C. Detection and treatment of bacterial infections related to acnes.

Abstract

The present invention relates to a method for treating or preventing a Cutibacterium acnes-related disease in a subject, comprising the step of modulating, in particular reducing, the ratio of the amount of a newly identified category of C. acnes bacteria called type α to the amount of a newly identified category of C. acnes bacteria called type β, wherein the type α category efficiently defines acne-related strains and the type β category defines non-acne-related strains.

Description

Technical Field

[0001] The present invention relates to a method for treating C. acnes bacteria-related diseases in a subject, particularly for treating acne, more particularly, acne vulgaris.

Background Art

[0002] Cutibacterium acnes is a major commensal bacterium of the skin microbiome and becomes the most abundant bacterium in hair follicles. It plays a strong role in maintaining skin health, but is also involved in several diseases and infections including acne vulgaris (Bruggemann et al. (2021) Front Microbiol. 12:673845) or progressive macular hypomelanosis (McDowell et al. (2021) J. Eur. Acad. Dermatol. Venereol. 35:338-344).

[0003] Acne vulgaris is a chronic inflammatory disorder of hair follicles in which C. acnes is listed as one of the virulence factors. In fact, previous studies have shown that (i) the effectiveness of antimicrobial treatment correlates with a reduction in C. acnes load (Lessin et al. (2020) Skin Microbiome Handbook: From Basic Research to Product Development, edited by Nava Dayan, pp. 289-302), and (ii) isotretinoin, the most efficient drug available to treat acne to date, resulted in a reduction in C. acnes load (Oprica et al. (2007) Acta Derm Venerol 87:246-254; Nolan et al. (2023) Exp. Dermatol. 32:955-964; McCoy et al. (2019) J Invest. Dermatol. 139:732-735; Kelhala et al. (2017) Exp. Dermatol. (27:30~36) (iii) Antibiotic ineffectiveness was correlated with the presence of antibiotic-resistant strains of C. acnes (Simonart et al. (2005) British J. Dermatol. 153:395~403); (iv) C. acnes induced acneiform inflammation in different in vitro (Laclaverie et al. (2021) Exp. Dermatol. 30:347~357) and in vivo models (Kolar et al. (2019) JCI Insight 4(5):e124687); and (v) patients with acne vulgaris had anti-C. acnes antibodies (Wang et al. (2018) J. Invest. Dermatol. 138:2355~2364; Huang et al. (2021) Front. Microbiol. 12:709562).

[0004] Since C. acnes also plays an important role in maintaining skin health, identifying C. acnes types involved in inflammatory disorders (e.g., acne vulgaris) and differentiating them from non-inflammatory disorder-related C. acnes types is of great importance.

[0005] Different studies have attempted to achieve such identification, but the results have been insufficient. In 2013, Fitz-Gibbon et al. compared the skin microbiome of C. acnes at the strain and genomic levels between acne patients and healthy individuals. They showed significant enrichment of certain C. acnes ribotypes (i.e., RT4, RT5, RT8, and RT10 ribotypes) in acne patients and significant enrichment of another specific C. acnes ribotype (i.e., RT6 ribotype) in healthy subjects (Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152~2160). However, not all acne patients showed a clear presence of C. acnes bacteria belonging to acne-associated ribotypes. Therefore, the distinction of C. acnes bacteria between different ribotypes has not enabled effective identification of C. acnes bacteria involved in acne.

[0006] Based on whole-genome sequencing of C. acnes clones belonging to different ribotypes, Fitz-Gibbon et al. also showed that three loci (referred to by the authors as loci 1, 2, and 3) were specific to ribotypes 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 again does not enable the specific identification of acne-associated strains, because C. acnes strains belonging to the RT8 ribotype (enriched in acne patients) are not enriched at these three loci, while C. acnes strains belonging to the RT1 ribotype (abundant in both acne patients and healthy subjects) may possess loci 1, 2, and 3.

[0007] Later, the same laboratory performed metagenomic profiling of acne and healthy follicular plugs and showed that RT4, RT5, and RT8 ribotypes were more abundant and common in acne patients, while RT2 and RT6 ribotypes were more abundant and common in healthy subjects, and that there was enrichment of specific genes contained in previously identified loci 1, 2, and 3 (Barnard et al. (2016) Scientific Reports 6:39491). However, a large proportion of acne metagenomic samples did not possess loci 1, 2, and 3, while some healthy metagenomic samples did possess loci 1 or 3. This confirms that ribotypes and loci 1, 2, and 3 are not appropriate for efficiently identifying acne-related strains.

[0008] Other different typing methods (including multi-locus sequence typing (MLST), single-locus sequence typing (SLST), the Belfast scheme using seven target genes, multiple touchdown PCR, the Aarhus scheme using nine target genes, MALDI-TOF MS-based typing, and MLVA typing using 13 VNTR polymorphisms) have been used to attempt to distinguish between acne-related and non-acne-related strains; however, the types defined using these methods are inconsistent when compared to one another, and none of them enable clear and efficient identification of acne-related strains (Mayslich et al. (2021) Microorganisms 9:203).

[0009] Therefore, there is a critical need for tools that enable clear and efficient identification of acne-related strains, allowing for the specific targeting of these strains while maintaining non-acne-related strains in a viable and well-formed state.

[0010] Several studies have reported higher production of certain porphyrins (primarily coproporphyrin III) by acne-associated strains (Johnson et al. (2016) mSphere 1(1):e00023~15; Barnard et al. (2020) mSphere 5:e00793~19). Porphyrins were considered interesting because, when extracted from acne-associated strains, they have been shown to activate inflammasomes and provide an explanation for the role of C. acnes in inflammation (Spittaels et al. (2021) iScience 24:102575). Therefore, using differences in porphyrin production may be a 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 across C. acnes strains, as shown in Figure 5. Furthermore, Huiying Li's team reported the presence of putative repressors from the deoR family (also known as glpR) adjacent to 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 this deoR gene may be of interest in the diagnosis and / or treatment of acne vulgaris (WO2017 / 136738). However, as the authors emphasized, “deorR was found to be expressed in both high-level and low-level porphyrin-producing strains [so] [they] attempted to determine whether there were differences in the deoR gene sequence that could explain the variations in regulation and porphyrin production between strains. (...) [However, they] did not identify any single nucleotide polymorphisms (SNPs) that were uniquely shared by strains from clades IB-3 and IC and could potentially explain the increased porphyrin production in these lines” (see Barnard et al. (2020) mSphere 5:e00793~19). [Prior art documents] [Patent Documents]

[0012] [Patent Document 1] WO2017 / 136738 [Patent Document 2] WO2018 / 236548 [Patent Document 3] WO2017 / 141173 [Patent Document 4] WO2020181180 [Patent Document 5] WO2020181202 [Patent Document 6] WO2020181193 [Patent Document 7] WO2020181178 [Patent Document 8] WO2020181195 [Patent Document 9] U.S. Patent Application Publication No. 2015 / 0166980 [Patent Document 10] US Patent No. 10,113,163 [Non-patent literature]

[0013] [Non-Patent Document 1] Bruggemann et al. (2021) Front Microbiol. 12:673845 [Non-Patent Document 2] McDowell et al. (2021) J. Eur. Acad. Dermatol. Venereol. 35:338~344 [Non-Patent Document 3] Lessin et al. (2020) Skin Microbiome Handbook: From Basic Research to Product Development, edited by Nava Dayan, pp. 289-302 [Non-Patent Document 4] Oprica et al. (2007) Acta Derm Venerol 87:246~254

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[0014] Therefore, there remains a critical need for tools that enable robust and efficient identification of acne-related strains, allowing for the specific targeting of these strains while maintaining non-acne-related strains in a viable and well-formed state. [Means for solving the problem]

[0015] This invention satisfies this need.

[0016] This invention arises from an unexpected discovery by the inventors that a set of 218 SNPs across the hem locus (including genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) allows for the classification of known C. acnes strain diversity into two groups, hereafter referred to as α-type and β-type. Importantly, this novel typing correlates tightly with published porphyrin production levels, in contrast to the deoR gene, with α-type encompassing all C. acnes producing high amounts of porphyrin, while β-type encompassing all C. acnes producing low or absent amounts of porphyrin. Furthermore, after developing a method for estimating the relative abundance of α- and β-type C. acnes strains in shotgun metagenomic sequencing data and applying it to public datasets related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491), the inventors demonstrated that α-type C. acnes strains formed a significantly larger proportion of the C. acnes population in patients with acne vulgaris than in healthy subjects.

[0017] Therefore, the present invention relates to a method for treating or preventing a Cutibacterium acnes-related disease in a subject, comprising the step of modulating, in particular reducing, the ratio of the amount of α-type C. acnes to the amount of β-type C. acnes in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. Regarding the method.

[0018] The present invention also provides a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of specifically reducing the amount of α-type C. acnes bacteria in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Regarding the method.

[0019] The present invention also provides a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of genetically modifying the DNA sequence of C. acnes alpha-type in the subject, preferably generating at least one change at the hem locus of C. acnes alpha-type, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Regarding the method.

[0020] The present invention also provides a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of increasing the amount of β-type C. acnes bacteria in the subject. β-type C. acnes is a type of C. acnes that is not α-type C. acnes. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Regarding the method.

[0021] The present invention further comprises a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that induces modulation, preferably reduction, of the ratio of the amount of α-type C. acnes to the amount of β-type C. acnes in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. This relates to compositions for use.

[0022] The present invention also comprises a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that specifically reduces the amount of α-type C. acnes bacteria in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. This relates to compositions for use.

[0023] The present invention also comprises a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that genetically modifies the DNA sequence in C. acnes alpha-type in the subject, preferably producing at least one change at the hem locus of C. acnes alpha-type, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. This relates to compositions for use.

[0024] The present invention further comprises a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that increases the amount of β-type C. acnes bacteria in the subject, β-type C. acnes is a type of C. acnes that is not α-type C. acnes. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. This relates to compositions for use.

[0025] The present invention also provides a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of specifically reducing the expression of at least one hem locus protein in α-type C. acnes in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Regarding the method.

[0026] The present invention also includes a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that specifically reduces the expression of at least one hem locus protein in C. acnes α-type in the subject by genetically modifying the DNA sequence in C. acnes α-type in the subject, preferably by generating at least one change at the hem locus of C. acnes α-type, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. This relates to compositions for use.

[0027] Another object of the present invention is a pharmaceutical composition comprising a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium, encoding a programmable nuclease or gene editing enzyme or system designed to specifically target type α C. acnes. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Regarding pharmaceutical compositions.

[0028] Another object of the present invention is a method for determining whether a subject is at risk of developing acne, in particular acne vulgaris. a) A step of determining the presence and / or amount of α-type C. acnes bacteria in a sample, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Process, and b) A step of determining whether the subject is at risk of developing acne, in particular acne vulgaris, based on the presence and / or quantity determined in step a). Regarding methods including

[0029] Another object of the present invention is a method for diagnosing acne, particularly acne vulgaris, in a subject, a) A step of determining the presence and / or amount of α-type C. acnes bacteria in a sample, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of sequence number 1. C. acnes is a bacterium. Process, and b) A step of diagnosing acne, particularly acne vulgaris, in the subject based on the presence and / or quantity determined in step a). Regarding methods including [Modes for carrying out the invention]

[0030] α-type C. acnes and β-type C. acnes Cutibacterium acnes (formerly Propionibacterium acnes) is a Gram-positive, rod-shaped, air-resistant bacterium first isolated from skin in 1897. It belongs to the order Actinomycetes, the family Propionibacteridae, and the genus Cutibacterium. C. acnes is one of the most common and abundant bacteria on human skin and can be found both on the skin surface (stratum corneum) and in hair follicles. Unlike on the stratum corneum, where it is mostly in contact with dead keratinocytes, inside the hair follicle, it is in direct contact with a great diversity of living cells, such as keratinocytes, stem cells, sebaceous gland cells, and immune cells. C. acnes is a symbiotic bacterium but is also associated with several skin diseases, such as acne vulgaris or progressive macular hyperpigmentation.

[0031] C. acnes strains were previously classified into two main types, I and II, based on their cell wall carbohydrate contents and serum lectin response (Johnson et al. (1982) J Bacteriol. 109(3):1047~66). Subsequently, subclusters of these types were identified based on the use of RecA and tly genes, as well as QUBPa1 and QUBPa2 antibodies (McDowell et al. (2005) J Clin Microbiol. 43(1):326~334). Then, a further phylotype, type III, corresponding to strains with filamentous appendages, was added to the classification (McDowell et al. (2008) J Medical Microbiol. 57:218~224). Multilocus sequencing (MLST) methods were also developed to increase the resolution of the typing. The Belfast scheme, based on seven target genes, differentiates type I into clades IA1, IA2, IB, and IC (McDowell et al. (2011) Microbiology 157:1990-2003), while the Aarhus scheme, based on nine target genes, differentiates type I into clades I-1a, I-1b, and I-2 (Lomholt et al. (2010) PLoS ONE 5(8):e12277). Subsequently, a new method was developed to differentiate C. acnes strains into SLST types using SLST and whole-genome sequencing (WGS) techniques (Scholz et al. (2014) PLoS ONE 9(8):e104199).

[0032] Mass spectrometry-based methods have also been used to characterize the C. acnes strain, and when associated with profiling of ribosomal subunit proteins in MALDI-MS prototyping, they enabled the discrimination of all the phyllotypes mentioned above (Teramoto et al. (2019) Proc. Jpn. Acad. Ser. B 95:612~623).

[0033] Based on 16S rRNA gene analysis, the C. acnes strain was also classified according to the ribotype defined and mentioned by Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152~2160.

[0034] However, as highlighted by Mayslich et al. (Mayslich et al. (2021) Microorganisms 9:303), there is a critical need for standardization among all of the above nomenclature, and as highlighted above, none of them allow for a robust and efficient distinction between acne strains and non-acne-related strains.

[0035] The inventors have identified a set of 218 SNPs across the hem locus (including genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) that allows for the classification of known C. acnes strain diversity into two groups referred to herein as α-type and β-type. Importantly, this novel typing correlates tightly with published porphyrin production levels, in contrast to the deoR gene, with α-type containing all C. acnes producing high amounts of porphyrin, while β-type containing all C. acnes producing low or absent amounts of porphyrin. Furthermore, after developing a method for estimating the relative abundance of α- and β-type C. acnes strains in shotgun metagenomic sequencing data and applying it to public datasets related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491), the inventors demonstrated that α-type C. acnes strains formed a significantly larger proportion of the C. acnes population in patients with acne vulgaris than in healthy subjects.

[0036] The inventors thereby identified α-type C. acnes as a C. acnes bacterium in which at least 90% of the marker positions defined in Table 1 below have nucleotide variants defined as "alpha variants," and the positions are defined with respect to the following reference genes: sequence SEQ ID NO: 3 for the hemA gene, sequence SEQ ID NO: 4 for the hemB gene, sequence SEQ ID NO: 5 for the hemC gene, sequence SEQ ID NO: 6 for the hemD gene, sequence SEQ ID NO: 7 for the hemE gene, sequence SEQ ID NO: 8 for the hemH gene, sequence SEQ ID NO: 9 for the hemL gene, and sequence SEQ ID NO: 10 for the hemY gene.

[0037] The values ​​shown in the column titled "Reference Position (0-Based)" are 0-based, meaning that the first nucleotide in the gene sequence is indexed as 0. As will be readily apparent to those skilled in the art, positions may also be defined in a "1-based" manner, meaning that the first nucleotide in the gene sequence is indexed as 1. In this case, all "0-based" defined positions are incremented by 1. For example, position T173 defined in the "0-based" manner in the hemA gene is identical to position T174 defined in the "1-based" manner in the hemA gene. The values ​​shown in the column titled "Reference Position (1-Based)" are 1-based. In this specification, unless otherwise specifically indicated, the values ​​of reference positions are 0-based.

[0038] [Table 1A]

[0039] [Table 1B]

[0040] [Table 1C]

[0041] [Table 1D]

[0042] [Table 1E]

[0043] [Table 1F]

[0044] [Table 1G]

[0045] In the context of the present invention, therefore, α-type C. acnes bacteria are preferably C. acnes bacteria comprising at least 90%, in particular 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 variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10).

[0046] Alternatively, α-type C. acnes bacteria may contain 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 alpha nucleotide variants defined in Table 1.

[0047] Alternatively, using a position defined as "1-base," alpha-type C. acnes bacteria may contain at least 90%, in particular 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 variants in the hem locus: - In the hemA gene: T174, A480, T507, A615, T630, C672, T972, A990, T1086 and T1095 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T242, T477, A531, T705, A729, G768, T835, A868, A873, A883 and A958 (positions are defined by referring to the sequence of Sequence 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, T 1040, T1047, C1072, G1096, C1110, T1154, T1359, G1497, C1512, C1528, G1533, T1599, T1713, A1851, G1902, A1927, C1932 and C1998 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T108, C198, T230, A243, C311, A339, A375, T390, G393, T443, C468, G471, C483, G519 and C642 (positions are defined by referring to the sequence of SEQ ID NO: 9), and - In hemY gene: A90, A237, A355, C384, C393, A396, T399, T466, T475, C522, T539, C567, A 594, A768, T783, G864, G921, T928, A933, G936, C980, G990, C1020, T1056, G1092, T1 137, G1144, G1153, T1167, T1173, A1177, T1185, C1200, C1206, G1269, G1279, T1296, T1319, A1337, G1344, C1347, G1356, T1360 and C1396 (the position is defined by referring to the array of sequence number 10).

[0048] In this specification, "hem locus" means a locus contained within the porphyrin biosynthesis locus of C. acnes that includes eight hem genes, namely hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY genes.

[0049] Or, or further, in the context of the present invention, type α C. acnes bacterium is defined as having nucleic acid sequences of the hem locus (including genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) that are at least 97% identical to the sequence of SEQ ID NO: 1, in particular at least 97.1% identical, at least 97.2% identical, at least 97.3% identical, at least 97.4% identical, at least 97.5% identical, at least 97.6% identical, at least 97.7% identical, at least 97.8% identical, at least 97.9% identical, at least 98% identical, and at least 98.1% identical. C. acnes is at least 98.2% identical, at least 98.3% identical, at least 98.4% identical, at least 98.5% identical, at least 98.6% identical, at least 98.7% identical, at least 98.8% identical, at least 98.9% identical, at least 99% identical, at least 99.1% identical, at least 99.2% identical, at least 99.3% identical, at least 99.4% identical, at least 99.5% identical, at least 99.6% identical, at least 99.7% identical, at least 99.8% identical, at least 99.9% identical, or 100% identical.

[0050] Preferably, type α C. acnes bacteria, (i) containing at least 90% of the alpha nucleotide variants defined in Table 1, in particular 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 Table 1 (Table 1) 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 alpha nucleotide variants defined in Table 1, and (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of SEQ ID NO: 1, in particular at least 97.1% identical, at least 97.2% identical, at least 97.3% identical, at least 97.4% identical, at least 97.5% identical, at least 97.6% identical, at least 97.7% identical, at least 97.8% identical, at least 97.9% identical, at least 98% identical, at least 98.1% identical, at least 98.2% identical, at least 98.3% identical, at least They are 98.4% identical, at least 98.5% identical, at least 98.6% identical, at least 98.7% identical, at least 98.8% identical, at least 98.9% identical, at least 99% identical, at least 99.1% identical, at least 99.2% identical, at least 99.3% identical, at least 99.4% identical, at least 99.5% identical, at least 99.6% identical, at least 99.7% identical, at least 99.8% identical, at least 99.9% identical, or 100% identical. This is *C. acnes*.

[0051] In the context of this invention, β-type C. acnes is a C. acnes bacterium that is not the α-type C. acnes bacterium defined above.

[0052] Preferably, β-type C. acnes bacteria are C. acnes bacteria containing at least 90%, in particular 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 variants in the hem locus: - In the hemA gene: G173, G479, C506, G614, G629, A671, C971, G989, C1085 and C1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: C241, C476, G530, C704, G728, C767, A834, G867, G872, C882 and G957 (positions are defined by referring to the sequence of Sequence 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, C 1039, C1046, G1071, A1095, T1109, C1153, C1358, C1496, T1511, T1527, A1532, C1598, C1712, G1850, C1901, G1926, T1931 and T1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: C107, T197, A229, G242, A310, G338, G374, C389, T392, C442, T467, A470, T482, T518 and G641 (positions are defined by referring to the sequence of Sequence ID No. 9), and - In hemY gene: G89, G236, G354, T383, T392, G395, C398, C465, C474, T521, C538, T566, C 593, C767, A782, A863, A920, A927, G932, A935, A979, C989, G1019, C1055, A1091, C1 136, A1143, T1152, C1166, G1172, G1176, C1184, T1199, T1205, A1268, A1278, C1295, C1318, G1336, A1343, T1346, C1355, G1359 and G1395 (the position is defined by referring to the array of sequence number 10).

[0053] Alternatively, using a position defined as "1-base," a β-type C. acnes bacterium may contain at least 90%, in particular, 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 variants in the hem locus. - In the hemA gene: G174, G480, C507, G615, G630, A672, C972, G990, C1086 and C1095 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: C242, C477, G531, C705, G729, C768, A835, G868, G873, C883 and G958 (positions are defined by referring to the sequence of Sequence 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, C 1040, C1047, G1072, A1096, T1110, C1154, C1359, C1497, T1512, T1528, A1533, C1599, C1713, G1851, C1902, G1927, T1932 and T1998 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: C108, T198, A230, G243, A311, G339, G375, C390, T393, C443, T468, A471, T483, T519 and G642 (positions are defined by referring to the sequence of SEQ ID NO: 9), and - In hemY gene: G90, G237, G355, T384, T393, G396, C399, C466, C475, T522, C539, T567, C 594, C768, A783, A864, A921, A928, G933, A936, A980, C990, G1020, C1056, A1092, C1 137, A1144, T1153, C1167, G1173, G1177, C1185, T1200, T1206, A1269, A1279, C1296, C1319, G1337, A1344, T1347, C1356, G1360 and G1396 (the position is defined by referring to the array of sequence number 10).

[0054] Alternatively, a β-type C. acnes bacterium may contain 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 beta nucleotide variants defined in Table 1.

[0055] Alternatively, the β-type C. acnes bacterium preferably has nucleic acid sequences of the hem locus (including genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) that are at least 97% identical to the sequence of SEQ ID NO: 2, particularly at least 97.1% identical, at least 97.2% identical, at least 97.3% identical, at least 97.4% identical, at least 97.5% identical, at least 97.6% identical, at least 97.7% identical, at least 97.8% identical, at least 97.9% identical, at least 98% identical, and at least 98.1% identical. It is a C. acnes bacterium that is at least 98.2% identical, at least 98.3% identical, at least 98.4% identical, at least 98.5% identical, at least 98.6% identical, at least 98.7% identical, at least 98.8% identical, at least 98.9% identical, at least 99% identical, at least 99.1% identical, at least 99.2% identical, at least 99.3% identical, at least 99.4% identical, at least 99.5% identical, at least 99.6% identical, at least 99.7% identical, at least 99.8% identical, at least 99.9% identical, or 100% identical.

[0056] Preferably, β-type C. acnes bacteria, (i) containing at least 90% of the beta-nucleotide variants defined in Table 1, in particular 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 Table The beta nucleotide variants defined in 1 (Table 1) include 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 them, and (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of SEQ ID NO: 2, in particular at least 97.1% identical, at least 97.2% identical, at least 97.3% identical, at least 97.4% identical, at least 97.5% identical, at least 97.6% identical, at least 97.7% identical, at least 97.8% identical, at least 97.9% identical, at least 98% identical, at least 98.1% identical, at least 98.2% identical, at least 98.3% identical, at least They are 98.4% identical, at least 98.5% identical, at least 98.6% identical, at least 98.7% identical, at least 98.8% identical, at least 98.9% identical, at least 99% identical, at least 99.1% identical, at least 99.2% identical, at least 99.3% identical, at least 99.4% identical, at least 99.5% identical, at least 99.6% identical, at least 99.7% identical, at least 99.8% identical, at least 99.9% identical, or 100% identical. This is *C. acnes*.

[0057] As used herein, “percent identity” between two sequences means the percentage of identical nucleotides or amino acids between the two sequences being compared, obtained using the best alignment of the sequences. As used herein, “best alignment” or “optimal alignment” means the alignment with the highest determined percentage of identity (see below). Sequence comparison between two sequences is typically achieved by comparing these sequences previously aligned according to the best alignment; this comparison is performed on segments of the comparison to identify and compare local regions of similarity. The best sequence alignment for comparison can be achieved manually, by using the global homology algorithm developed by Smith and Waterman (Smith and Waterman (1981) Ad. App. Math. 2:482), by using the local homology algorithm developed by Needleman and Wunsch (Needleman and Wunsch (1970) J. Mol. Biol 48:443), by using the similarity method developed by Pearson and Lipman (Pearson and Lipman (1988) Proc. Natl. Acd. Sci. USA 85:2444), by using computer software that employs such algorithms (GAP, BESTFIT, BLAST P, BLAST N, FASTA, TFASTA, etc.), or by using the MUSCLE multiple alignment algorithm (Edgar (2004) Nucleic Acids Research 32:1792). To obtain the best local alignment, the Needleman-Wunsch algorithm can preferably be used. The percentage of identity between two sequences is determined by comparing these two optimally aligned sequences, and these sequences may include additions or deletions to the reference sequence in order to obtain the best alignment between these two sequences.The percentage of identity can be calculated by determining the number of identical positions between the two sequences, dividing this number by the total number of positions compared, and multiplying the result by 100 to obtain the percentage of identity between the two sequences. Preferably, for the purposes of this specification, the percentage identity value refers to the value generated using the pairwise sequence alignment program EMBOSS Needle, which uses the Needleman-Wunsch algorithm to create the best overall alignment of the two sequences, where all search parameters are set to their default values, i.e., scoring matrix = BLOSUM62 for protein sequences, DNAfull for DNA sequences, gap open = 10, gap elongation = 0.5, end gap penalty = false, end gap open = 10, and end gap elongation = 0.5.

[0058] C. Treatment or prevention of bacterial infections related to acne The present invention relates to a method for treating or preventing a Cutibacterium acnes-related disease in a subject, comprising the step of modulating the ratio of the amount of α-type C. acnes to the amount of β-type C. acnes in the subject. α-type C. acnes is defined as described in the above section "α-type C. acnes and β-type C. acnes", and β-type C. acnes is defined as described in the section "α-type C. acnes and β-type C. acnes" above. Regarding the method.

[0059] The present invention also comprises a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that induces modulation of the ratio of the amount of α-type C. acnes to the amount of β-type C. acnes in the subject, α-type C. acnes is defined as described in the above section "α-type C. acnes and β-type C. acnes", and β-type C. acnes is defined as described in the section "α-type C. acnes and β-type C. acnes" above. This relates to compositions for use.

[0060] The present invention further relates to the use of a therapeutic or prophylactic agent for the manufacture of a pharmaceutical for the treatment or prevention of C. acnes-related diseases, which induces modulation of the ratio of the amount of α-type C. acnes bacteria to the amount of β-type C. acnes bacteria, α-type C. acnes is defined as described in the above section "α-type C. acnes and β-type C. acnes", and β-type C. acnes is defined as described in the section "α-type C. acnes and β-type C. acnes" above. Regarding use.

[0061] "C. acnes-related disease" means, in this specification, a disease, particularly a skin disease, caused by, associated with, or negatively affected by C. acnes bacteria.

[0062] Examples of C. acnes-related diseases include acne (e.g., acne vulgaris, acne inversa, acne clusters, or acne fulminans), keratitis, synovitis, prosopus pustulosis, osteopathy (SAPHO) syndrome, endocarditis, medical implant biofilm infections, prosthesis infections, surgical wound infections, vascular graft infections, anaerobic arthritis, cardiovascular device-related infections (e.g., prosthetic valve endocarditis), ocular implant infections, breast implant disease, sciatica, conjunctivitis, shunt-related and / or spinal hardware central nervous system infections, shunt-related central nervous system infections, sarcoidosis, endophthalmitis, osteomyelitis, allergic alveolitis, rheumatoid arthritis, infectious arthritis, chronic juvenile arthritis, and chronic destructive oligoarthritis. This includes, but is not limited to, oligoarthritis, degenerative disc disease, dental infections, ulcerative colitis, hyperthermia, brain abscess, subdural abscess, peritonitis, periodontitis, endodontic infection, chronic sinusitis, folliculitis, corneal ulcer, prostatitis, chronic prostatitis, primary biliary cirrhosis, hidradenitis suppurativa, pulmonary vasculitis, atherosclerosis, prostate cancer, progressive macular pigment deficiency, eczema, psoriasis, seborrheic dermatitis, rosacea, lichen sclerosus, lichen planus, nodular prurigo, and chronic simple lichen.

[0063] In certain embodiments, the C. acnes-related disease is a C. acnes-related skin disease. Examples of C. acnes-related skin diseases include, but are not limited to, acne (e.g., acne vulgaris, acne variola, acne clusters, or fulminant acne), surgical wound infections, folliculitis, eczema, psoriasis, seborrheic dermatitis, rosacea, lichen sclerosus, lichen planus, prurigo nodularis, and chronic lichen simplex.

[0064] In certain embodiments, the C. acnes-related disease is a C. acnes-related inflammatory disease. Examples of C. acnes-related inflammatory diseases are well known to those skilled in the art and include, without limitation, acne (e.g., acne vulgaris, anti-acne, acne clusters, or fulminant acne), sarcoidosis, SAPHO syndrome, eczema, psoriasis, seborrheic dermatitis, rosacea, lichen sclerosus, lichen planus, prurigo nodularis, and lichen simplex chronicus.

[0065] Therefore, in a preferred embodiment, the C. acnes-related disease is selected from the group consisting of acne (e.g., acne vulgaris, anti-acne, acne clusters, or fulminant acne), sarcoidosis, SAPHO syndrome, eczema, psoriasis, seborrheic dermatitis, rosacea, lichen sclerosus, lichen planus, prurigo nodosa, and chronic lichen simplex.

[0066] In a more preferred embodiment, the C. acnes-related disease is acne, and more particularly acne vulgaris.

[0067] When used in the context of this invention, acne vulgaris is a chronic inflammatory disorder of the follicular sebaceous glands. It affects almost all people at some point in their lives, with 15–20% suffering from moderate to severe forms of acne. Acne can be classified as mild, moderate, or severe. Mild acne typically corresponds to cases with 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 cases with between 20 and 100 comedones and / or between 15 and 50 inflammatory lesions and / or a total lesion count between 30 and 125. Severe acne typically corresponds to cases with more than 5 pseudocysts and / or more than 100 comedones and / or more than 50 inflammatory lesions.

[0068] In certain embodiments, the C. acnes-related disease is severe acne.

[0069] As used herein, the terms “treatment,” “to treat,” etc., refer to obtaining a desired pharmacological or physiological effect. This effect may be therapeutic in the sense of partial or complete cure of a disease or disorder, or the symptoms of a disease or disorder, or adverse effects attributable to a disease or disorder. As used herein, “treatment” includes inhibiting a disease, disorder or condition, i.e., stopping its onset; and reducing a disease, disorder or condition, i.e., causing regression of the disease, disorder or condition.

[0070] When applied to acne, the term “treatment” includes, for example, a reduction in the number of acne lesions, sebum discharge, follicular keratinization, comedone formation, bacterial colonization of hair follicles, C. acnes proliferation, and / or inflammation. This further includes, for example, a reduction in the severity of the disease, such as a reduction from severe acne to moderate or mild acne, or from moderate acne to mild acne.

[0071] As used herein, the terms “prevention,” “prevent,” etc., include preventing or reducing the likelihood or severity of developing a disease. This includes preventive measures for persons at increased risk of developing such disease. Increased risk indicates a above-average risk of developing the disease, which may be determined, for example, through family history, detection of genes that cause a predisposition to the disease, or treatment with antibiotics.

[0072] When applied to acne, the term “prevention” encompasses, for example, the fact of avoiding reaching a given stage of acne severity, such as severe acne, moderate acne, or mild acne.

[0073] In certain embodiments of the present invention, treatment and / or prevention of C. acnes-related diseases is obtained by modulating the ratio of the amount of C. acnes α, as defined in the above section "C. acnes α and C. acnes β", to the amount of C. acnes β, as defined in the above section "C. acnes α and C. acnes β".

[0074] In this specification, "quantity" means a relative (e.g., relative to the entire bacterial population of interest, in particular to the cutaneous bacterial population, or relative to the entire C. acnes population of interest, in particular to the cutaneous C. acnes population) or absolute quantity (or concentration) that can be determined by any suitable technique known to those skilled in the art. Examples of suitable techniques for determining the quantity of a given bacterial species include direct cell counting, indirect cell counting, PCR (including real-time and quantitative PCR), and shotgun metagenomic sequencing.

[0075] "Modulation of the ratio" means, as used herein, an increase or decrease in the ratio after the execution of the method and / or administration of the therapeutic or prophylactic agent, compared to the ratio in the absence of or prior to the execution of the method and / or administration of the therapeutic or prophylactic agent.

[0076] In certain embodiments, the modulation of the ratio is a statistically significant modulation.

[0077] In a preferred embodiment, treatment and / or prevention of C. acnes-related diseases, particularly C. acnes-related inflammatory diseases, is achieved by reducing the ratio of the amount of C. acnes-type α, as defined in the above section "C. acnes-type α and C. acnes-type β", to the amount of C. acnes-type β, as defined in the above section "C. acnes-type α and C. acnes-type β".

[0078] "Reduction in the ratio" means, as used herein, a reduction in the ratio after the execution of the method and / or administration of the therapeutic or prophylactic agent, compared to the ratio in the absence of or prior to the execution of the method and / or administration of the therapeutic or prophylactic agent.

[0079] Preferably, the reduction in the ratio is a statistically significant reduction.

[0080] In certain embodiments, the modulation, preferably reduction, of the ratio is observed one day after the first run of the method and / or the first administration of the therapeutic or prophylactic agent, and in particular 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 run of the method and / or the first administration of the therapeutic or prophylactic agent.

[0081] In certain embodiments, the modulation, preferably reduction, of the ratio is maintained for one day after the first run of the method and / or the first administration of the therapeutic or prophylactic agent, and in particular for 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 (not necessarily at the same level) after the first run of the method and / or the first administration of the therapeutic or prophylactic agent.

[0082] In certain embodiments, the modulation, preferably reduction, of the ratio is maintained (not necessarily at the same level) throughout the entire period during which the method is performed and / or the therapeutic or prophylactic agent is administered.

[0083] Preferably, the ratio is the ratio of the amount of α-type C. acnes bacteria, as defined in the section "α-type C. acnes and β-type C. acnes bacteria", on the skin of the subject to the ratio of the amount of β-type C. acnes bacteria, as defined in the section "α-type C. acnes and β-type C. acnes bacteria", on the skin of the subject.

[0084] According to the present invention, skin refers to the skin of the arms, especially the hands, the legs, especially the feet, the armpits, the neck, the chest, the back, the scalp, and / or the face. In preferred embodiments, skin is the skin of the face, neck, chest, and / or back. In preferred embodiments, skin is the skin of the face.

[0085] It specifically reduces the amount of α-type C. acnes bacteria. In certain embodiments, the treatment or preventive method of the present invention includes a step of specifically reducing the amount of α-type C. acnes, as defined in the above section "α-type C. acnes and β-type C. acnes," on a subject, particularly on the skin of the subject.

[0086] Accordingly, the present invention relates to a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of specifically reducing the amount of C. acnes type α in the subject, wherein C. acnes type α is as defined in the above section "C. acnes type α and C. acnes type β". The present invention also relates to a composition for use in treating or preventing a C. acnes-related disease in a subject, comprising a therapeutic or prophylactic agent that specifically reduces the amount of C. acnes type α in the subject, wherein C. acnes type α is as defined in the above section "C. acnes type α and C. acnes type β". The present invention further relates to the use of a therapeutic or prophylactic agent that specifically reduces the amount of C. acnes type α in a subject for the manufacture of a pharmacopoeia for treating or preventing a C. acnes-related disease, wherein C. acnes type α is as defined in the above section "C. acnes type α and C. acnes type β".

[0087] As used herein, the term “quantity” has the same meaning as disclosed in the above section “C. Methods for the treatment or prevention of bacterial diseases of acne.”

[0088] "Specifically reducing the amount of α-type C. acnes" means, in this specification, that the amount of other types of C. acnes, particularly β-type C. acnes, in the subject, in particular on the skin of the subject, is not significantly reduced, and / or the amount of other bacterial species, in the subject, in particular on the skin of the subject, is not significantly reduced. Preferably, "specifically reducing the amount of α-type C. acnes" means, in this specification, that the amount of other types of C. acnes, particularly β-type C. acnes, in the subject, in particular on the skin of the subject, is not significantly reduced.

[0089] "Reduction in quantity" in this specification means a reduction in quantity after the execution of the method and / or administration of the therapeutic or prophylactic agent, compared to the quantity before or in the absence of the execution of the method and / or administration of the therapeutic or prophylactic agent.

[0090] Preferably, the reduction in quantity is a statistically significant reduction.

[0091] In certain embodiments, the reduction in quantity is observed one day after the first execution of the method and / or the first administration of the therapeutic or prophylactic agent, and in particular two, three, four, five, six, seven, two weeks, three weeks, or one month after the first execution of the method and / or the first administration of the therapeutic or prophylactic agent.

[0092] In certain embodiments, the reduction in quantity is maintained for one day after the first run of the method and / or the first administration of the therapeutic or prophylactic agent, and in particular for 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 (not necessarily at the same level) after the first run of the method and / or the first administration of the therapeutic or prophylactic agent.

[0093] In certain embodiments, the reduction in quantity is maintained (not necessarily at the same level) throughout the entire period during which the method is performed and / or the therapeutic or prophylactic agent is administered.

[0094] In certain embodiments, the treatment or preventive method of the present invention includes the step of specifically killing or specifically inhibiting the growth of α-type C. acnes, as defined in the above section "α-type C. acnes and β-type C. acnes," on a subject, particularly on the skin of the subject.

[0095] Accordingly, the present invention relates to a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of specifically killing or specifically inhibiting the growth of C. acnes α in the subject, wherein C. acnes α is as defined in the above section "C. acnes α and C. acnes β". The present invention also relates to a composition for use in treating or preventing a C. acnes-related disease in a subject, comprising a therapeutic or prophylactic agent that specifically kills or specifically inhibits the growth of C. acnes α in the subject, wherein C. acnes α is as defined in the above section "C. acnes α and C. acnes β". The present invention further relates to the use of therapeutic or prophylactic agents for the manufacture of pharmaceuticals for the treatment or prevention of C. acnes-related diseases, which specifically kill or specifically inhibit the growth of C. acnes type α, where C. acnes type α is as defined in the above section “C. acnes type α and C. acnes type β”.

[0096] In certain embodiments, the α-C. acnes bacteria are killed to a level corresponding to 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% reduction of the α-C. acnes bacteria population in the subject, particularly the α-C. acnes bacteria cutaneous population, compared to an untreated population, or to the α-C. acnes bacteria population in the subject before the execution of the method and / or administration of the therapeutic or prophylactic agent, particularly the α-C. acnes bacteria cutaneous population, preferably at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% reduction.

[0097] In a preferred embodiment, the α-C. acnes bacteria are killed to 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 of the α-C. acnes bacteria population in the subject, particularly the α-C. acnes bacteria cutaneous population, compared to an untreated population, or compared to the α-C. acnes bacteria population in the subject before the execution of the method and / or administration of the therapeutic or prophylactic agent, particularly the α-C. acnes bacteria cutaneous population.

[0098] As used herein, the term "log" refers to the logarithm with base 10 (log 10 This refers to the common logarithm (as also shown by ).

[0099] "Specifically kills α-type C. acnes" means, in this specification, that, in the subject, other types of C. acnes present on the skin of the subject, particularly β-type C. acnes, and / or other bacterial species, are not significantly killed, in particular, are killed at a level at least 1 log, at least 2 log, at least 3 log, or at least 4 log lower than that of α-type C. acnes. Preferably, "specifically kills α-type C. acnes" means, in this specification, that, in the subject, other types of C. acnes present on the skin of the subject, particularly β-type C. acnes, are not significantly killed, in particular, are killed at a level at least 1 log, at least 2 log, at least 3 log, or at least 4 log lower than that of α-type C. acnes. In some specific embodiments, "specifically kill type α C. acnes" means, as used herein, that in the subject, in particular, types of C. acnes other than type α, especially type β C. acnes, and / or other bacterial species, preferably type β C. acnes, present on the skin of the subject are killed to a level corresponding to a reduction of less than 20%, preferably less than 10%, of the population of types of C. acnes other than type α, especially type β C. acnes, and / or other bacterial species, preferably type β C. acnes, in the subject, compared to an untreated population, or compared to the population of types of C. acnes other than type α, especially type β C. acnes, and / or other bacterial species, preferably type β C. acnes, in the subject, preferably on the skin of the subject, before the execution of the method and / or administration of the therapeutic or prophylactic agent.

[0100] In certain embodiments, the growth of the α-C. 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%, of the α-C. acnes bacteria population in the subject, particularly the α-C. acnes bacteria cutaneous population, compared to an untreated population, or compared to the α-C. acnes bacteria population in the subject before the execution of the method and / or administration of the therapeutic or prophylactic agent, particularly the α-C. acnes bacteria cutaneous population.

[0101] In a preferred embodiment, the growth of the α-C. acnes bacteria is inhibited to 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 of the α-C. acnes bacteria population in the subject, particularly the α-C. acnes bacteria cutaneous population, compared to an untreated population or compared to the α-C. acnes bacteria population in the subject before the execution of the method and / or administration of the therapeutic or prophylactic agent, particularly the α-C. acnes bacteria cutaneous population.

[0102] "Specifically inhibits the growth of α-type C. acnes" means, in this specification, that in the subject, in particular, the growth of other types of C. acnes present on the skin of the subject, in particular β-type C. acnes, and / or other bacterial species is not significantly inhibited, in particular at a level at least 1 log, at least 2 log, at least 3 log, or at least 4 log lower than that of α-type C. acnes. Preferably, "specifically inhibits the growth of α-type C. acnes" means, in this specification, that in the subject, in particular, the growth of other types of C. acnes present on the skin of the subject, in particular β-type C. acnes, is not significantly inhibited, in particular at a level at least 1 log, at least 2 log, at least 3 log, or at least 4 log lower than that of α-type C. acnes. In some specific embodiments, "specifically inhibits the growth of α-type C. acnes" means herein that the growth of C. acnes of a different type than α, particularly β-type C. acnes, and / or other bacterial species, preferably β-type C. acnes, present in the subject, in particular on the subject's skin, is inhibited to a level corresponding to a reduction of less than 20%, preferably less than 10%, compared to an untreated population, or in the subject before the execution of the method and / or administration of the therapeutic or prophylactic agent, preferably compared to the population of α-type C. acnes, particularly β-type C. acnes, and / or other bacterial species, preferably β-type C. acnes, on the subject's skin.

[0103] In certain embodiments, the treatment or preventive method of the present invention includes administering to the subject a therapeutic or preventive dose of an antibacterial agent, phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium that specifically targets the α-type C. acnes bacterium as defined in the above section "α-type C. acnes and β-type C. acnes bacterium".

[0104] Similarly, in specific embodiments of the use of compositions for use according to the present invention or therapeutic or prophylactic agents according to the present invention, the therapeutic or prophylactic agent is an antibacterial agent, phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium that specifically targets the α-type C. acnes bacterium as defined in the above section “α-type C. acnes and β-type C. acnes.”

[0105] As used herein, the term “therapeutic dose” refers to a non-toxic but sufficient amount of active agent to provide the desired therapeutic effect.

[0106] As used herein, the term “preventive dose” refers to a non-toxic but sufficient amount of active agent to provide the desired preventive effect.

[0107] In this specification, "targeting the α-type C. acnes bacteria" means that the therapeutic or prophylactic agent recognizes, preferably specifically recognizes, the α-type C. acnes bacteria, and / or exerts, preferably specifically exerts, its activity against, the α-type C. acnes bacteria.

[0108] "Specifically targeting the α-type C. acnes" means, in this specification, that the therapeutic or prophylactic agent recognizes the α-type C. acnes and / or exerts its activity against the α-type C. acnes, but does not significantly recognize and / or exert its activity against other types of C. acnes present on the skin of the subject, particularly β-type C. acnes, and / or other bacterial species. Preferably, "specifically targeting the α-type C. acnes" means, in this specification, that the therapeutic or prophylactic agent recognizes the α-type C. acnes and / or exerts its activity against the α-type C. acnes, but does not significantly recognize and / or exert its activity against other types of C. acnes present on the skin of the subject, particularly β-type C. acnes.

[0109] In this specification, “antibacterial agent” means a compound that inhibits or prevents bacterial growth, kills bacteria, or reduces the number of bacteria. The antibacterial agent may typically be a small molecule, a protein, a peptide or polypeptide, or a nucleic acid, such as DNA or RNA. Examples of antibacterial agents include antibiotics, bacteriocins, and endolysins. Therefore, in certain embodiments, the antibacterial agent is an antibiotic, bacteriocin, and / or endolysin that specifically targets the α-type C. acnes bacteria as defined in the above section “α-type C. acnes and β-type C. acnes.”

[0110] In this specification, "bacteriocin" means a proteinotoxin produced by bacteria that kills or inhibits the growth of other bacteria. Bacteriocins are categorized in several ways, including by producing strain, common resistance mechanisms, and mechanisms of death. Such bacteriocins are described from Gram-negative bacteria (e.g., microsin, colicin-like bacteriocin, and tailocin) and from Gram-positive bacteria (e.g., Class I, Class II, Class III, or Class IV bacteriocins).

[0111] In the context of the present invention, the bacteriocin may be a wild-type bacteriocin, or an engineered bacteriocin, particularly a bacteriocin mutant, variant, or chimera, typically involving alterations and / or modifications of the amino acid sequence. Such alterations and / or modifications may include mutations of amino acid residues, e.g., deletions, insertions and additions, substitutions or combinations thereof, and / or chemical changes, e.g., biotinylation, acetylation, pegylation, or chemical changes of amino, thiol, or carboxyl groups. Such an engineered bacteriocin typically exhibits the solubility activity of a wild-type bacteriocin. However, this activity may be the same as, higher than, or lower than that of a wild-type bacteriocin. The activity may be approximately 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 bacteriocin. The activity may be measured by assays well known in the art to those skilled in the art, such as plate dissolution assays or liquid dissolution assays described in Briers et al. (2007) J. Biochem. Biophys Methods 70:531-533 or Donovan et al. (2006) FEMS Microbiol Lett. 265:133-139, etc. Alternatively, such modified bacteriocins may exhibit different solubility compared to wild-type bacteriocins, for example, solubility with different specificity compared to wild-type bacteriocins.

[0112] In this specification, “endolysin” or “lysin” refers to enzymes used by bacteriophages at the end of their replication cycle to break down peptidoglycans of bacterial hosts from within, resulting in cell lysis and the release of progeny virions. These are typically β(1,4)-glycosylase (lysozyme), transglycosylase, amidase, or endopeptidase.

[0113] In the context of the present invention, the endolysin may be wild-type endolysin, or an engineered endolysin, particularly an endolysin mutant, variant, or chimera, typically involving alterations and / or modifications of the amino acid sequence. Such alterations and / or modifications may include mutations of amino acid residues, e.g., deletions, insertions and additions, substitutions or combinations thereof, and / or chemical changes, e.g., biotinylation, acetylation, pegylation, or chemical changes of amino, SH, or carboxyl groups. Such an engineered endolysin typically exhibits the solubility activity of wild-type endolysin. However, this activity may be the same as, higher than, or lower than that of wild-type endolysin. The activity may be approximately 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 endolysin. The activity may be measured by assays well known in the art to those skilled in the art, such as plate dissolution assays or liquid dissolution assays described in Briers et al. (2007) J. Biochem. Biophys Methods 70:531~533 or Donovan et al. (2006) FEMS Microbiol Lett. 265:133~139, etc. Alternatively, such modified endolysin may exhibit different solubility compared to wild-type endolysin, for example, solubility with different specificity compared to wild-type endolysin.

[0114] In this specification, “phage” or “bacteriophage” means a bacterial virus. Bacteriophages are obligate intracellular parasites that grow inside bacteria by incorporating some or all of the host biosynthetic machinery. Bacteriophages can be found inside cells as prophages, in which their genome is incorporated into the bacterial chromosome, or as phage-plasmids, in which their 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., genomes) and proteins and may be covered by a lipid membrane. Depending on the phage, the nucleic acid genome can be either DNA or RNA and may exist in either a circular or linear form. The size of the phage genome varies depending on the phage. The simplest phages have genomes measuring 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. The number and amount of individual protein types in a phage particle vary depending on the phage.

[0115] In the context of the present invention, the terms “recombinant” and “manipulated” are used interchangeably. “Recombinant” as used herein means a nucleic acid, protein, or microorganism containing, or encoded by, genetic material derived from multiple different sources and / or obtained using molecular biology and / or synthetic biology tools. Therefore, in the context of the present invention, a “recombinant” nucleic acid, protein, or microorganism is not a wild-type nucleic acid, protein, or microorganism.

[0116] 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 the present invention, “recombinant phage” is a phage that is neither a wild-type phage nor a phage obtained after natural evolution, but rather a phage that has been spontaneously modified, for example, using tools of molecular biology and / or synthetic biology.

[0117] As used herein, the terms “phagemide” or “phasmid” are equivalent and refer to vectors derived from both plasmid and bacteriophage genomes. A phagemide typically includes a phage packaging site and, optionally, an origin of replication (ori), particularly a bacterial and / or phage origin of replication. In one embodiment, the phagemide does not include a functional bacterial origin of replication and therefore cannot replicate on its own when injected into bacteria. Alternatively, the phagemide may include a plasmid origin of replication, particularly a bacterial and / or phage origin of replication.

[0118] As used herein, the term “packaged phagemide” refers to a phagemide capsid-encapsulated within a bacteriophage scaffold, phage-derived delivery particle, or capsid. In particular, it refers to a bacteriophage scaffold, phage delivery particle, or capsid lacking a bacteriophage genome. Packaged phagemides can be produced using helper phage strategies well known to those skilled in the art. A helper phage typically contains all the genes encoding the structural and functional proteins essential for the capsid-encapsulation of the phagemide according to the present invention.

[0119] As used herein, the term “plasmid” refers to a circular nucleic acid molecule capable of autonomous replication in a host cell. The plasmid may be a conjugative plasmid. In certain embodiments, the plasmid is a recombinant plasmid.

[0120] As used herein, the term “DNA or RNA-containing vesicle” refers to an artificial delivery vehicle that encapsulates at least one nucleic acid molecule (which may be DNA, RNA, or a mixture thereof) within a core surrounded by a shell. The DNA or RNA-containing vesicle may be a chemically based vesicle, in particular a polymer-based vesicle, e.g., a polymersome or a nonionic surfactant, e.g., a niosome, a lipid-based vesicle, e.g., a liposome, a protein-based or peptide-based vesicle, or a nanoparticle-based vesicle.

[0121] As used herein, the terms “extracellular vesicle” or “cell-derived nanovesicle” refer to nanoscale structures in the form of particles released or secreted from a cell, in which biomolecules encapsulate biomolecules, such as proteins, nucleic acid molecules, lipids, or organelles, within a cell membrane typically identical to the cell membrane of the cell from which they originate, in a lipid layer. 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 formed extracellular vesicles (e.g., by fractionation centrifugation ending in ultrafiltration, density gradient / cushion centrifugation, and immunoaffinity-based capture) or obtained by artificial methods (e.g., by extrusion processes in which cells pass through microfluidic channels, multi-step filtration processes, etc.).

[0122] The bacteria used in the context of the present invention may be wild-type bacteria, for example, wild-type bacteria that are naturally capable of specifically targeting C. acnes as defined in the above section "C. acnes and C. acnes as defined" by naturally producing an antibacterial agent defined for specifically targeting C. acnes as

[0123] As used herein, “engineered bacteria” refers to bacteria modified at the protein and / or nucleic acid level. Therefore, in the context of the present invention, “engineered bacteria” are bacteria that are neither wild-type bacteria nor bacteria obtained after natural evolution, but are spontaneously modified, for example, using tools of molecular biology and / or synthetic biology.

[0124] In certain embodiments, the treatment or preventive method of the present invention includes administering to the subject a therapeutic or preventive dose of a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium defined to specifically target the α-type C. acnes bacterium as defined in the above section "α-type C. acnes and β-type C. acnes bacterium".

[0125] Similarly, in specific embodiments of the use of compositions for use according to the present invention or therapeutic or prophylactic agents according to the present invention, the therapeutic or prophylactic agent is a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium defined to specifically target the α-type C. acnes bacterium as defined in the above section "α-type C. acnes and β-type C. acnes bacterium".

[0126] In preferred embodiments, the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encodes (or comprises nucleic acids encoding) a programmable nuclease designed to specifically target the α-type C. acnes bacterium.

[0127] "Programmable nuclease" as used herein means an enzyme designed to recognize and cleave a specific nucleic acid sequence. Programmable nucleases are well known to those skilled in the art and include the CRISPR-Cas system (including CRISPR-Cas nucleases), TALENs and their variants, zinc finger nucleases (ZFNs) and their variants, natural, evolved, or engineered meganuclease or recombinase variants, and any combination and hybrid thereof.

[0128] Therefore, in certain embodiments, the programmable nuclease is selected from CRISPR-Cas nucleases, TALENs and their variants, ZFNs and their variants, natural, evolved or engineered meganuclease or recombinase variants, and any combination and hybrid thereof.

[0129] As used herein, the terms “TALEN” or “activator-like effector nuclease” refer to recombinant proteins comprising an “activator-like effector (TALE) binding domain” and an endonuclease domain. An “activator-like effector (TALE) binding domain” refers to a protein containing a “repeat region” (also called a “repeat domain”) containing multiple repeated, highly conserved sequences of 33-34 amino acids (called “repeat modules” and “repeat modules”), wherein the last repeat module at the C-terminus is partially or half (approximately 20 amino acids) long. The combination of repeat modules in the repeat region binds to specific nucleotide sequences in target DNA and / or RNA sequences, and as a result, TALEN modifies target DNA and / or RNA in or adjacent to specific nucleotide sequences in cells or their offspring.

[0130] As used herein, the terms “zinc finger nuclease” or “ZFN” refer to a chimeric protein containing a zinc finger DNA-binding domain fused to a nuclease domain derived from an endonuclease or exonuclease.

[0131] As used herein, the term “meganucleases” refers to endonucleases that bind to double-stranded DNA at recognition sequences larger than 12 base pairs. Naturally occurring meganucleases may be monomeric (e.g., I-Scel) or dimeric (e.g., I-Crel). As used herein, the term meganuclease may be used to refer to monomeric meganucleases, dimeric meganucleases, or monomers that associate to form dimeric meganucleases. Due to the large recognition site of meganucleases, this site generally exists only once in any given genome.

[0132] As used herein, the term “recombinase” refers to a DNA-modifying enzyme (i.e., an enzyme capable of performing DNA recombination) that binds, cleaves, exchanges strands, and rejoins DNA at its respective recombination sites.

[0133] The "CRISPR-Cas system" refers to clustered, regularly arranged short palindromic sequence repeats and their CRISPR-associated (Cas) proteins. These systems include multiple diverse RNA-guided prokaryotic adaptive immune systems employed by these organisms to defend against foreign parasitic nucleic acids.

[0134] The CRISPR-Cas system contains two distinct elements: i) an endonuclease, 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 may be in the form of a chimeric RNA consisting of a combination of CRISPR (crRNA) bacterial RNA and tracrRNA (transactivatable RNA CRISPR) (Jinek et al. (2012) Science 337(6096):816~21). The guide RNA combines the targeting specificity of the crRNA corresponding to a "spacing sequence" that functions as a guide to the Cas protein, and the conformational properties of the tracrRNA, in a single transcript. When the guide RNA and Cas protein are expressed simultaneously in a cell, the target genomic sequence may be permanently disrupted (depending on the location, causing loss of the targeted and surrounding sequences and / or cell death) or modified. Modifications may be guided by the repair matrix.

[0135] The CRISPR-Cas system includes two main classes, depending on the nuclease action mechanism: - Class 1 consists of multi-subunit effector complexes, which include types I, III, and IV; - Class 2 consists of single-unit effector modules such as Cas9 nuclease, which include Type II (II-A, II-B, II-C, II-C variant), 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).

[0136] In certain embodiments, the programmable nuclease is a CRISPR-Cas nuclease (also referred herein as Cas nuclease or CRISPR enzyme). Various CRISPR enzymes are available for use in the context of the present invention. In some embodiments, the CRISPR enzyme is a type II CRISPR enzyme, type II-A, or type II-B CRISPR enzyme. In other embodiments, the CRISPR enzyme is a type I CRISPR enzyme or a type III CRISPR enzyme. In some embodiments, the CRISPR enzyme catalyzes DNA cleavage. In some other embodiments, the CRISPR enzyme catalyzes RNA cleavage.

[0137] Non-exclusive examples of Cas proteins as part of a multi-subunit effector or as 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), Cas13b(C2c6), Cas13c(C2c7), Cas13d, Csa5, Csc1, Csc2, Cs e1, Cse2, Csy1, Csy2, Csy3, Csf1, Csf2, Csf3, Csf4, Csm1, Csm2, Csm3, Csm4, Csm5, Csm6, Cm r1, Cmr3, Cmr4, Cmr5, Cmr6, Csn2, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx1 3, Csx1, Csx15, SdCpf1, CmtCpf1, TsCpf1, CmaCpf1, PcCpf1, ErCpf1, FbCpf1, UbcCpf1, AsCpf1, LbCpf1, Mad4, Mad7, Cms1, their homologs, their orthologues, their variants, or modified versions thereof. In some embodiments, the CRISPR enzyme cleaves both strands of the target nucleic acid at the protospacer adjacent motif (PAM) site.

[0138] In certain embodiments, the CRISPR enzyme is any Cas9 protein, for example, any naturally occurring bacterial Cas9 and any variant, homolog, or orthologue thereof.

[0139] "Cas9" refers to the protein Cas9 (also known as Csn1 or Csx12) or its functional protein, peptide, or polypeptide fragment, i.e., a substance capable of interacting with guide RNA and exhibiting enzymatic activity (nuclease) that enables it to perform double-strand breaks in target genome DNA. Therefore, "Cas9" may also refer to a modified protein, for example, one in which a protein has been shortened by removing a protein domain that is not essential for the protein's predetermined function, particularly a domain that is not necessary for interaction with gRNA.

[0140] The sequence encoding Cas9 (the whole protein or a fragment thereof) can be obtained from any known Cas9 protein when used in the context of the present invention (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 useful in the present invention include, but are not limited to, those of Streptococcus pyogenes (SpCas9), Streptococcus thermophiles (St1Cas9, St3Cas9), Streptococcus mutans, Staphylococcus aureus (SaCas9), Campylobacter jejuni (CjCas9), Francisella novicida (FnCas9), and Neisseria meningitides (NmCas9).

[0141] In certain embodiments, the CRISPR enzyme is dCas9.

[0142] The sequence encoding Cpf1(Cas12a) (the whole protein or a fragment thereof) can be obtained from any known Cpf1(Cas12a) protein when used in the context of the present invention (Koonin et al. (2017) Curr Opin Microbiol. 37:67~78). Examples of Cpf1(Cas12a) proteins useful in the present invention include, but are not limited to, Cpf1(Cas12a) proteins from Acidaminococcus sp., Lachnospiraceae bacteria, and Francisella nobicida.

[0143] The sequence encoding Cas13a (the whole protein or a fragment thereof), when used in the context of the present invention, can be obtained from any known Cas13a(C2c2) protein (Abudayyeh et al. (2017) Nature 550(7675):280~284). Examples of Cas13a(C2c2) proteins useful in the present invention include, but are not limited to, the Cas13a(C2c2) protein from Leptotrichia wadei (LwaCas13a).

[0144] The sequence encoding Cas13d (the whole protein or a fragment thereof) can be obtained from any known Cas13d protein when used in the context of the present invention (Yan et al. (2018) Mol Cell. 70(2):327~339.e5.). Examples of Cas13d proteins useful in the present invention include, but are not limited to, the Cas13d proteins of Eubacterium siraeum and Ruminococcus sp.

[0145] The sequence encoding Mad4 (the whole protein or a fragment thereof), when used in the context of the present invention, is disclosed in international application WO2018 / 236548.

[0146] The sequence encoding Mad7 (the whole protein or a fragment thereof) is disclosed in international application WO2018 / 236548 when used in the context of the present invention.

[0147] The sequence encoding Cms1 (the whole protein or a fragment thereof) is disclosed in international patent application WO2017 / 141173 when used in the context of the present invention.

[0148] In one embodiment, the CRISPR enzyme can be coupled to a guide RNA or a single guide RNA (sgRNA).

[0149] Therefore, in a preferred embodiment, the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium further encodes a guide RNA designed to specifically target the α-type C. acnes bacterium.

[0150] As used herein, the term "guide RNA" refers to either a crRNA (also known as CRISPR RNA) or a combination of a crRNA and a trRNA (also known as tracrRNA). The crRNA and trRNA can associate as a single RNA molecule (single guide RNA, sgRNA) or as two separate RNA molecules (dual guide RNA, dgRNA). The trRNA can be a naturally occurring sequence or a trRNA sequence having modifications or variations compared to a naturally occurring sequence. For clarity, the term "guide RNA", as used herein, refers to an RNA molecule (comprising A, C, G, and U nucleotides) or a DNA molecule (comprising A, C, G, and T nucleotides) encoding such an RNA molecule or their complementary sequences, unless otherwise specifically stated. As is well known to those skilled in the art, the "guide RNA" in the CRISPR-Cas system is utilized for the detection of a target nucleic acid and is responsible for recognizing a portion of the sequence carried 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 specificity of the detection of the target nucleic acid in the CRISPR-Cas system. The guide RNA is typically designed to match the Cas protein with which it is co-administered. Methods for designing and producing guide RNAs are well known.

[0151] In certain embodiments, the guide RNA is designed to specifically target an α-type C. acnes bacterium-specific sequence, gene, or locus.

[0152] In certain embodiments, the guide RNA is designed to specifically target the hem locus of the α-type C. acnes bacterium.

[0153] In a more preferred embodiment, the guide RNA is designed to specifically target at least one of the nucleotide variants in the hem locus associated with C. acnes, as defined in the section "C. acnes α and C. acnes β". Preferably, the guide RNA is selected to have at least one mismatch, preferably two, between C. acnes α and C. acnes β, and / or one mismatch in the PAM site.

[0154] Therefore, in more specific embodiments, the guide RNA is designed to specifically target at least one of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10).

[0155] Preferably, the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encodes multiple (at least 2, 3, 4, 5 or more) guide RNAs that specifically target multiple (at least 2, 3, 4, 5 or more) nucleotide variants in the hem locus associated with C. acnes bacterium α as defined in the section "C. acnes bacterium α and C. acnes bacterium β".

[0156] In certain embodiments, the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium includes a sequence encoding a guide RNA selected from the group consisting of SEQ ID NOs: 13-16.

[0157] Genetic modification of the DNA sequence in α-type C. acnes bacteria. In certain embodiments, the treatment or preventive method of the present invention includes the step of genetically modifying the DNA sequence of the α-type C. acnes bacteria, as defined in the above section "α-type C. acnes and β-type C. acnes bacteria", on the skin of the subject to produce at least one change in the α-type C. acnes bacteria, preferably at the hem locus of the α-type C. acnes bacteria.

[0158] Similarly, in a particular embodiment of the use of a composition for use according to the present invention or a therapeutic or prophylactic agent according to the present invention, the therapeutic or prophylactic agent induces a genetic alteration of the DNA sequence in the α-type C. acnes bacteria, as defined in the above section "α-type C. acnes and β-type C. acnes bacteria," on the skin of the subject, thereby producing at least one change in the α-type C. acnes bacteria, preferably at the hem locus of the α-type C. acnes bacteria.

[0159] Accordingly, the present invention relates to a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of genetically modifying the DNA sequence of C. acnes α-type on the skin of the subject to produce at least one change in the C. acnes α-type, preferably at the hem locus of the C. acnes α-type. The present invention also relates to a composition for use in treating or preventing a C. acnes-related disease in a subject, comprising a therapeutic or prophylactic agent for genetically modifying the DNA sequence of C. acnes α-type on the skin of the subject to produce at least one change in the C. acnes α-type, preferably at the hem locus of the C. acnes α-type. The present invention further relates to the use of a therapeutic or prophylactic agent for the manufacture of a pharmaceutical for the treatment or prevention of C. acnes-related diseases, wherein the DNA sequence of C. acnes α-type on the skin of the subject is genetically modified to produce at least one change in the C. acnes α-type, preferably at the hem locus of the C. acnes α-type.

[0160] "Genetically modifying a DNA sequence" or "genetically modifying a DNA sequence" means, as used herein, that at least one nucleotide of the DNA sequence is modified. 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 nucleic acid base of at least one nucleotide (e.g., methylation).

[0161] In the context of the present invention, the gene modification preferably occurs at the hem locus of the α-type C. acnes bacterium; in other words, the gene modification preferably produces at least one change at the hem locus of the α-type C. acnes bacterium.

[0162] In certain embodiments, the gene modification preferably produces at least one change in at least one of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence 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 (positions are defined by referring to the sequence of Sequence ID No. 6), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (positions are defined by referring to the sequence of Sequence ID No. 7), - In hemH gene: T11, T23, A48, T89, C188, G338, T464, T470, G536, T548, T608, G626, T 632, T641, T671, T674, C683, C689, A740, G745, G787, A797, T893, A898, T1034, T 1039, T1046, C1071, G1095, C1109, T1153, T1358, G1496, C1511, C1527, G1532, T1598, T1712, A1850, G1901, A1926, C1931 and C1997 (the position is defined by referring to the array of sequence number 8), - In the hemL gene: T107, C197, T229, A242, C310, A338, A374, T389, G392, T442, C467, G470, C482, G518 and C641 (positions are defined by referring to the sequence of Sequence 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, T1 136, G1143, G1152, T1166, T1172, A1176, T1184, C1199, C1205, G1268, G1278, T1295, T1318, A1336, G1343, C1346, G1355, T1359 and C1395 (the position is defined by referring to the array of sequence number 10).

[0163] In certain embodiments, the gene modification produces at least one change in at least one of the nucleotide variants in the hem locus associated with α-type C. acnes, as defined in the section “α-type C. acnes and β-type C. acnes,” to a nucleotide variant in the hem locus associated with β-type C. acnes.

[0164] Therefore, in certain embodiments, the gene modification generates 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 changes at the hem locus: - In the hemA gene: T173G, A479G, T506C, A614G, T629G, C671A, T971C, A989G, T1085C and T1094C (positions are defined by referring to the sequence of 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 (positions are defined by referring to the sequence of Sequence 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, A644G, A66 5G, C710T, C713G, A737G, A770G, A776G, T785A, T802C, G830A, C842T, T845C, G855A, C893G, A896T, C897T, G902A, G908T, A941G and A947G (the position is defined by referring to the array of sequence number 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 (position is defined by referring to the sequence of Sequence ID No. 6), - in the hemE gene: T241C, T476C, A530G, T704C, A728G, G767C, T834A, A867G, A872G, A882C, and A957G (positions are defined by reference to the sequence of 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, A898T, T1034C, T1039C, T1046C, C1071G, G1095A, C1109T, T1153C, T1358C, G1496C, C1511T, C1527T, G1532A, T1598C, T1712C, A1850G, G1901C, A1926G, C1931T, and C1997T (positions are defined by reference to the sequence of SEQ ID NO: 8), - in the hemL gene: T107C, C197T, T229A, A242G, C310A, A338G, A374G, T389C, G392T, T442C, C467T, G470A, C482T, G518T, and C641G (positions are defined by reference to the sequence of 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, T1055C, G1091A, T1136C, G1143A, G1152T, T1166C, T1172G, A1176G, T1184C, C1199T, C1205T, G1268A, G1278A, T1295C, T1318C, A1336G, G1343A, C1346T, G1355C, T1359G, and C1395G (positions are defined by reference to the sequence of SEQ ID NO: 10).

[0165] Genetic modification can be a point mutation, deletion, insertion, or any combination thereof. Preferably, the genetic modification is a point mutation.

[0166] Genetic modification preferably involves eliminating, reducing, or increasing gene expression. Genetic modification may occur in the coding or uncoding regions of a gene. Genetic modification may occur in the promoter region of a gene or in any other region involved in gene regulation.

[0167] In certain embodiments, the genetic modification eliminates and / or reduces the expression of one or more genes at the hem locus in C. acnes, preferably in α-type C. acnes, namely the hemA, hemB, hemC, hemD, hemE, hemH, hemL, and / or hemY genes. In more specific embodiments, the genetic modification eliminates or reduces porphyrin production by C. acnes, particularly by α-type C. acnes.

[0168] In some embodiments, the gene modification results in a change to a different amino acid in 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, 500, etc. In some embodiments, the gene modification introduces a stop codon. In some embodiments, the gene modification is outside the protein coding sequence, within the RNA, or within a regulatory sequence. In some embodiments, the gene modification introduces one or more rare codons such that protein expression is affected, preferably reduced. In some embodiments, the start codon is modified so that normal initiation is altered or invalidated.

[0169] In certain embodiments, the genetic modification results in the modified C. acnes bacteria no longer belonging to the group of α-type C. acnes bacteria as defined in the section "α-type C. acnes bacteria and β-type C. acnes bacteria". In preferred embodiments, the genetic modification results in the modified C. acnes bacteria becoming β-type C. acnes bacteria as defined in the section "α-type C. acnes bacteria and β-type C. acnes bacteria".

[0170] A therapeutic or preventive agent that genetically modifies the DNA sequence in C. acnes α-type to produce at least one change in the C. acnes α-type, preferably at the hem locus of the C. acnes α-type, may be a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a gene editing enzyme or system that targets the hem locus in the C. acnes α-type, particularly at least one of the nucleotide variants defined above.

[0171] In certain embodiments, the treatment or preventive method of the present invention includes administering to the subject a therapeutic or preventive dose of a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a gene editing enzyme or system that targets the hem locus in the α-type C. acnes bacterium, in particular, at least one of the nucleotide variants defined above.

[0172] Similarly, in specific embodiments of the use of compositions for use according to the present invention or therapeutic or prophylactic agents according to the present invention, the therapeutic or prophylactic agent is a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a gene editing enzyme or system that targets and modifies the hem locus in the α-type C. acnes bacterium, in particular, at least one of the nucleotide variants defined above.

[0173] As used herein, the term “gene editing” refers to a type of genetic manipulation in which DNA is inserted, deleted, altered, or replaced in the genome of a living organism.

[0174] In this specification, "gene editing system" refers to a combination of components required for gene editing of the genome in a cell. The various components of the system, such as polypeptides and gRNAs, may exist independently of each other or in any combination thereof.

[0175] In this specification, "gene editing enzyme" means an enzyme that enables gene editing of the genome in a cell. The gene editing enzyme may typically be part of the gene editing system defined above and may be used in conjunction with other components of the system.

[0176] In certain embodiments, the gene editing enzyme or system is a base editing enzyme or system.

[0177] Base editing (BE) refers to the ability to replace specific nucleotide base pairs on a DNA or RNA molecule with other nucleotide base pairs. In base editing techniques, no DNA exchange occurs; instead, an enzymatic reaction converts one nucleotide to another, resulting in a mismatch at the dsDNA level that is then corrected by the cellular machinery.

[0178] In some embodiments, the base editing system includes one or more of the following enzymes and systems:

[0179] Cytosine base editors (CBEs) and adenosine base editors (ABEs) described in Rees and Liu (2018) Nat Rev Genet 19:770~788.

[0180] Examples of DNA base editors include: - Cytosine base editor (CBE) for converting C:G to T:A (Komor et al. (2016) Nature 533:420~4); - Adenine base editor (ABE) for converting A:T to G:C (Gaudelli et al. (2017) Nature 551(7681):464~471); - C:G to G:C conversion C:Singanine base editor (CGBE) (Chen et al. (2020) Precise and programmable C:G to G:C base editing in genomic DNA. Biorxiv; Kurt et al. (2020) CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nature Biotechnology); - Cytosine adenine base editor (CABE) that converts C:G to A:T (Zhao et al. (2020) New base editors change C to A in bacteria and C to G in mammalian cells. Nature Biotechnology); - Adenine cytosine base editor (ACBE) (WO2020181180) for converting A:T to C:G; - Adenine thymine base editor (ATBE) for converting A:T to T:A (WO2020181202); - Thymine-adenine base editor (TABE) that converts T:A to A:T (WO2020181193;WO2020181178;WO2020181195).

[0181] Base editors differ in their base-modifying enzymes. CBEs depend on ssDNA cytidine deaminases, particularly APOBEC1, rAPOBEC1, APOBEC1 variants or evolved versions (evoAPOBEC1), and APOBEC homologs (APOBEC3A (eA3A), Anc689), cytidine deaminase 1 (CDA1), evoCDA1, FERNY, and evoFERNY.

[0182] ABE relies on the deoxyadenosine deaminase activity of the tandem fusion TadA-TadA*, where TadA* is an evolved version of the E. coli tRNA adenosine deaminase enzyme TadA, capable of converting adenosine on ssDNA to inosine. TadA* includes TadA-8a-e and TadA-7.10.

[0183] Apart from base-modifying enzymes, modifications to base editors have also been made to increase the effectiveness, precision, and modularity of the editing process. - Addition of one or two uracil DNA glycosylase inhibitor domains (UGIs) to prevent the base excision repair mechanism from reversing base editing; - Addition of Mu-GAM to reduce insertion-deletion rates by inhibiting the non-homologous end joining mechanism (NHEJ) in cells; - The use of nickase-active Cas9 (nCas9 D10A) that works favorably for repair by creating nicks on the unedited strand, and consequently favorably for fixing the edited bases; - For example, the use of diverse Cas proteins from different organisms, variants with different PAM motifs, different fidelity, or different families (e.g., Cas12a).

[0184] Non-exclusive examples of DNA-based editor 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 ABE. 7.9, 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-NG- Includes ABE, SpCas9-NG-CBE4, enAsBE1.1, enAsBE1.2, enAsBE1.3, enAsBE1.4, AsBE1.1, AsBE1.4, CRISPR-Abest, CRISPR-Cbest, eA3A-BE3, AncBE4.

[0185] The Citrous Anine Base Editor (CGBE) consists of the following fused nicasse CRISPR: - 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 Escherichia coli-derived uracil DNA N-glycosylase (eUNG) (Kurt et al. (2020) CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nature Biotechnology).

[0186] Cytosine adenine base editors (CABEs) consist of Cas9 nickase, cytidine deaminase (e.g., AID), and uracil-DNA glycosylase (Ung) (Zhao et al. (2020) New base editors change C to A in bacteria and C to G in mammalian cells. Nature Biotechnology).

[0187] ACBE contains nucleic acid programmable DNA-binding protein and adenine oxidase (WO2020181180).

[0188] ATBE consists of Cas9 nickase and one or more adenosine deaminases or one oxidase domain (WO2020181202).

[0189] TABE consists of Cas9 nickase and adenosine methyltransferase, thymine alkyltransferase, or adenosine deaminase domains (WO2020181193;WO2020181178;WO2020181195).

[0190] Base editor molecules can also consist of two or more of the editor enzymes listed above, fused to a Cas protein (e.g., a combination of ABE and CBE). These biomolecules are called dual base 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 adenine base editors, Nature Biotechnology).

[0191] In certain embodiments, 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 enzyme, e.g., APOBEC enzyme, or an adenosine deaminase enzyme, e.g., ADAT enzyme, as disclosed, for example, in U.S. Patent Application Publication 2015 / 0166980. In one embodiment, the deaminase is ACF1 / ASE deaminase. In various embodiments, the APOBEC enzyme is selected from the group consisting of 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 glycosylase inhibitor (UGI) domain. In one embodiment, the deaminase is an adenosine deaminase that deaminates adenosine in DNA, such as disclosed in U.S. Patent No. 10,113,163. In some embodiments, the base editing system further comprises a base repair inhibitor, such as a nuclease-inactive inosine-specific nuclease (dISN), as disclosed in U.S. Patent No. 10,113,163.

[0192] In certain embodiments, the base editing system includes a cytosine base editor (CBE) and / or an adenosine base editor (ABE) as defined above.

[0193] In another specific embodiment, the gene editing enzyme or system is a prime editing enzyme or system.

[0194] Prime editing (PE) enables the introduction of insertions, deletions (indels), and multi-base-to-base conversions. Prime editing typically relies on the ability of reverse transcriptase (RT) fused to a Cas nickase variant to convert an RNA sequence provided by prime editing guide RNA (pegRNA) into DNA at a nick site generated by the Cas protein. The resulting DNA flap is then either present or absent in the targeted DNA sequence.

[0195] The prime editor described by Anzalone et al. (2019) Nature 576:149-157 typically consists of nCas9 fused to a reverse transcriptase used in combination with prime editing RNA (pegRNA; guide RNA containing a template region for reverse transcription).

[0196] A prime editing system typically includes: - Cas nickerse variants fused to the reverse transcriptase domain, e.g., M-MLV RT or its variant versions (M-MLV RT(D200N), M-MLV RT(D200N / L603W), M-MLV RT(D200N / L603W / T330P / T306K / W313F), e.g., Cas9-H840A, and - Prime editing guide RNA (pegRNA).

[0197] To facilitate editing, the prime editing system may include the expression of additional sgRNAs that ideally target Cas nickase activity toward the unedited DNA strand only after the degradation of the edited strand flap, by designing sgRNAs that anneal to the edited strand but not to the original strand.

[0198] Non-exclusive examples of prime editing systems include PE1, PE1-M1, PE1-M2, PE1-M3, PE1-M6, PE1-M15, PE1-M3inv, PE2, PE3, and PE3b.

[0199] In various embodiments, the prime editing system comprises a fusion protein containing a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that identifies a target site and encodes the desired edit, as described, for example, in (2019) Nature 576:149-157.

[0200] Other suitable gene editing systems or enzymes include: - Cas9 Retron precISe Parallel Editing via homologY ("CRISPEY"), retron RNA fused to sgRNA and expressed together with Cas9, and retron proteins containing at least reverse transcriptase (Sharon et al. (2018) Cell 175:544~557.e16). - SCRIBE strategy: A retron system expressed in combination with a recombinase that promotes single-stranded DNA recombination, also known as a single-stranded annealing protein (SSAP) (Farzadfard and Lu (2014) Science 346:1256272). Such recombinases include, but are not limited to, phage recombinases described by Wannier et al., Improved bacterial recombineering by parallelized protein discovery. Biorxiv 2020.01.14.906594 (2020) doi:10.1101 / 2020.01.14.906594, such as lambda red, recET, Sak, Sak4, and SSAP. - A targetron system based on group II introns, described by Karberg et al. in Nat Biotechnol (2001) 19:1162~7, which has been adapted to many bacterial species. - Other retron-based gene targeting approaches described in Simon et al. (2019) Nucleic Acids Res 47:11007~11019. - A bridge system using non-coding RNA (ncRNA) with two distinct binding loops that separately recognize IS DNA donors and their genomic insertion target sites, based on IS1111 and IS110 insertion sequence (IS) family members. By bridging the donor and target DNA molecules via direct base-pairing interactions, the bispecific bridge RNA facilitates DNA recombination by IS recombinase (Durrant et al., Nature. June 2024; 630(8018): 984-993; Siddiquee et al. Nat Commun 15, 5235 (2024)).

[0201] In certain embodiments, the gene editing system or enzyme is a base editor or prime editor as defined above.

[0202] The present invention also relates to a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of specifically reducing the expression of at least one hem locus protein in C. acnes α-type in the subject, wherein C. acnes α-type is C. acnes as defined in the above section "C. acnes α-type and C. acnes β-type".

[0203] The present invention also relates to a composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that specifically reduces the expression of at least one hem locus protein in C. acnes α in the subject by genetically modifying the DNA sequence of C. acnes α in the subject, preferably by generating at least one change at the hem locus of C. acnes α, wherein C. acnes α is C. acnes as defined in the above section "C. acnes α and C. acnes β".

[0204] The present invention further relates to the use of a therapeutic or prophylactic agent for the manufacture of a pharmaceutical for the treatment or prevention of C. acnes-related diseases in a subject, wherein the therapeutic or prophylactic agent specifically reduces the expression of at least one hem locus protein in C. acnes α in the subject by genetically modifying the DNA sequence in C. acnes α in the subject, preferably by generating at least one change at the hem locus of C. acnes α, wherein C. acnes α is C. acnes as defined in the above section "C. acnes α and C. acnes β".

[0205] The therapeutic or prophylactic agent may be as defined above.

[0206] In certain embodiments, therapeutic or prophylactic agents that specifically reduce the expression of at least one hem locus protein in α-C. acnes in a subject by genetically modifying the DNA sequence in the α-C. acnes in the subject are phages, recombinant phages, packaged phagemids, plasmids, DNA or RNA-containing vesicles, extracellular vesicles, bacteria, or engineered bacteria encoding a gene editing enzyme or system that targets the hem locus in α-C. acnes, in particular, at least one of the nucleotide variants defined above.

[0207] In certain embodiments, the treatment or preventive method of the present invention comprises administering to the subject a therapeutic or preventive amount of a therapeutic or preventive agent that specifically reduces the expression of at least one hem locus protein in α-C. acnes in the subject by genetically modifying the DNA sequence in α-C. acnes in the subject. Preferably, the therapeutic or preventive agent is a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a gene editing enzyme or system that targets the hem locus, in particular at least one of the nucleotide variants defined above.

[0208] Genetic modification can be performed as defined above and can be carried out as described above.

[0209] In certain embodiments, the genetic modification eliminates and / or reduces the expression of one or more genes at the hem locus in α-type C. acnes, namely the hemA, hemB, hemC, hemD, hemE, hemH, hemL, and / or hemY genes.

[0210] In more specific embodiments, the genetic modification eliminates or reduces porphyrin production by α-type C. acnes bacteria.

[0211] "Specifically reducing the expression of at least one hem locus protein in α-type C. acnes" means, in this specification, that the expression of at least one hem locus protein, i.e., hemA, hemB, hemC, hemD, hemE, hemH, hemL, and / or hemY proteins, of a type of C. acnes other than α-type, particularly β-type C. acnes, and / or other bacterial species, in the subject, particularly on the skin of the subject, is not significantly reduced; preferably, the expression of at least one hem locus protein of a type of C. acnes other than α-type, particularly β-type C. acnes, in the subject, particularly on the skin of the subject, is not significantly reduced. Preferably, the expression of the at least one hem locus protein of a type of C. acnes other than α-type, particularly β-type C. acnes, and / or other bacterial species, is reduced by less than 20%, preferably less than 10%, compared to an untreated population, or compared to a population of a type of C. acnes other than α-type, particularly β-type C. acnes, and / or other bacterial species in the subject before the execution of the method and / or administration of the therapeutic or prophylactic agent.

[0212] Genetic modifications that induce a reduction in the expression of at least one hem locus protein may or may not affect the ratio of α-type C. acnes to β-type C. acnes, i.e., the genetic modification may or may not result in the modified C. acnes no longer belonging to the group of α-type C. acnes as defined in the above section "α-type C. acnes and β-type C. acnes". In some specific embodiments, the ratio of α-type C. acnes to β-type C. acnes is not affected by the genetic modification.

[0213] Increases the amount of β-type C. acnes bacteria. In certain embodiments, the treatment or preventive method of the present invention includes a step of increasing the amount of β-type C. acnes, as defined in the above section "α-type C. acnes and β-type C. acnes," on the skin of the subject.

[0214] Accordingly, the present invention relates to a method for treating or preventing a C. acnes-related disease in a subject, comprising the step of increasing the amount of β-type C. acnes bacteria on the skin of the subject. The present invention also relates to a composition for use in treating or preventing a C. acnes-related disease in a subject, comprising a therapeutic or prophylactic agent for increasing the amount of β-type C. acnes bacteria on the skin of the subject. The present invention further relates to the use of a therapeutic or prophylactic agent for increasing the amount of β-type C. acnes bacteria on the skin of the subject, for the manufacture of a pharmacopoeia for treating or preventing a C. acnes-related disease in a subject.

[0215] As used herein, the term “quantity” has the same meaning as disclosed in the above section “C. Methods for the treatment or prevention of bacterial diseases of acne.”

[0216] In certain embodiments, the amount of β-type C. acnes, as defined in the above section "α-type C. acnes and β-type C. acnes," is specifically increased in the subject, particularly on the skin of the subject.

[0217] "Specifically increasing the amount of β-type C. acnes" means, in this specification, that the amount of other types of C. acnes, particularly α-type C. acnes, in the subject, in particular on the skin of the subject, is not significantly increased, and / or the amount of other bacterial species in the subject, in particular on the skin of the subject, is not significantly increased.

[0218] "Increase in quantity" in this specification means an increase in quantity after the implementation of the method, compared to the quantity in the absence of the implementation of the method or before its implementation.

[0219] In certain embodiments, the increase in quantity is a statistically significant increase.

[0220] In certain embodiments, the increase in quantity is observed one day after the first execution of the method, and in particular two, three, four, five, six, seven days, two weeks, three weeks, or one month after the first execution of the method.

[0221] In certain embodiments, the aforementioned increase in quantity is maintained for one day after the first run of the method, and in particular for two days, three days, four days, five days, six days, seven days, two weeks, three weeks, one month, two months, three months, four months, five months, six months, or one year (not necessarily at the same level) after the first run of the method.

[0222] In certain embodiments, the aforementioned increase in quantity is maintained (not necessarily at the same level) throughout the entire duration that the method is performed.

[0223] In certain embodiments, the treatment or prevention method of the present invention includes the step of administering, in particular, the β-type C. acnes, as defined in the section "α-type C. acnes and β-type C. acnes," to the subject, and especially to the skin of the subject.

[0224] In particular, therapeutic or prophylactic agents that increase the amount of β-type C. acnes bacteria may be phages, recombinant phages, packaged phagemids, plasmids, DNA or RNA-containing vesicles, extracellular vesicles, bacteria, or engineered bacteria that encode gene editing enzymes or systems that target the hem locus of α-type C. acnes bacteria, in particular the alpha nucleotide variant as defined in Table 1, thereby causing a change in the α-type C. acnes bacteria, resulting in the modified α-type C. acnes bacteria becoming β-type C. acnes bacteria.

[0225] Subjects, regimens, and administration The subjects of the present invention are animals, preferably mammals, and more preferably humans. However, the term "subject" may also refer to non-human animals, in particular mammals.

[0226] Human subjects according to the present invention may be newborns, children, infants, adolescents, or adults of any age. In certain embodiments, the human subjects are adolescents.

[0227] In a preferred embodiment, the subject has been diagnosed with acne, particularly acne vulgaris, or is at risk of developing acne, particularly acne vulgaris. In a preferred embodiment, the subject has been diagnosed with acne, particularly acne vulgaris, using the diagnostic methods disclosed in the following section, “Risk and Diagnosis of Developing Acne.” In a preferred embodiment, the subject has been identified as being at risk of developing acne, particularly acne vulgaris, using the methods disclosed in the following section, “Risk and Diagnosis of Developing Acne.”

[0228] In certain embodiments, the subject has not received any treatment prior to the treatment or preventive method of the present invention.

[0229] In certain embodiments, the subject has already received at least one treatment plan, preferably several treatment plans, prior to the treatment or preventive method of the present invention.

[0230] Preferably, the treatment is administered regularly, preferably daily to monthly, more preferably daily to every two weeks, and even more preferably daily to weekly. In certain embodiments, the treatment is administered several times a day, preferably twice a day.

[0231] The duration of treatment according to the present invention is preferably from one day to one year, more preferably from one week to six months, even more preferably from two weeks to three months, and even more preferably from three weeks to two months. In certain embodiments, the duration of treatment is about one month. Alternatively, the treatment may continue for as long as the disease persists.

[0232] The form of the pharmaceutical composition, the route of administration of the therapeutic or prophylactic agent according to the present invention, and the dosage can be adjusted by those skilled in the art according to the type and severity of the disease, and according to the patient or subject, in particular their age, weight, sex, and overall physical condition.

[0233] In particular, the amount of therapeutic or prophylactic agent to be administered must be determined by standard procedures well known to those skilled in the art. Physiological data of the patient or subject (e.g., age, size, and weight) and the route of administration must be taken into consideration to determine the appropriate dosage, so that a therapeutic or prophylactic effective dose is administered to the patient or subject.

[0234] For example, the total amount of phages, manipulated phages, or packaged phagemids according to the present invention for each dose is typically 10 4 From the delivery vehicle 10 15 It is included between individual delivery vehicles.

[0235] In the context of the present invention, the preferred route of administration is topical administration.

[0236] The treatment or preventive method of the present invention is intended to be used in combination with other standard treatments. For example, in some embodiments, the treatment or preventive method of the present invention is performed before, after, or concurrently with the administration of a further therapeutic agent or the execution of a further treatment or preventive method. In some embodiments, the further therapeutic agent may be a topical antibiotic. Non-limiting examples of topical antibiotics include clindamycin, doxycycline, erythromycin, and tetracycline. In some embodiments, the further therapeutic agent may be an oral antibiotic. Non-limiting examples of oral antibiotics include erythromycin; or tetracycline, for example, doxycycline or minocycline. Other further therapeutic agents may include anti-inflammatory agents, antioxidants, acids, or combinations thereof.

[0237] In some embodiments, the further treatment or preventive method is phototherapy. In some embodiments, the further treatment or preventive method is laser treatment. In some embodiments, the further treatment or preventive method includes treating the subject with blue light. In some embodiments, the further treatment or preventive method includes treating the subject with red light. In some embodiments, the further treatment or preventive method includes treating the subject with a targeted laser device. In some embodiments, the further treatment or preventive method includes treating the subject with a laser that targets porphyrins.

[0238] The combinations of further therapeutic agents and further treatment or preventive methods disclosed above may also be used.

[0239] Pharmaceutical composition The present invention also relates to a pharmaceutical composition comprising a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium, as defined in the section "Specifically reducing the amount of C. acnes", which encodes a programmable nuclease as defined in the section "Specifically reducing the amount of C. acnes" above, or a gene editing enzyme or system as defined in the section "Genetically modifying the DNA sequence in C. acnes" above, where C. acnes is as defined in the section "C. acnes and C. acnes".

[0240] In certain embodiments, the pharmaceutical composition further comprises a pharmaceutically acceptable vehicle.

[0241] "Pharmacologically acceptable vehicle" as used herein means a pharmaceutical component known to be useful for preparing a pharmaceutical composition to be administered to a patient in need. Such a component is safe and non-sensitizing under the conditions of use.

[0242] Pharmacopoeia-acceptable vehicles are known to those skilled in the art and include common excipients, diluents, or carriers.

[0243] In certain embodiments, the pharmaceutical composition further comprises at least one pharmaceutically acceptable excipient and / or adjuvant.

[0244] "Pharmacologically acceptable excipients" as used herein means non-pharmaceutically active additives used in the manufacture of a pharmaceutical composition that enable the production of pharmaceutically active components into a pharmaceutical composition or galenic preparation that provides the necessary bioavailability of the medicine to the patient upon administration of the pharmaceutical composition. The excipients are preferably compatible with the other components of the composition and do not cause adverse effects, allergic reactions, or other undesirable reactions when administered to humans or animals.

[0245] "Pharmacologically acceptable adjuvant" as used herein means a substance added to a pharmaceutical composition to enhance the role of an excipient or therapeutically active component, which is non-toxic, bioacceptable, and otherwise bioappropriate for administration to a subject.

[0246] In certain embodiments, the pharmaceutical composition further comprises an additional therapeutically active agent.

[0247] "Further therapeutically active agents" in this specification means any chemical, biochemical, organic, inorganic compound, composition, element, or substance that is designated for or may be used for the treatment of diseases, disorders, dysfunctions, etc., of organisms or biological substances in general, and is different from therapeutic or prophylactic agents as defined in the above sections "Methods for the treatment or prevention of C. acnes-related diseases," "Specifically reducing the amount of C. acnes α," "Genetically modifying the DNA sequence in C. acnes α" and / or "Increasing the amount of C. acnes β."

[0248] The aforementioned further therapeutically active agents include nonsteroidal anti-inflammatory drugs (NSAIDs) analgesics; opioid agonist analgesics; salicylate analgesics; H1-blocker antihistamines; H2-blocker antihistamines; anti-infective agents; anti-anaerobic anti-infective agents; antifungal antibiotic anti-infective agents; macrolide antibiotic anti-infective agents; various beta-lactam antibiotic anti-infective agents; penicillin antibiotic anti-infective agents; quinolone antibiotic anti-infective agents; tetracycline antibiotic anti-infective agents; anti-tuberculous anti-mycobacterial anti-infective agents; anti- Protozoan anti-infective agents; antimalarial anti-infective agents; antiretroviral anti-infective agents; antiviral anti-infective agents; antineoplastic alkylating agents; nitrosourea antineoplastic alkylating agents; antimetabolites antineoplastic agents; pyrimidine analog antimetabolites antineoplastic agents; hormonal antineoplastic agents; natural antineoplastic agents; antibiotics natural antineoplastic agents; vinca alkaloids natural antineoplastic agents; autonomic neurogenic agents; anticholinergic autonomic neurogenic agents; antimuscarinic anticholinergic autonomic neurogenic agents; ergot alkaloids autonomic neurogenic agents; cholinergic agents Gonist parasympathetic agents; cholinesterase inhibitors parasympathetic agents; alpha-blockers sympathetic blockers; beta-blockers sympathetic blockers; adrenergic agonists sympathetic agents; cardiovascular agents; beta-blockers antianginal agents; calcium channel blockers antianginal agents; nitrate antianginal agents; cardiac glycoside antiarrhythmic agents; class I antiarrhythmic agents; class II antiarrhythmic agents; class III antiarrhythmic agents; class IV antiarrhythmic agents; alpha-blockers antihypertensive agents; angiotensin-converting enzyme inhibitors Harmful agents (ACE inhibitors) antihypertensive drugs; beta-blocker antihypertensive drugs; calcium channel blocker antihypertensive drugs; centrally acting adrenergic antihypertensive drugs; diuretic antihypertensive drugs; peripheral vasodilator antihypertensive drugs; antihyperlipidemia drugs; bile acid metal ion sequestering antihyperlipidemia drugs; HMG-CoA reductase inhibitors antihyperlipidemia drugs; inotropic substances; cardiac glycoside inotropic substances; thrombolytic agents or enzymes; dermatological agents; dermatological corticosteroid anti-inflammatory agents; antifungal topical anti-infective agents; antiviral topical anti-infective agents; topical antineoplastic agents; electrolytic and renal agents; loop diuretics; potassium-sparing diuretics; thiazide diuretics; uric acid excretion agents; enzymes, e.g., RNase and DNase; immunosuppressants; antiemetics; salicylate gastrointestinal anti-inflammatory agents; gastric acid pump inhibitors anti-ulcer agents;H2-blockers (anti-ulcer agents); digestive agents; intestinal motility stimulants; opioid agonists (intravenous anesthetics); hematopoietic anti-anemia agents; coagulants; anticoagulants; growth receptor inhibitors; abortifacients; antidiabetic agents; oral contraceptives; progestin contraceptives; estrogen; fertility agents; parathyroid agents; pituitary hormones; progestin; thyroid hormones; immunobiological agents; immunoglobulins; amide local anesthetics; ester local anesthetics; musculoskeletal corticosteroids (anti-inflammatory agents); musculoskeletal anti-inflammatory immunosuppressants; musculoskeletal nonsteroidal anti-inflammatory drugs (NSAIDs); skeletal muscle relaxants; reverse neuromuscular blockers (skeletal muscle relaxants); neurological agents; anticonvulsants; barbiturates (anticonvulsants); benzodiazepines (anticonvulsants); antiparkinsonian agents; antivertigo Agent); Opiate agonists; Opiate antagonists; Beta-blocker antiglaucoma agents; Miotic antiglaucoma agents; Ophthalmic aminoglycosides anti-infective agents; Ophthalmic quinolone anti-infective agents; Ophthalmic corticosteroid anti-inflammatory agents; Ophthalmic non-steroidal anti-inflammatory drugs (NSAIDs); Antipsychotics; Benzodiazepine anxiolytics, sedatives and hypnotics; Stimulants; Antitussives; Bronchodilators; Adrenaline agonists bronchodilators; Respiratory corticosteroid anti-inflammatory agents; Antidotes; Heavy metal antagonists / chelators; Drug abuse deterrents; Drug abuse withdrawal agents; Minerals, for example Iron, calcium, and magnesium; vitamin B compounds, e.g., cyanocobalamin (vitamin B12) and niacin (vitamin B3); vitamin C compounds; vitamin D compounds, e.g., calcitriol; vitamin A, vitamin E, and vitamin E compounds; antihemorrhagic agents; anthelmintic and anti-infective agents; sclerosing agents; anabolic agents; antacids; anti-asthmatic agents; anticholesterolemic and anti-lipid agents; antidiarrheal agents; anti-manic agents; antiemetics; anti-obesity agents; antipyretics and analgesics; antispasmodics; antithrombotic agents; anti-uricemia agents; antitussives; antitussives; appetite suppressants; cerebral dilators; coronary vasodilators; decongestants; diagnostic agents; erythropoiesis; expectorants; gastrointestinal sedatives; hyperglycemic agents; hypoglycemic agents; ion exchange resins; laxatives; mucolytics; neuromuscular drugs; peripheral vasodilators; psychotropic and stimulant agents; thyroid agents and antithyroid agents;The following may be selected from the group consisting of uterine relaxants as well.

[0249] In certain embodiments, the pharmaceutical composition may further include a skincare agent.

[0250] "Skin care agent" as used herein means an agent having one or more beneficial effects on skin care and / or hygiene. Skin care agents may be selected from the group consisting of antioxidants, free radical scavengers, skin protectants, skin conditioning agents, skin soothing agents, exfoliators, moisturizers, emollients, and humectants.

[0251] In this specification, "skin conditioning agent" means a drug that can maintain the skin in good condition. Examples of skin conditioning agents include urea, guanidine, aloe vera, glycolic acid and glycolates, e.g., ammonium and quaternary alkylammonium, lactic acid and lactates, e.g., sodium lactate, ammonium lactate and quaternary alkylammonium lactate, polyhydroxy alcohols, e.g., sorbitol, glycerol, hexanetriol, tocopherol, propylene glycol, butylene glycol, hexylene glycol, polyethylene glycol, carbohydrates, e.g., alkoxylated glucose, starch, starch derivatives, glycerin, pyrrolidone carboxylic acid (PCA), lactamide monoethanolamine, acetamide monoethanolamine, volatile silicone oils, non-volatile silicone oils, Helianthus annuus seed oil, phospholipids, Salix alba (willow) bark extract, glycine soja seed extract, and mixtures thereof.

[0252] Examples of skin sedatives include bisabolol.

[0253] As used herein, “skin protectant” includes sunscreens, chemical and / or physical irritants, agents that protect the skin from UV light, anti-wrinkle and anti-skin atrophy agents.

[0254] Examples of UV blocking agents include 2-ethylhexyl p-methoxycinnamate, 2-ethylhexyl N,N-dimethyl-p-aminobenzoate, p-aminobenzoic acid, 2-phenylbenzimidazole-5-sulfonic acid, octocrylene, oxybenzone, homomenthyl salicylate, octyl salicylate, 4,4'-methoxy-t-butyldibenzoylmethane, 4-isopropyldibenzoylmethane, 3-benzylidene camphor, 3-(4-methylbenzylidene) camphor, anthranilates, and ultrafine titanium dioxide. It contains zinc oxide, iron oxide, silica, 4-N,N-(2-ethylhexyl)methylaminobenzoate of 2,4-dihydroxybenzophenone, 4-N,N-(2-ethylhexyl)-methylaminobenzoate of 4-hydroxydibenzoylmethane, 4-N,N-(2-ethylhexyl)-methylaminobenzoate of 2-hydroxy-4-(2-hydroxyethoxy)benzophenone, and 4-N,N(2-ethylhexyl)-methylaminobenzoate of 4-(2-hydroxyethoxy)dibenzoylmethane.

[0255] 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 excluding cysteine, alpha-hydroxy acids (e.g., glycolic acid and lactic acid), phytic acid, lipoic acid, and lysophosphatidic acid.

[0256] Examples of antioxidants and / or free radical scavengers include ascorbic acid, salts of ascorbic acid, e.g., ascorbyl palmitate and sodium ascorbate, ascorbyl glucosamine, vitamin E (i.e., tocopherol, e.g., α-tocopherol), derivatives of vitamin E (e.g., tocopheryl acetate), retinoids, e.g., 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, tetinyl palmitate). It contains (also known as palmitate), lipoic acid, sodium citrate, sodium sulfite, lycopene, anthocyanides, bioflavonoids (e.g., hesperitin, naringen, rutin, and quercetin), superoxide dismutase, glutathione peroxidase, butylated hydroxytoluene (BHT), butylated hydroxyanisole (BHA), indole-3-carbinol, pycnogenol, melatonin, sulforaphane, pregnenolone, lipoic acid, and 4-hydroxy-5-methyl-3[2H]-furanone.

[0257] Examples of exfoliants include hydroxycarboxylic acids, such as alpha-hydroxy or beta-hydroxy acids, keto acids, and hydroxybenzoic acids.

[0258] Examples of moisturizers include lactic acid and other hydroxy acids and their salts, glycerol, propylene glycol, butylene glycol, sodium PCA, sodium hyaluronate, Carbowax 200, Carbowax 400, and Carbowax 800.

[0259] Examples of softening or moisturizing agents include panthenol, cetyl palmitate, glycerol (glycerin), PPG-15 stearyl ether, lanolin alcohol, lanolin, lanolin derivatives, cholesterol, petrolatum, isostearyl neopentanoate, octyl stearate, mineral oil, isocetyl stearate, myristyl myristate, octyldodecanol, 2-ethylhexyl palmitate (octyl palmitate), dimethicone, phenyl trimethicone, cyclomethicone, and C benzoate. 12 ~C 15 Alkyl, dimethiconol, propylene glycol, Theobroma grandiflorum seed butter, ceramide (e.g., ceramide 2 or ceramide 3), hydroxypropyl bispalmitamide MEA, hydroxypropyl bislauramide MEA, hydroxypropyl bisisostearamide MEA, 1,3-bis(N-2-(hydroxyethyl)stearoylamino)-2-hydroxypropane, bis-hydroxyethyl tocopherylsuccinoylamide hydroxypropane It contains hydroxypropane, urea, aloe, allantoin, glycyrrhetinic acid, safflower oil, oleyl alcohol, oleic acid, stearic acid, dicaprylate / dicaplate, diethyl sebacate, isostearyl alcohol, pentylene glycol, isononyl isononanoate, and 1,3-bis(N-2-(hydroxyethyl)palmitoylamino)-2-hydroxypropane.

[0260] The pharmaceutical composition of the present invention can be formulated in any suitable form that is well known to those skilled in the art.

[0261] In certain embodiments, the composition is an aqueous, aqueous-alcoholic, or oily solution, a dispersion in the form of a lotion or serum-type solution or dispersion, typically an emulsion having a particularly large emulsion-type liquid or semi-liquid consistency obtained by a dispersion of a fatty 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 in the form of a cream, an aqueous or anhydrous gel, a microemulsion, a nanoemulsion, a microcapsule, a microparticle, an ionic and / or nonionic vesicular dispersion, in the form of a stick, an aerosol spray, a pump spray, or a foam. In certain embodiments, the composition is in the form of an emulsion, a microemulsion, or a nanoemulsion.

[0262] The pharmaceutical composition of the present invention may typically take any form well known to those skilled in the art, depending on its route of administration.

[0263] 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, or lipid or polymer vesicles that provide controlled release.

[0264] For parenteral administration, the pharmaceutical composition may be in the form of a solution or suspension for infusion or injection.

[0265] For topical application, the pharmaceutical composition may be in the form of an unguent, cream, emulsion, ointment, powder, impregnated tampon, solution, gel, spray, lotion, or suspension. The pharmaceutical composition may also be in the form of a suspension of microspheres or nanospheres providing controlled release, or in the form of lipid or polymer vesicles, polymer patches, or hydrogels. This formulation for topical application may be in the form of anhydrous, aqueous, or emulsion.

[0266] Preferably, the pharmaceutical composition of the present invention is intended for external application.

[0267] A pharmaceutical composition according to the present invention can be prepared by mixing essential components and optional components as needed.

[0268] The methods and means for mixing the above-mentioned essential and optional components are not limited. Any conventional methods and means may be used to mix the above-mentioned essential and optional components in order to prepare a formulation according to the present invention.

[0269] Risk and diagnosis of developing acne The present invention also relates to a method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, a) A step of determining the presence and / or amount of α-type C. acnes in the subject sample, in particular a skin sample, wherein α-type C. acnes is as defined in the above section "α-type C. acnes and β-type C. acnes", and b) A step of determining whether the subject is at risk of developing acne, in particular acne vulgaris, based on the presence and / or quantity determined in step a). Regarding methods including

[0270] The present invention also relates to a method for determining whether a subject is at risk of developing acne, particularly acne vulgaris, a) A step of determining the presence and / or amount of β-type C. acnes in the subject sample, in particular a skin sample, wherein β-type C. acnes is as defined in the above section "α-type C. acnes and β-type C. acnes", and b) A step of determining whether the subject is at risk of developing acne, in particular acne vulgaris, based on the presence and / or quantity determined in step a). Regarding methods including

[0271] The present invention also relates to a method for diagnosing acne, particularly acne vulgaris, in a subject, a) A step of determining the presence and / or amount of α-type C. acnes in the subject sample, in particular a skin sample, wherein α-type C. acnes is as defined in the above section "α-type C. acnes and β-type C. acnes", and b) A step of diagnosing acne, particularly acne vulgaris, in the subject based on the presence and / or quantity determined in step a). Regarding methods including

[0272] The present invention also relates to a method for diagnosing acne, particularly acne vulgaris, in a subject, a) A step of determining the presence and / or amount of β-type C. acnes in the subject sample, in particular a skin sample, wherein β-type C. acnes is as defined in the above section "α-type C. acnes and β-type C. acnes", and b) A step of diagnosing acne, particularly acne vulgaris, in the subject based on the presence and / or quantity determined in step a). Regarding methods including

[0273] As used herein, the term “quantity” has the same meaning as disclosed in the above section “C. Methods for the treatment or prevention of bacterial diseases of acne.”

[0274] In a preferred embodiment of the above method, the amount of α-type C. acnes or β-type C. acnes is the relative abundance of α-type C. acnes or β-type C. acnes.

[0275] As used herein, the term “present” means that the amount of the α-type C. acnes or β-type C. acnes in the sample is within the detectable range of the technique used to detect the bacteria, more particularly the α-type C. acnes or β-type C. acnes. In other words, if it is determined that the α-type C. acnes or β-type C. acnes are not present in the sample, it means that they are below the detection threshold of the technique used for this determination step.

[0276] Preferably, the sample is a skin sample.

[0277] A skin sample can be any sample obtained from the skin of the subject. A skin sample 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 Q-tip or cotton swab), placing an adhesive or tape on the surface of the skin and removing the adhesive or tape to obtain a skin sample on the adhesive or tape, or via biopsy (e.g., shave biopsy, punch biopsy, incisional biopsy, saucerization biopsy, or excision biopsy). As will be understood by those skilled in the art, a skin sample must be obtained by any means that allows for the collection of bacteria present on the skin of the subject, preferably in the hair follicles of the subject. Therefore, a skin sample includes at least a portion of the skin microbiome.

[0278] In some embodiments, the skin sample further includes epithelial cells, epidermal cells, dermal cells, hair / skin follicles, adipose tissue (i.e., subcutaneous fat), and / or connective tissue.

[0279] As highlighted in the examples above and below, we have shown that a set of 218 SNPs across the hem locus (including genes hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY) can separate known C. acnes strain diversity into two groups referred to herein as α-type and β-type. Importantly, this novel typing correlates more accurately with published porphyrin production levels than the deoR gene. Furthermore, after developing a method for estimating the relative abundance of α-type and β-type C. acnes strains in shotgun metagenomic sequencing data and applying it to publicly available datasets associated with a study characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491), we demonstrated that α-type C. acnes strains were significantly more abundant in patients with acne vulgaris than in healthy subjects.

[0280] 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 determined to be at risk of developing acne, particularly acne vulgaris, if (i) it is determined that α-type C. acnes bacteria are present in the sample and / or the amount of α-type C. acnes bacteria, particularly the relative abundance (e.g., relative to the entire bacterial population of the subject, particularly to the skin bacterial population, or the entire C. acnes population of the subject, particularly to the skin C. acnes population) is determined to be higher than a reference value, or (ii) it is determined that β-type C. acnes bacteria are present in the sample and / or the amount of β-type C. acnes bacteria, particularly the relative abundance (e.g., relative to the entire bacterial population of the subject, particularly to the skin bacterial population, or the entire C. acnes population of the subject, particularly to the skin C. acnes population) is determined to be lower than a reference value. Similarly, in the diagnostic method of the present invention, a subject is diagnosed with acne, particularly acne vulgaris, if (i) it is determined that α-type C. acnes bacteria are present in the sample and / or the amount of α-type C. acnes bacteria, particularly the relative abundance (e.g., relative to the entire bacterial population of the subject, particularly to the skin bacterial population, or the entire C. acnes population of the subject, particularly to the skin C. acnes population) is determined to be higher than a reference value, or (ii) it is determined that β-type C. acnes bacteria are present in the sample and / or the amount of β-type C. acnes bacteria, particularly the relative abundance (e.g., relative to the entire bacterial population of the subject, particularly to the skin bacterial population, or the entire C. acnes population of the subject, particularly to the skin C. acnes population) is determined to be lower than a reference value.

[0281] In certain embodiments, the reference value is the amount of α-type C. acnes bacteria relative to β-type C. acnes bacteria in a corresponding sample of a healthy subject, particularly a skin sample, in particular the relative abundance (e.g., relative to the entire bacterial population of the subject, particularly to the skin bacterial population, or to the entire C. acnes population of the subject, particularly to the skin C. acnes population).

[0282] "Healthy subject" in this specification means a subject that does not have acne, in particular acne vulgaris, preferably a subject that does not have acne-related diseases, in particular skin diseases and / or inflammatory diseases and / or skin diseases, and more preferably a subject that does not exhibit any signs of skin discomfort, such as signs associated with sensitive skin, sensitized skin, fragile skin or weakened skin, or any unpleasant and non-aesthetic findings of sensitized, fragile and / or weakened skin.

[0283] "Sensitive skin" as used herein means skin that does not readily tolerate invasive factors, particularly environmental factors such as pollutants, climatic factors (wind, low temperature, heat), emotional factors, particularly stress, and / or chemical agents (heavy metals, detergents, compounds contained in cosmetic compositions, e.g., fragrances, preservatives, alcohol, pH, AHA, or dermatological treatments, e.g., vitamin A acid), as well as / or sweating and mechanical irritation, e.g., hair removal, shaving, friction, and even water, particularly hard water. Sensitive skin is not pathological skin, unlike allergic skin. Nevertheless, sensitive skin may react to invasive factors and / or conditions by producing non-aesthetic and / or unpleasant skin findings, e.g., stinging, a sensation of heat or warmth, tension, tingling, tightness, and redness. Therefore, the characteristics of "sensitive skin" can be estimated by the individual themselves based on their subjective skin sensations, or by a dermatologist based on objective skin reactions.

[0284] "Sensitive skin" in this specification means skin and / or mucous membranes that have become temporarily sensitive, as defined above, and therefore are non-pathological in themselves.

[0285] "Vulnerable" and / or "weakened skin" (i.e., temporarily weakened skin) means, as used herein, skin whose barrier function is weakened. This can be associated with the individual's circumstances; for example, the elderly and infants have more vulnerable skin. This condition can result from chemical or physical aggression (e.g., abrasion, friction).

[0286] The unpleasant and non-aesthetic findings of sensitive, fragile, and / or weakened skin are the same as those of sensitive skin, and these findings and / or skin conditions are not considered to be related to the prevention and / or treatment of pathology.

[0287] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as those generally understood by those skilled in the art to which this invention pertains.

[0288] When used herein, the singular forms “a,” “an,” and “the” should be noted to include plural referents unless the context explicitly indicates otherwise. Therefore, for example, a reference to “a cell” includes multiple such cells (e.g., a group of such cells). Similarly, a reference to “a nucleic acid” includes one or more such nucleic acids.

[0289] While the present invention has been described in conjunction with its specific embodiments, many alternative methods, modifications, and variations will be apparent to those skilled in the art. Therefore, it is intended to encompass all such alternative methods, modifications, and variations that fall within the spirit and broad scope of the appended claims.

[0290] All publications, patents, and patent applications referenced herein are incorporated herein by reference in whole to the same extent that each individual publication, patent, or patent application is specifically and individually indicated as being incorporated herein by reference. Furthermore, any citation or specification of references in this application should not be construed as a declaration that such references are available as prior art to the present invention. Section headings, to the extent in which they are used, should not necessarily be construed as limitations.

[0291] The following examples are provided for the purpose of illustrating various embodiments of the present invention and are not intended to limit the present invention in any way. A brief explanation of arrays

[0292] [Table 2] [Brief explanation of the drawing]

[0293] [Figure 1] Figure 1 shows a phylogenetic tree of the hem locus, along with the annotated SLST clusters and α / β typing divisions disclosed herein. [Figure 2A] Figure 2A shows the published porphyrin production levels along with the presence (deoR+) or absence (deoR-) of their assigned α / β types and deoR repressors. Adapted from Figure 1 of Barnard et al. (2020) mSphere 5:e00793~19. [Figure 2B] Figure 2B shows the published porphyrin production levels along with their assigned α / β types and the presence (deoR+) or absence (deoR-) of deoR repressors. This figure was adapted from Figure 1 of Johnson et al. (2016) mSphere 1(1):e00023~15. [Figure 2C]Figure 2C shows the published porphyrin production levels along with their assigned α / β types and the presence (deoR+) or absence (deoR-) of deoR repressors. This figure was adapted from Figure S4 of Johnson et al. (2016) mSphere 1(1):e00023~15. [Figure 3] Figure 3 shows the extraction of the alignment of the glpR / deoR reference DNA sequence with the consensus glpR / deoR DNA sequence for most strains of the SLST D cluster. The insertion of poly-G in the SLST D variant DNA sequence results in a frameshift and the generation of an immature stop codon at position 105, while the glpR / DeoR reference protein is 310AA long. [Figure 4] Figure 4 shows the difference in the ratio of C. acnes population classified as type α between healthy skin metagenomics and skin metagenomics of patients with acne vulgaris. [Figure 5] Figure 5 shows the hem locus containing eight hem genes conserved across C. acnes strains: hemA, hemB, hemC, hemD, hemE, hemH, hemL, and hemY. Representatives from each SLST cluster are shown. [Figure 6A] Figure 6A shows the specific nuclease-mediated death of alpha-type C. acnes strains. Specific nuclease-mediated death of C. acnes phylotypes and alpha vs. beta strains. Each diluted population of four C. acnes strains (one alpha-type strain: SLST A5; three beta-type strains: SLST D1, D2, K9) was transduced with three different packaged phagemids, each packaged with either a chloramphenicol cassette, a DNA payload containing a nuclease (SEQ ID NO: 11) expression cassette and a non-targeting gRNA (SEQ ID NO: 12, black bar), or a gRNA targeting strains A5, D1, and D2 (SEQ ID NO: 13, gray bar), or a HemB gRNA targeting only strain SLST A5 (SEQ ID NO: 14, white bar). Y-axis: Colony-forming units (cfu) per μL of packaged phagemid on a BHI+ 3 μg / mL chloramphenicol plate. [Figure 6B] Figure 6B shows the specific nuclease-mediated death of the alpha-type C. acnes strain. Specific nuclease-mediated death of C. acnes alpha strain versus beta strain. Each diluted population of four C. acnes strains (three alpha strains: 2×SLST A1, SLST A5; one beta strain: SLST K9) was transduced with six different packaged phagemids, each packaged with either a chloramphenicol cassette, a DNA payload containing a nuclease (SEQ ID NO: 11) expression cassette, and a non-targeting gRNA (SEQ ID NO: 12), or with the following sets of Hem gRNAs targeting the three alpha strains at different locations on the hem locus: HemB_1 gRNA (SEQ ID NO: 14) targets HemB alpha nucleotide variant A155; HemL_2 gRNA (SEQ ID NO: 15) targets HemL alpha nucleotide variants C389 and T392; HemY_2 gRNA (SEQ ID NO: 16) targets HemY alpha nucleotide variants T1199 and T1205. Y-axis: Colony-forming units per 1 μL of packaged phagemid on a BHI+ 3 μg / mL chloramphenicol plate. [Examples]

[0294] (Example 1) The Heme molecule, a porphyrin ring complexed with iron, is an enzyme cofactor and a source of iron essential for the survival of bacterial pathogens (Choby et al. (2016) J. Mol. Biol. 428:3408~3428). Cutibacterium acnes (hereinafter referred to as C. acnes) is the most abundant bacterium inhabiting human skin (Fitz-Gibbon et al. (2013) J. Invest. Dermatol. 133:2152~2160, Oh et al. (2014) Nature 515-59~64). C. acnes is also known to be involved in acne vulgaris, an inflammatory skin disease that affects a large portion of adolescents and young adults (Bhate et al. (2013) British Journal of Dermatology 168:474~485). C. acnes has been shown to produce porphyrins that induce inflammation (Schaller et al. (2005) British J Dermatol. 153:66~71, Spittaels et al. (2021) iScience 24:102575). Interestingly, C. acnes strains from different lineages exhibit different levels of porphyrin production (Johnson et al. (2016) mSphere 1:e00023~15, Barnard et al. (2020) mSphere 5:e00793~19), and it has been previously hypothesized that the presence of putative repressor genes from the deoR family is responsible for low levels of porphyrin production (Johnson et al. (2016) mSphere 1:e00023~15). However, this explanation is not complete, as high levels of porphyrin production have also been observed in some strains that encode deoR in their genomes (Barnard et al. (2020) mSphere 5:e00793~19). Furthermore, while strain lines typically exhibit their low / high porphyrin production, exceptions have been documented in the literature (Johnson et al. (2016) mSphere 1:e00023~15).

[0295] The key enzymes involved in the porphyrin biosynthesis pathway in C. acnes are encoded by eight genes (hemA, hemB, hemC, hemD, hemE, hemH, hemL, hemY). These genes are clustered within a conserved locus (hereinafter referred to as the hem locus) across all C. acnes strains.

[0296] The inventors have found that a set of 218 SNPs across the hem locus gene can separate known C. acnes strain diversity into two groups: α-type and β-type. While types from the classical C. acnes typing scheme (SLST, recA) can be clearly assigned to either α-type or β-type, α-type and β-type are not monophyletic based on core genome phylogeny (i.e., overall similarity of strain genomes does not predict whether a strain is α or β). Importantly, α / β typing correlates tightly with presence / absence, along with published porphyrin production levels, with α-type strains being high-producing and β-type strains being low-producing.

[0297] Furthermore, the inventors developed a method for estimating the relative abundance of α- and β-type C. acnes strains in shotgun metagenomic sequencing data and applied it to public datasets related to studies characterizing the skin microbiome in acne vulgaris (Barnard et al. (2016) Scientific Reports 6:39491). The inventors found that α-type strains form a significantly larger proportion of the C. acnes population in acne vulgaris patients than in healthy volunteers. Therefore, treatment modalities to specifically kill α-type C. acnes strains, specifically inhibit the growth of α-type C. acnes strains, or inactivate porphyrin production in α-type C. acnes strains have the potential to prevent and / or cure acne vulgaris.

[0298] SLST cluster definition The genome assemblies of 475 C. acnes strains were sequenced by Eligo Bioscience or downloaded from the public repertoire. For each assembly, a single-locus sequence type (SLST) was predicted using in silico PCR amplification and sequence alignment with primers and reference sequences as described by Scholz et al. (Scholz et al. (2014) PloS ONE 9:e104199). Pan-genomic 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 lengths of the core genome phylogenetic tree, the inventors defined SLST clusters, which are a coarser typing scheme consisting of SLST type groups that begin with the same letter (for example, SLST cluster A includes SLST A1, A2, etc.).

[0299] Definitions of α-type and β-type Hem locus genes were extracted from all available assemblies, and phylogenetic trees were constructed based on their linked amino acid sequences using the IQ-TREE (Minh et al. (2020) Mol. Biol. Evol. 37:1530~1534) along with the edge-equal partition model (Chernomor et al. (2016) Syst. Biol. 65:997~1008) and the revised Dayhoff matrix substitution model (Kosiol et al. (2005) Mol Biol Evol 22:193~199). In the resulting trees (Figure 1), the inventors observed two distinct groups that did not correspond to core genome phylogeny: a group containing SLST clusters A, B, C, E, F, G, and H (named type α) and a group containing SLST clusters D, K, and L (named type β). Importantly, no SLST clusters spanned between types.

[0300] To obtain a set of marker SNPs for these types, the inventors calculated multiple sequence alignments at the nucleotide level for each gene using MUSCLE (Edgar (2004) Nucleic Acids Res 32:1792~1797) and identified conserved but distinguishable locations between α and β types in more than 90% of the genome from each type. This procedure identified 218 marker locations (see Table 1 above). Based on these results, the inventors defined α (and β) as strains having α-specific (or β-specific) nucleotide variants in at least 90% of the aforementioned locations.

[0301] Analysis of published porphyrin levels We searched available scientific literature for reported levels of porphyrin production by C. acnes strains. Data from two papers (Johnson et al. (2016) mSphere 1:e00023~15, Barnard et al. (2020) mSphere 5:e00793~19) were aggregated, and the strains used were typed using available genome sequences and SLST schemes. Where genome sequences were unavailable, SLST clusters were inferred from the authors' reported lineages.

[0302] Based on the SLST cluster, strains were assigned to either α-type or β-type. The inventors observed that strains classified by the authors as high or low porphyrin producers precisely corresponded to α-type and β-type strains, respectively (Figure 2), providing a more reliable explanation for production levels than the presence of deoR repressors. Furthermore, through multiple sequence alignment of the deoR gene, the inventors found that SLST cluster D strains possess a poly-G insertion in this gene, which, in the majority of cases including HL025PA1, results in a shifted leading frame and nonsense mutation (Figure 3). Therefore, it was anticipated that deoR in SLST cluster D is non-functional and cannot explain the measured low porphyrin production. Accordingly, the inventors considered the SNPs in Table 1 above as biomarkers for high porphyrin production (α-type). Conversely, β-type is associated with low porphyrin production.

[0303] Metagenome analysis Metagenomic shotgun sequencing data from Barnard et al. (2016) Scientific Reports 6:39491, including keratin plug samples from 42 acne vulgaris patients and 40 healthy volunteers, was obtained from the NCBI dbGaP resource (accession number phs001655). Raw reads were pre-processed using fastp (Chen et al. (2018) Bioinformatics 34:i884~i890) and aligned to the human reference genome and PhiX genome using bowtie2 (Langmead et al. (2012) Nature Methods 9:357~359). Reads that aligned to either the host or PhiX were removed, while those that passed QC were mapped to the reference hem locus using bwa mem (Li (2013) arXiv:1303.3997), and only properly paired mappings were retained for downstream analysis.

[0304] Since this locus is always a single copy in the available C. acnes genome and has no closely related orthologues in other species (the closest related species, Cutibacterium modestum, has 86% identity at the nucleotide level), we did not include other reference sequences in the alignment database. However, to validate our approach, we also used Kraken2 (Wood et al. (2019) Genome Biology 20:257) to remove reads assigned to other species other than C. acnes from the dataset, but no difference was observed in our results.

[0305] For each of the 218 discriminant sites, the proportions of α- and β- variants were calculated from the alignment pile-up. The overall relative abundance of each type within the C. acnes population was calculated using the median frequency of its signature SNP across the 218 sites. The α- variant was found to be significantly more abundant in acne vulgaris patients than in healthy controls (p-value 0.0112; Mann-Whitney U test) (Figure 4).

[0306] (Example 2) Specific nuclease-mediated death of C. acnes phylotype and alpha vs. beta strains. This embodiment demonstrates nuclease-mediated specific killing of Cutibacterium acnes phylotypes and alpha versus beta strains. The nuclease can be programmed to target and kill specific phylotypes (in this embodiment, phylotypes IA1 and II) encompassing both alpha and beta strains as defined in the above section, “α-type C. acnes and β-type C. acnes” (Figure 6A). Similarly, the nuclease can be programmed to target and kill only the alpha strain while leaving the beta strain intact (Figure 6B).

[0307] Four C. acnes strains (one alpha-type strain: SLST A5; three beta-type strains: SLST D1, D2, and K9) were grown anaerobically overnight at 37°C, and the following day they were diluted to an OD600 of 0.05. Strains SLST A5, SLST D1, and SLST D2 belong to phyllotype IA1. SLST K9 belongs to phyllotype II. Each diluted C. acnes population was transduced with three different packaged phagemids, each packaged with a chloramphenicol cassette, a DNA payload containing a Mad4 nuclease (SEQ ID NO: 11) expression cassette and a non-targeting gRNA (SEQ ID NO: 12), or a gRNA targeting phylotype IA1, i.e., strains A5, D1, and D2 (SEQ ID NO: 13), or a HemB gRNA (HemB_1 gRNA) (SEQ ID NO: 14) that targets HemB alpha nucleotide variant A155, and therefore targets only alpha-type C. acnes strains, such as strain SLST A5. Transduced cells were serially diluted after transduction, plated on BHI agar containing 3 μg / ml chloramphenicol, and incubated in an anaerobic chamber at 37°C.

[0308] As shown in Figure 6A, packaged phagemids programmed with HemB_1 gRNA targeting HemB alpha nucleotide variant A155 selectively reduced the number of alpha strains (SLST A5) by more than 4 log, but did not affect the growth of any of the beta strains (SLST D1, D2, and K9). Packaged phagemids programmed with IA1 gRNA reduced the number of colonies from strains SLST A5, D1, and D2 by 10 log. 4 The reduction was selectively reduced to less than 1 / 2, but as expected, it did not affect the number of colonies from strain SLST K9.

[0309] Specific nuclease-mediated death of C. acnes alpha strain versus beta strain. Four C. acnes strains (three alpha-type strains: 2×SLST A1, SLST A5; one beta-type strain: SLST K9) were grown anaerobically overnight at 37°C, and the following day they were diluted to an OD600 of 0.05. Each diluted C. acnes population was transduced with six different packaged phagemids, each packaged with either a chloramphenicol cassette, a DNA payload containing a Mad4 nuclease (SEQ ID NO: 11) expression cassette, and a non-targeting gRNA (SEQ ID NO: 12), or with the following sets of Hem gRNAs targeting three alpha-type strains at different locations on the hem locus: HemB_1 gRNA (SEQ ID NO: 14) targets HemB alpha nucleotide variant A155; HemL_2 gRNA (SEQ ID NO: 15) targets HemL alpha nucleotide variants C389 and T392; and HemY_2 gRNA (SEQ ID NO: 16) targets HemY alpha nucleotide variants T1199 and T1205. Transduced cells were serially diluted after transduction and plated on BHI agar containing 3 μg / ml chloramphenicol. The plates were incubated in an anaerobic chamber at 37°C.

[0310] As shown in Figure 6B, packaged phagemids programmed with Hem gRNA targeting alpha nucleotide variants selectively reduced the number of colonies from the three alpha-type strains by more than 99.9%, but did not affect the number of colonies from the beta-type strains.

Claims

1. A method for treating or preventing a Cutibacterium acnes-related disease in a subject, comprising a step of modulating, in particular reducing, the ratio of the amount of α-type C. acnes bacteria to the amount of β-type C. acnes bacteria in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. method.

2. The method according to claim 1, wherein the ratio is the ratio of the amount of α-type C. acnes bacteria on the target skin to the amount of β-type C. acnes bacteria on the skin.

3. The method according to claim 1 or 2, further comprising the step of specifically reducing the amount of α-type C. acnes bacteria on the skin of the subject.

4. The method according to claim 3, further comprising the step of specifically killing or specifically inhibiting the growth of α-type C. acnes bacteria on the skin of the subject.

5. The method according to claim 4, comprising the step of administering to the subject a therapeutically effective or prophylactic amount of an antibacterial agent, phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium that specifically targets the α-type C. acnes bacterium.

6. The method according to claim 5, comprising the step of administering to the subject a therapeutically effective or prophylactically effective amount of a phage that specifically targets the α-type C. acnes bacterium, a recombinant phage, a packaged phagemid, a plasmid, a DNA or RNA-containing vesicle, an extracellular vesicle, a bacterium, or a manipulated bacterium.

7. The method according to claim 6, wherein the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium encodes a programmable nuclease designed to specifically target the α-type C. acnes bacterium.

8. The method according to claim 7, wherein the programmable nuclease is selected from the group consisting of CRISPR-Cas nucleases, TALENs and their variants, zinc finger nucleases (ZFNs) and their variants, natural, evolved or engineered meganucleases or recombinase variants, and any combination and hybrids thereof.

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

10. The method according to claim 9, wherein the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium further encodes a guide RNA designed to specifically target the α-type C. acnes bacterium.

11. The method according to claim 10, wherein the guide RNA is designed to specifically target the hem locus of the α-type C. acnes bacterium, and is selected in particular from the group consisting of SEQ ID NOs. 13 to 16.

12. The method according to any one of claims 5 to 11, wherein the administration is topical administration.

13. The method according to claim 3, further comprising the step of genetically modifying the DNA sequence of α-type C. acnes bacteria on the skin of the subject to generate at least one change in the hem locus of the α-type C. acnes bacteria.

14. The method according to claim 13, comprising the step of administering to the subject a therapeutically effective or prophylactically effective amount of a phage encoding a gene editing enzyme or system that targets the hem locus in the alpha-type C. acnes bacterium, a recombinant phage, a packaged phagemid, a plasmid, a DNA or RNA-containing vesicle, an extracellular vesicle, a bacterium, or a manipulated bacterium.

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

16. The method according to claim 14, wherein the gene editing enzyme is a base editor or a prime editor.

17. The method according to any one of claims 14 to 16, wherein the administration is topical administration.

18. The method according to claim 1 or 2, further comprising the step of increasing the amount of β-type C. acnes bacteria on the skin of the subject.

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

20. The method according to any one of claims 1 to 19, wherein the C. acnes-related disease is acne, in particular acne vulgaris.

21. A method for treating or preventing C. acnes-related diseases in a subject, comprising the step of specifically reducing the expression of at least one hem locus protein in α-type C. acnes in the subject, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. method.

22. The method according to claim 21, comprising the step of administering to the subject a therapeutic or prophylactic dose of a therapeutic or prophylactic agent that specifically reduces the expression of at least one hem locus protein in α-type C. acnes in the subject by genetically modifying the DNA sequence in the α-type C. acnes in the subject, preferably the agent is a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a gene editing enzyme or system that targets the hem locus.

23. A composition for use in the treatment or prevention of Cutibacterium acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that induces a reduction in the ratio of the amount of α-type C. acnes to the amount of β-type C. acnes in the subject, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. Composition for use.

24. The composition for use according to claim 23, wherein the therapeutic or prophylactic agent is an antibacterial agent, phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium that specifically targets the α-type C. acnes bacterium.

25. The composition for use according to claim 24, wherein the therapeutic or prophylactic agent is a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a programmable nuclease designed to specifically target the α-type C. acnes bacterium.

26. The composition for use according to claim 25, wherein the programmable nuclease is selected from the group consisting of CRISPR-Cas nucleases, TALENs and their variants, zinc finger nucleases (ZFNs) and their variants, natural, evolved or engineered meganucleases or recombinase variants, and any combination and hybrids thereof.

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

28. The composition for use according to claim 27, wherein the phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium further encodes a guide RNA designed to specifically target the α-type C. acnes bacterium.

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 C. acnes bacterium, and is selected in particular from the group consisting of SEQ ID NOs. 13 to 16.

30. The composition for use according to claim 23, wherein the therapeutic or prophylactic agent is a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium, or engineered bacterium encoding a gene editing enzyme or system that targets and genetically modifies the hem locus in the α-type C. acnes bacterium.

31. The composition for use according to claim 30, wherein the gene modification is a point modification.

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

33. The composition for use according to any one of claims 23 to 32, wherein the C. acnes-related disease is a C. acnes-related inflammatory disease.

34. The composition for use according to any one of claims 23 to 33, wherein the C. acnes-related disease is acne, in particular acne vulgaris.

35. A composition for use according to any one of claims 23 to 34, for external administration.

36. A composition for use in the treatment or prevention of C. acnes-related diseases in a subject, comprising a therapeutic or prophylactic agent that specifically reduces the expression of at least one hem locus protein in C. acnes α-type in the subject by genetically modifying the DNA sequence of C. acnes α-type in the subject, preferably by generating at least one change at the hem locus of C. acnes α-type, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. Composition for use.

37. A pharmaceutical composition comprising a phage, recombinant phage, packaged phagemid, plasmid, DNA or RNA-containing vesicle, extracellular vesicle, bacterium or engineered bacterium encoding a programmable nuclease or gene-editing enzyme or system designed to specifically target α-type C. acnes bacteria, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium. Pharmaceutical composition.

38. A method for determining whether a subject is at risk of developing acne, particularly acne vulgaris. a) A step of determining the presence and / or amount of α-type C. acnes bacteria in the target sample, in particular a skin sample, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium. Process, and b) A step of determining whether the subject is at risk of developing acne, in particular acne vulgaris, based on the presence and / or quantity determined in step a). A method that includes this.

39. A method for diagnosing acne, particularly acne vulgaris, in a subject, a) A step of determining the presence and / or amount of α-type C. acnes bacteria in the target sample, in particular a skin sample, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (positions are defined by referring to the sequence of Sequence 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium. Process, and b) A step of diagnosing acne, particularly acne vulgaris, in the subject based on the presence and / or quantity determined in step a). A method that includes this.

40. A method for determining whether a subject is at risk of developing acne, particularly acne vulgaris. a) A step of determining the presence and / or amount of β-type C. acnes bacteria in the target sample, in particular a skin sample, β-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: G173, G479, C506, G614, G629, A671, C971, G989, C1085 and C1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: C241, C476, G530, C704, G728, C767, A834, G867, G872, C882 and G957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

2. C. acnes is a bacterium. Process, and b) A step of determining whether the subject is at risk of developing acne, in particular acne vulgaris, based on the presence and / or quantity determined in step a). A method that includes this.

41. A method for diagnosing acne, particularly acne vulgaris, in a subject, a) A step of determining the presence and / or amount of β-type C. acnes bacteria in the target sample, in particular a skin sample, β-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: G173, G479, C506, G614, G629, A671, C971, G989, C1085 and C1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: C241, C476, G530, C704, G728, C767, A834, G867, G872, C882 and G957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

2. C. acnes is a bacterium. Process, and b) A step of diagnosing acne, particularly acne vulgaris, in the subject based on the presence and / or quantity determined in step a). A method that includes this.

42. The use of a therapeutic or prophylactic agent for the manufacture of a pharmaceutical product for the treatment or prevention of C. acnes-related disease in a subject, wherein the therapeutic or prophylactic agent induces a reduction in the ratio of the amount of α-type C. acnes bacteria to the amount of β-type C. acnes bacteria in the subject. α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium; and β-type C. acnes is a C. acnes bacterium that is not α-type C. acnes bacterium. use.

43. The use of a therapeutic or prophylactic agent for the manufacture of a pharmaceutical product for the treatment or prevention of a C. acnes-related disease in a subject, wherein the therapeutic or prophylactic agent specifically reduces the expression of at least one hem locus protein in C. acnes α-type in the subject by genetically modifying the DNA sequence in C. acnes α-type in the subject, preferably by generating at least one change at the hem locus of C. acnes α-type, α-type C. acnes bacteria, (i) Contains at least 90% of the following nucleotide variants in the hem locus: - In the hemA gene: T173, A479, T506, A614, T629, C671, T971, A989, T1085 and T1094 (the positions are defined by reference to the sequence of Sequence ID No. 3, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 4, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 5, and the first nucleotide in the 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 (the positions are defined by reference to the sequence of Sequence ID No. 6, and the first nucleotide in the sequence is indexed as 0), - In the hemE gene: T241, T476, A530, T704, A728, G767, T834, A867, A872, A882 and A957 (the positions are defined by reference to the sequence of Sequence ID No. 7, and the first nucleotide in the 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 (the position is defined by reference to the sequence of sequence number 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 (the positions are defined by reference to the sequence of Sequence ID No. 9, and the first nucleotide in the sequence is indexed as 0), and - In 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 (the positions are defined by reference to the sequence of sequence number 10, and the first nucleotide in the sequence is indexed as 0), and / or (ii) The nucleic acid sequence of the hem gene locus is at least 97% identical to the sequence of Sequence ID No.

1. C. acnes is a bacterium. use.

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