979, G989, C1019, T1055, G1091, T1136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359, and C1395, wherein the positions are defined with reference to the sequence SEQ ID NO: 10, and the first nucleotide in said sequence is indexed as 0. and / or (ii) wherein the nucleic acid sequence of the hem locus has at least 97% identity with the sequence SEQ ID NO: 1.

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