Bifidobacterium longum (transitional microorganism)

Abstract

The present invention relates to a Bifidobacterium longum transitional microbial strain deposited with CNCM under depositary number CNCM I-5942, or a B. longum transitional strain having the distinguishing characteristics of a B. longum transitional strain deposited under depositary number CNCM I-5942.

Description

Technical Field

[0001] The present invention relates to a transitional strain of Bifidobacterium longum.

Background Art

[0002] Nutrition plays an important role in all areas of development (including cognitive development, motor-sensory development, dental development, musculoskeletal development, immune development, and social development) in infants and young children. Furthermore, the gastrointestinal microbiota or "gut" microbiota in infancy can play an important role in the health and development of infants not only during infancy but also in later life (see, for example, Tanaka and Nakayama. 2017. Allergol. Int. 66(4):515-522). Various factors, including diet, can greatly affect the composition of the microbiota and thus affect the health and growth of infants not only during infancy but also in later life.

[0003] During infancy, mammals, including humans, transition from a diet consisting solely of breast milk or primarily of breast milk to solid food. This transition is called the "transition period," "transition period," or "weaning." Once the transition occurs, dietary changes and other stressors during the transition period can lead to significant changes in the composition of the gut microbiome (see, for example, Vatanen et al., 2019. Nature Microbiology. 4:470-479; Dizzell et al., 2021. PLOS ONE. https: / / doi.org / 10.1371 / journal.pone.0248924; Moore and Townsend. 2019. Open Biol. Sep; 9(9):190128; Magne et al. 2006. FEMS Microbiology Ecology, 58(3):563-571; and Edwards CAAnn Nutr Metab 2017; 70:246-250). Changes in the composition of the microbiome can, in turn, affect the physiological state or characteristics, cognitive state or characteristics, anatomical state or characteristics, health state or characteristics, or other states or characteristics of mammals. Although several studies have investigated the gut microbiome during infancy and early childhood, the impact of the gut microbiome on the immediate and lifelong health and well-being of infants remains unclear. Alongside the insufficient assessment and understanding of the gut microbiome in infancy and early childhood, there is also a lack of compositions and formulations that are appropriate for use by infants or young children and can promote a healthy gut microbiome. Therefore, there is a need to improve the assessment and understanding of the gut microbiome, compositions, and methods in order to support and / or establish a healthy gut microbiome, particularly in infants and young children.

[0004] The transition between a full milk-based diet, whether breast milk or formula, and a protein- and fiber-rich solid diet results in an increase in gut bacteria and progresses to a microbial composition associated with adult individuals. Weaning is considered a stressful and complex process, and disruption of the gut microbiota can lead to microbial dysbiosis associated with the pathogenesis of both intestinal disorders, such as diarrhea, IBD, IBS, and celiac disease, and extraintestinal disorders, such as allergies, asthma, metabolic syndrome, cardiovascular disease, and obesity. To develop and maintain a healthy gut microbiota, it is desirable to reduce the stress caused by weaning.

[0005] Vatanen et al. reported on the Bifidobacterium longum subspecies of clade present in the gut microbiome of mammals, particularly humans, during the transition period, demonstrating that this remarkable Bifidobacterium longum clade expanded with the introduction of solid food and possessed enzymes for utilizing both breast milk and solid food substrates (Cell;2022 Nov 10;185(23):4280-4297.e12). International Publication No. 2023 / 278441 states that during the transition period (e.g., weaning), the relative abundance of this Bifidobacterium longum clade is greater than that of either B. longum subsp. infantis (iB. longum subsp. infantis) or B. longum subsp. longum (B. longum subsp. longum). Furthermore, the relative abundance of B. longum subspecies infantis decreases from the start to the end of the transitional feeding period, while the abundance of B. longum subspecies longum begins to increase.

[0006] However, there is a need for compositions and methods that are particularly suitable and advantageous for supporting the transition between milk-based foods and solid foods in infants and young children. [Overview of the project]

[0007] This invention is at least in part based on the provision of a novel Bifidobacterium longum transitional microbial strain. The B. longum transitional strain is referred to herein as NCC5025 and was deposited on March 29, 2023, by SOCIETE DES PRODUITS NESTLE SA in accordance with the Budapest Convention with the Collection Nationale de Cultures de Micro-organisms (CNCM) of the Pasteur Institute, and has been given deposit number CNCM I-5942.

[0008] Accordingly, in the first aspect, the present invention provides a B. longum transitional microbial strain deposited with the Collection Nationale de Cultures de Micro-organismes (CNCM) under deposit number CNCM I-5942, or a B. longum transitional strain having the distinguishing characteristics of the B. longum transitional strain deposited under deposit number CNCM I-5942.

[0009] In a further embodiment, the present invention provides a B. longum transitional microbial strain having at least 99% mean base identity (ANI) compared to the B. longum strain deposited with the CNCM under depositary number CNCM I-5942. Preferably, the B. longum transitional microbial strain has at least one of the identifying characteristics of the B. longum transitional strain deposited under depositary number CNCM I-5942, as described herein.

[0010] In another embodiment, the present invention provides a composition comprising a transitional strain of B. longum according to the present invention, preferably the composition comprising at least one further probiotic and / or prebiotic.

[0011] The present invention further provides the use of the B. longum transitional strain according to the present invention to promote and / or support the transition from milk-based foods to solid foods in infants and / or toddlers.

[0012] In a further embodiment, the present invention provides a method for promoting and / or assisting the transition from milk-based foods to solid foods in infants and / or toddlers, the method comprising administering a transitional strain of B. longum according to the present invention to infants and / or toddlers.

[0013] The B. longum transitional strain of the present invention is thought to possess several advantageous properties that make it particularly suitable for supporting the transition between milk-based foods and solids in infants and young children, for example, when used as a probiotic or as part of a synbiotic.

[0014] While we do not wish to be bound by theory, the B. longum transition strain of the present invention may offer one or more of the following advantages: a) No antibiotic resistance to the set of antibiotics considered relevant by EFSA; b) A unique carbohydrate-related enzyme (CaZy) profile, including the presence of 17 enzymes from the GH43 subfamily that have not been evaluated in B. longum to date; c) It proliferates favorably in 3-FL; although we do not wish to be bound by theory, this ability is thought to make the transitional strain of B. longum competitive in the intestinal environment of weaning infants; d) Favorably proliferates with a set of dietary fibers (e.g., inulin and arabinan).

[0015] Overall, the B. longum transitional strain of the present invention is particularly well-suited to the weaning period and may perform better than other B. longum transitional strains in this environment. Furthermore, the B. longum transitional strain of the present invention may also perform better than other B. longum transitional strains in diets containing dietary fiber (for example, in adulthood). [Brief explanation of the drawing]

[0016] [Figure 1] UPGMA phylogenetic tree of the B. longum genome [Figure 2]Carbohydrate-related enzymes (CAZyme) found in B. longum transitional strains, including NCC5025. [Figure 3] The gene region of NCC5025 containing the unique GH43_17 coding gene. [Figure 4-1] Growth profiles of transitional B. longum strains, including NCC5025, against 3-FL as the sole carbon source. [Figure 4-2] Growth profiles of transitional B. longum strains containing NCC5025 against 3-FL as the sole carbon source. The graph shows the growth rate k obtained for each strain tested. [Figure 5] Growth profiles of various B. longum transitional strains in response to A) inulin and B) arabinan as substrates. [Modes for carrying out the invention]

[0017] Herein, various preferred features and embodiments of the present invention are described by non-limiting examples. Those skilled in the art will understand that all features of the present invention disclosed herein can be combined without departing from the scope of the disclosed invention.

[0018] No reference to prior art documents in this specification should be considered an acknowledgment that such prior art is well known or that it forms part of a common general understanding in the art. All publications referenced herein are incorporated herein by reference.

[0019] As used herein, the words “comprises,” “comprising,” and similar words should not be interpreted as exclusive or exhaustive. In other words, they mean “including, but not limited to.” The terms “comprises,” “comprising,” etc., also include the term “consisting of.”

[0020] The implementation of the present invention will employ conventional techniques within the ability of those skilled in the art, unless otherwise described. Such techniques are described in the literature. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

[0021] Numeric ranges include the numbers defining the range, and all percentages disclosed herein are by weight / weight unless otherwise specified. As used herein, the term "about" means approximately, nearly, generally, or in the vicinity of. When the term "about" is used with a numerical value or range, the value or range is modified by expanding the upper and lower boundaries of the recited numerical value. Generally, the terms "about" and "substantially" are used herein to adjust numerical values that are more than 10% above and below the defined value.

[0022] All percentages (%) are by weight unless otherwise specified.

[0023] As used herein, the term "about" or "substantially" when referring to a measurable value, e.g., a parameter, quantity, period of time, means including variations of a particular value, or from a particular value, such as variations of 1% to -10% or less, 1% to -5% or less, 1% to -1% or less, and +0.1% or less from a particular value, as long as such variations are appropriate for implementing the disclosed invention. It should be understood that the value to which the modifier "about" or "substantially" refers is also specifically and preferably disclosed.

[0024] Reference to an array having a certain percentage identity to any one of the SEQ ID numbers detailed herein may refer to an array having the recited percentage identity to the full length of such reference SEQ ID number.

[0025] The comparison of identity can be performed visually, or more generally, with the help of readily available sequence comparison programs. These commercially available computer programs can calculate the percentage of homology or identity between two or more sequences.

[0026] Identity percentages can be calculated over continuous sequences. That is, one sequence is aligned with the other, and each amino acid in one sequence is directly compared one residue at a time with its corresponding amino acid in the other sequence. This is called a "gapless" alignment. Typically, such gapless alignments are performed only for relatively short sequences.

[0027] While this is an extremely simple and consistent method, it does not take into account that, for example, a single insertion or deletion in a nucleotide sequence may cause subsequent codons to deviate from the alignment in otherwise identical sequence pairs. Therefore, when performing global alignment, the identity percentage can be significantly reduced. For this reason, most sequence comparison methods are designed to produce optimal alignments that take possible insertions and deletions into account without excessively lowering the overall identity score. This is achieved by inserting "gaps" during sequence alignment to maximize local identity.

[0028] However, these more complex methods assign a "gap penalty" to each gap that occurs during alignment, so that for the same number of identical amino acids, a sequence alignment with as few gaps as possible—reflecting a higher relatedness between the two comparison sequences—achieves a higher score than a sequence alignment with many gaps. Typically, an "affine gap cost" is used, which imposes a relatively high cost on the presence of gaps and a small penalty on each subsequent residue within the gap. This is the most commonly used gap scoring system. Naturally, a higher gap penalty results in an optimized alignment with fewer gaps. Most alignment programs allow you to change the gap penalty. However, when using such software for sequence comparison, it is preferable to use the default values. For example, with the GCG Wisconsin Bestfit package, the default gap penalty for amino acid sequences is -12 for gaps and -4 for each extension.

[0029] Therefore, calculating the maximum identity percentage first requires generating an optimal alignment that takes gap penalties into account. Suitable computer programs for performing such alignments include the GCG Wisconsin Bestfit package (University of Wisconsin, USA; Devereux et al. (1984) Nucleic Acids Res. 12:387), minimap, or Burrows-Wheeler Aligner (BWA). Other software capable of sequence comparison includes, but is not limited to, the BLAST package (see Ausubel et al. (1999), Chapter 18), FASTA (Atschul et al. (1990) J.Mol. Biol. 403-410), and GENEWORKS formula comparison tools. Both BLAST and FASTA are available for offline and online searching (see Ausubel et al. (1999), pp. 7-58 to 7-60). However, for some applications, the GCG Bestfit program is preferable. Another tool called BLAST2 Sequences can also be used to compare protein and nucleotide sequences (FEMS Microbiol. Lett. (1999) 174:247-50; FEMS Microbiol. Lett. (1999) 177:187-8).

[0030] Preferably, the identity percentage can be calculated over a common minimum coverage between two sequences aligned with coverage of at least 80%, at least 85%, at least 90%, at least 95%, or at least 99%.

[0031] The alignment process itself is not typically based on all-or-nothing pairwise comparisons. Rather, a scaled similarity score matrix is ​​usually used, which assigns a score to each pairwise comparison based on chemical similarity or evolutionary distance. An example of such a commonly used matrix is ​​the BLOSUM62 matrix (the default matrix for the BLAST program family). The GCG Wisconsin program typically uses either public default values ​​or custom symbol comparison tables, if provided (see the user manual for further details). For some applications, it is preferable to use the public default values ​​for the GCG package, or, in the case of other software, to use a default matrix such as BLOSUM62.

[0032] Once the software generates the optimal alignment, homology (%), preferably sequence identity (%), can be calculated. Typically, the software does this as part of the sequence comparison and generates a numerical result.

[0033] The terms “subject,” “individual,” and “patient” are used interchangeably to refer to vertebrates, preferably mammals, and more preferably humans. Mammals include, but are not limited to, mice, monkeys, humans, livestock, sporting animals, and pets.

[0034] The term "infant" refers to a human subject under 12 months of age or a non-human animal of equivalent age.

[0035] As used herein, the terms “young child” or “toddler” may refer to human subjects between 12 months and 5 years of age. Preferably, “young child” may refer to non-human animals of equivalent age.

[0036] The terms “complementary feeding period,” “complementary period,” “transition period,” “transition period,” and “weaning period” can be used interchangeably and refer to the period in an infant's or toddler's diet during which either breast milk or formula is replaced by another food. Infants or toddlers are typically gradually moved or transitioned from being fed only breast milk or formula to a mixed diet that includes milk and / or solid foods. The transition period varies from infant to toddler, but is typically between approximately 4 months and 18 months of age, for example, between approximately 6 months and 18 months of age, although in some cases it may extend to approximately 24 months or longer. In humans, the weaning period typically begins between 4 and 6 months of age and is considered complete when the infant or toddler is no longer given breast milk or infant formula, typically around 24 months of age. In some embodiments, the weaning period is between 4 and 24 months.

[0037] The terms "composition" or "nutritional composition" refer to any composition or formulation of any kind that provides nutritional benefits to an individual and is safe for human or animal consumption. A nutritional composition may be in solid (e.g., powder), semi-solid, or liquid form and may contain one or more major nutrients, micronutrients, food additives, water, etc. For example, a nutritional composition may contain the following major nutrients: sources of protein, sources of lipids, sources of carbohydrates, and any combination thereof. Furthermore, a nutritional composition may contain the following micronutrients: vitamins, minerals, fiber, phytochemicals, antioxidants, prebiotics, probiotics, bioactive substances, metabolites (e.g., butyrates, docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), gamma-linolenic acid (GLA)), and any combination thereof. A composition may also contain food additives, such as stabilizers (if provided in liquid or solid form) or emulsifiers (if provided in liquid form). The amounts of various raw materials (e.g., oligosaccharides) can be expressed in grams per 100 g of composition on a dry weight basis if the raw material is in solid form, e.g., powder, or as a concentration in grams per 1 L of composition if the raw material refers to a liquid form (the latter also includes liquid compositions that can be obtained after reconstituting powder with a liquid, e.g., milk, water, e.g., reconstituted infant formula or follow-on / follow-up formula, or infant cereal product, or any other formulation designed for the nutrition of infants or toddlers). Generally, nutritional compositions can be formulated for enteral, oral, parenteral, or intravenous administration and usually contain one or more nutrients selected from lipid or fat sources, protein sources, and carbohydrate sources. Preferably, nutritional compositions are for oral use.

[0038] In certain embodiments, the nutritional composition is a "synthetic nutritional composition." The expression "synthetic nutritional composition" means a mixture obtained by chemical and / or biological means.

[0039] Preferably, the nutritional composition may include fiber; for example, fiber as defined herein.

[0040] As used herein, the term “infant formula” refers to a food intended for specific nutritional purposes of an infant during the first month of life, which, by itself, satisfies the nutritional requirements for infants in this category (Article 2(c) of the European Commission Directive 91 / 321 / EEC 2006 / 141 / EC of 22 December 2006, relating to infant formulas and follow-on formulas). This term also refers to nutritional compositions intended for infants, as defined in Codex Alimentarius (Codex STAN72-1981), and special infant foods (including foods for special medical purposes). The expression “infant formula” encompasses any of “infant starter formulas” and “follow-up formulas” or “follow-on formulas.”

[0041] "Follow-up formulas" or "follow-on formulas" are given from six months of age onward. These formulas constitute the main liquid component in the increasingly diverse diet of infants in this category.

[0042] The term "baby food" refers to food intended for specific nutritional purposes during the first year of life for infants or toddlers.

[0043] The term "infant cereal composition" refers to food intended for specific nutritional purposes for infants or young children during the first few years of life.

[0044] The term "growing-up milk" (or GUM) refers to a milk beverage intended for infants or children, generally fortified with vitamins and minerals.

[0045] The term "fortifier" refers to a liquid or solid nutritional composition suitable for fortifying or mixing with human milk, infant formula, growing-up milk, or human breast milk fortified with other nutrients. Therefore, fortifiers can be administered after being dissolved in human breast milk, after being dissolved in infant formula, after being dissolved in growing-up milk, or after being dissolved in human breast milk fortified with other nutrients, or otherwise, as a standalone composition.

[0046] The composition of the present invention may be a supplement.

[0047] The supplement may be in the form of, for example, tablets, capsules, lozenges, or liquids. The supplement may further contain protective hydrophilic colloids (such as gums, proteins, and modified starches), binders, film-forming agents, capsule encapsulants / capsule encapsulating materials, wall / shell wall materials, matrix compounds, coatings, emulsifiers, surfactants, solubilizers (such as oils, fats, waxes, and lecithin), adsorbents, carriers, fillers, co-compounds, dispersants, wetting agents, processing aids (solvents), flowing agents, taste masking agents, bulking agents, gelling agents, and gel-forming agents. The supplement may also contain conventional pharmaceutical additives and auxiliaries, excipients, and diluents, including but not limited to water, gelatin derived from any source, vegetable gums, lignin sulfonates, talc, sugars, starches, gum arabic, vegetable oils, polyalkylene glycols, flavoring agents, preservatives, stabilizers, emulsifiers, buffers, lubricants, colorants, wetting agents, and fillers.

[0048] Furthermore, supplements may also contain vitamins, minerals, trace elements, and other micronutrients, in accordance with the recommendations of government agencies such as the USRDA, in addition to organic or inorganic carrier materials suitable for oral or parenteral administration.

[0049] The term "metabolize" is used herein to mean that a substrate can be broken down, adsorbed, and / or utilized by microorganisms. For example, a substrate may promote the growth and / or survival of microorganisms, and / or contribute to their growth and / or survival.

[0050] Preferably, the term "able to metabolize glycan substrates" may mean that the B. longum transitional strain encodes at least one CAZyme that can utilize glycan substrates. For example, a CAZyme may be capable of catalyzing the hydrolysis of glycosidic bonds within glycan substrates. Preferably, the B. longum transitional strain may encode at least one, at least two, at least three, at least four, or at least five CAZymes that can utilize glycan substrates. Preferably, the term "able to metabolize glycan substrates" may mean that glycan substrates (or fibers or raw materials containing glycan substrates) can promote the growth and / or survival of the B. longum transitional strain (for example, when added to an anaerobic culture of the B. longum transitional strain). The growth and / or survival of the B. longum transitional strain over time can be measured by measuring the abundance using strain-specific genes, for example, by qPCR, or by measuring growth via the optical density of cells at 580 nm. An exemplary assay for measuring the growth of B. longum transitional strains in the presence of a glycan substrate (e.g., fibrous form) is provided in this embodiment.

[0051] Glycan substrates that can promote the growth and / or survival of B. longum transitional strains may increase the number of B. longum transitional bacteria in anaerobic cultures by at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, or at least 100% compared to the number of B. longum transitional bacteria in HMO-free control anaerobic cultures. Preferably, glycan substrates that can promote the growth and / or survival of B. longum transitional strains may increase the number of B. longum transitional bacteria in anaerobic cultures by a statistically significant amount (e.g., p-value < 0.05 calculated by one-way ANOVA) compared to the number of B. longum transitional bacteria in anaerobic cultures without glycan substrates.

[0052] "Glycan substrate" refers to glycans that can be metabolized by microorganisms. Glycan substrates may be, for example, complex carbohydrates, oligosaccharides, or polysaccharides. Complex carbohydrate glycans may include N-linked or O-linked glycans in glycoproteins and proteoglycans, or glycolipids. For example, O-linked glycans may include proteins or peptides in which the oxygen atom of a serine or threonine residue is linked to a monosaccharide, oligosaccharide, or polysaccharide, as in the case of glycosaminoglycans (GAGs). Further examples of "glycan substrates" are cellulose, a glycan composed of β-1,4-linked D-glucose, and chitin, a glycan composed of β-1,4-linked N-acetyl-D-glucosamine. Glycans may be homopolymers or heteropolymers of monosaccharide residues and may be linear or branched. As used herein, "glycan substrate" includes, for example, oligosaccharides and polysaccharides.

[0053] "Oligosaccharides" can refer to carbohydrates having more than two but relatively few monosaccharide units (typically 3, 4, 5, 6, and up to 10). Examples of oligosaccharides include, but are not limited to, fructooligosaccharides, galactooligosaccharides (raffinose, stachyose, beruvasose), maltooligosaccharides, gentiooligosaccharides, cellooligosaccharides, milk oligosaccharides (e.g., those found in mammary secretions), isomaltoligosaccharides, lactosucrose, mannooligosaccharides, melibiose-derived oligosaccharides, pectin oligosaccharides, and xylooligosaccharides.

[0054] The term "polysaccharide" may refer to carbohydrates having more than 10 monosaccharide units. Examples of polysaccharides include, but are not limited to, starch, arabinogalactan, arabinan, β-glucan, laminarin, chrysolaminan, xylan, arabinoxylan, mannan, fucoidan, rhamnogalacturonan, and galactomannan. It should be understood that there is no strict distinction or division between the terms oligosaccharide and polysaccharide, and such a distinction is not necessary for carrying out the present invention.

[0055] The term "glycosaminoglycan" (GAG), or mucopolysaccharide, refers to a long, linear polysaccharide composed of repeating disaccharide units (i.e., two-sugar units). The repeating of two sugar units consists of a uronic acid and an amino acid, with keratan being an exception, having galactose instead of uronic acid. GAGs are classified into four groups based on their core disaccharide structure.

[0056] As used herein, "mucin" may refer to a family of high molecular weight, highly glycosylated proteins (complex carbohydrates). A key property of mucin is its gel-forming ability. Therefore, mucin is an important component in most gel-like secretions and plays a role ranging from lubrication to cell signaling, mechanical barrier formation, and chemical barrier formation.

[0057] The term "HMO" or "HMO(plural)" refers to human milk oligosaccharides. These carbohydrates are highly resistant to enzymatic hydrolysis, suggesting that HMOs may exhibit important functions not directly related to their calorie value. In particular, they have been shown to play an essential role in the early development of infants and young children, such as the maturation of the immune system. Many types of HMOs are found in human breast milk. Each individual oligosaccharide is based on a combination of glucose, galactose, sialic acid (N-acetylneuraminic acid), fucose, and / or N-acetylglucosamine, with a wide variety of bonds between them, resulting in a very large number of oligosaccharide types in human breast milk, with over 130 structures identified to date. Almost all of these oligosaccharides have a lactose residue at the reducing end, and the non-reducing terminal position is occupied by sialic acid and / or fucose (if present). Depending on the presence of fucose and sialic acid in the oligosaccharide structure, HMOs can be classified as non-fucosylated molecules (neutral), or as fucosylated molecules (neutral) and sialylated molecules (acidic) and non-sialylated molecules, respectively.

[0058] The term "fucosylated oligosaccharide" refers to oligosaccharides that contain fucose residues. Such oligosaccharides are neutral in nature. Some examples include 2'-fucosyllactose (2-FL), 3-fucosyllactose (3-FL), difucosyllactose (DiFL), lacto-N-fucopentaose (e.g., lacto-N-fucopentaose I, lacto-N-fucopentaose II, lacto-N-fucopentaose III, lacto-N-fucopentaose V), lacto-N-fucohexaose, lacto-N-difucohexaose I, fucosyllacto-N-hexaose, fucosyllacto-N-neohexaose, difucosyllacto-N-hexaose I, difucosyllacto-N-neohexaose II, and any combination thereof. Fucosylated oligosaccharides are the largest fraction in human breast milk, with 2'-FL accounting for up to 30% of all HMOs. Fucosylated oligosaccharides are thought to reduce the risk of infection and inflammation, and to reduce inflammatory responses by enhancing the growth and metabolic activity of certain symbiotic microorganisms.

[0059] The term "N-acetylated oligosaccharide" encompasses both "N-acetyl-lactosamine" and "oligosaccharides containing N-acetyl-lactosamine." These are neutral oligosaccharides that have an N-acetyl-lactosamine residue. Appropriate examples include LNT (lacto-N-tetraose), para-lacto-N-neohexaose (para-LNnH), LNnT (lacto-N-neotetraose), DSLNT (dicialyllacto-N-tetraose), and any combination thereof. Other examples include lacto-N-hexaose, lacto-N-neohexaose, para-lacto-N-hexaose, para-lacto-N-neohexaose, lacto-N-octaose, lacto-N-neooctaose, isolact-N-octaose, para-lacto-N-octaose, and lacto-N-decaose.

[0060] The phrases "at least one type of fucosylated oligosaccharide" and "at least one type of N-acetylated oligosaccharide" should be understood as meaning "at least one type of fucosylated oligosaccharide" and "at least one type of N-acetylated oligosaccharide."

[0061] The term "sialylated oligosaccharide" refers to oligosaccharides that have a charged sialic acid residue. Sialylated oligosaccharides are acidic. Some examples include 3'-sialyl lactose (3-SL), 6'-sialyl lactose (6-SL), and sialyl lact-N-tetraose (Lst-, e.g., Lst-a, Lst-b, or Lst-c).

[0062] Preferably, the term "able to metabolize HMO" may mean that the B. longum transitional strain encodes at least one CAZyme that can utilize HMO. For example, the CAZyme may be capable of catalyzing the hydrolysis of glycosidic bonds within HMO. Preferably, the B. longum transitional strain may encode at least one, at least two, at least three, at least four, or at least five CAZymes that can utilize HMO. Preferably, the term "able to metabolize HMO" may mean that HMO can promote the growth and / or survival of the B. longum transitional strain (for example, when added to an anaerobic culture of the B. longum transitional strain). The growth and / or survival of the B. longum transitional strain over time can be measured by measuring the abundance using strain-specific genes, for example by qPCR, or by measuring growth via the optical density of cells at 580 nm.

[0063] The term "fiber" is used herein to refer to carbohydrates that are indigestible to humans or animals. Such fibers are also discussed herein in relation to carbohydrates. Preferably, the fibers can be fermented with the transitional strain of B. longum of the present invention. When used herein, the expressions "fiber" or "multiple fibers" or "dietary fiber" or "multiple dietary fibers" in the context of the present invention refer to the indigestible portion of a plant-derived food that is indigestible in the small intestine and reaches the large intestine, and which comprises two main components: water-soluble fiber and insoluble fiber. Mixtures of multiple fibers are included within the scope of the above terms. Soluble fiber readily ferments in the colon to form gas and physiologically active by-products, which may be prebiotics and viscous. Insoluble fiber does not dissolve in water, is not metabolized, provides bulk, or becomes a prebiotic in the large intestine and may undergo metabolic fermentation. Chemically, dietary fiber consists of carbohydrate polymers having three or more monomer units that are not hydrolyzed by endogenous enzymes in the small intestine or upper tract of the digestive system, such as arabinoxylan, cellulose, and many other plant components, such as resistant starch, undigestible dextrin, inulin, lignin, chitin, pectin, arabinan, arabinogalactan, galactan, xylan, β-glucan, and oligosaccharides. Non-limiting examples of dietary fiber include prebiotic fibers, such as fructooligosaccharides (FOS), inulin, galactooligosaccharides (GOS), fruit fiber, plant fiber, cereal fiber, undigestible starch, such as high-amylose corn starch.

[0064] As used herein, “added fiber” or “added dietary fiber” refers to fiber added to a complementary nutrition composition, which is primarily or entirely composed of fiber, and whose amount contributes to the total fiber content. The total fiber content of a complementary nutrition composition is provided by the sum of the amount of fiber naturally present in the raw materials used in the recipe (e.g., from whole grain flour) and the amount of added fiber.

[0065] Preferably, the composition of the present invention may be a probiotic composition.

[0066] The term "prebiotics" refers to non-digestible carbohydrates that have a beneficial effect on the host by selectively stimulating the growth and / or activity of healthy bacteria, such as Bifidobacterium in the human colon (Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics., J Nutr. 1995;125:1401-12).

[0067] The term "probiotics" refers to microbial cell preparations or microbial cell components that have beneficial effects on the health or well-being of the host (Salminen S, Ouwehand A, Benno Y. et al. "Probiotics: how should they be defined" Trends Food Sci. Technol. 1999:10 107-10). The microbial cells according to the present invention are generally bacteria.

[0068] The term "cfu" should be understood as a colony-forming unit.

[0069] The "intestinal microbiota" is the composition of microorganisms (including bacteria, archaea, and fungi) that inhabit the digestive tract.

[0070] The term "gut microbiome" can encompass both the "gut microbiota" and their "theatre of activity," which may include structural elements of the activity site (nucleic acids, proteins, lipids, polysaccharides), metabolites (signaling molecules, toxins, organic molecules, and inorganic molecules), and molecules produced by the coexisting host and structured by the surrounding environmental conditions (Berg, G., et al., 2020. Microbiome, 8(1), pp.1-22).

[0071] Bifidobacterium longum transitional microbial strain In a first aspect, the present invention provides a Bifidobacterium longum transitional microbial strain deposited with the Collection Nationale de Cultures de Micro-organismes (CNCM) under deposit number CNCM I-5942, or a B. longum transitional strain having the distinguishing characteristics of the B. longum transitional strain deposited under deposit number CNCM I-5942.

[0072] Preferably, the transitional strain of Bifidobacterium longum may be referred to herein as B. longum subsp. juvenis.

[0073] Preferably, the identifying characteristics of the B. longum transitional strain of the present invention may refer to one or more of the phenotypic or genotypic features described herein.

[0074] In another embodiment, the present invention provides a B. longum transitional microbial strain having at least 99% mean base match (ANI) to a B. longum transitional strain deposited with the CNCM under deposit number CNCM I-5942.

[0075] In some embodiments, the transitional strain of B. longum has at least 99.0%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% of the ANI compared to the B. longum strain deposited with CNCM under deposit number CNCM I-5942.

[0076] Preferably, the B. longum transition strain has at least 99.9% of the ANI compared to the B. longum strain deposited with CNCM under depositary number CNCM I-5942.

[0077] Preferably, the B. longum transition strain has at least 98.1%, at least 98.2%, at least 98.3%, at least 98.4%, at least 98.5%, at least 98.6%, at least 98.6%, at least 98.7%, at least 98.8%, at least 98.9%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% of the ANI of the B. longum transition strain deposited with CNCM under deposit number CNCM I-5942, as described herein, and has at least one of the identifying characteristics of the B. longum transition strain deposited under deposit number CNCM I-5942.

[0078] Preferably, the B. longum transition strain has at least 98.4%, at least 98.5%, at least 98.6%, at least 98.6%, at least 98.7%, at least 98.8%, at least 98.9%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% of the ANI compared to the B. longum strain deposited with CNCM under deposit number CNCM I-5942, as described herein, and has at least one of the identifying characteristics of the B. longum transition strain deposited under deposit number CNCM I-5942.

[0079] Methods for sequencing microbial genomes are well known in the art (see, for example, Segerman; Front.Cell.Infect.Microbiol.; 2020; 10; Article 527102 and Donkor; Genes; 2013; 4(4); 556-572). Metagenomics may be used as an example. A suitable metagenomics method may be performed, for example, using shotgun sequencing data. A suitable metagenomics method is publicly known in the art, such as MetaPhLaN 3.0 (see Beghini et al.; eLife 2021; 10:e65088; https: / / huttenhower.sph.harvard.edu / metaphlan).

[0080] Average Nucleotide Identity (ANI) is a technical term referring to a distance-based approach to describing species based on pairwise comparisons of their genome sequences, and is an in silico alternative to the conventional DNA-DNA hybridization (DDH) technique used for phylogenetic definition of species (Goris et al., 2007, "DNA-DNA hybridization values ​​and their relationship to whole-genome sequence similarities", Int. J. Syst. Evol. Microbiol. 57:81-91). Strains with more than 70% relatedness based on DDH are considered to belong to the same species (see, for example, Wayne et al., 1987, Report of the Ad-Hoc-Committee on Reconciliation of Approaches to Bacterial Systematics, Int J Syst Bacteriol 37:463-464). ANI is similar to the aforementioned 70% DDH cutoff value and can be used for species classification.ANI has been evaluated by multiple laboratories and has become the gold standard for species classification (see, for example, Kim et al., 2014, "Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes", Int.J.Syst.Evol.Micr.64:346-351; Richter et al., 2009, "Shifting the genomic gold standard for the prokaryotic species definition", P Natl Acad Sci USA 106:19126-19131; and Chan et al., 2012, "Defining bacterial species in the genomic era: insights from the genus Acinetobacter", Bmc.Microbiol.12).

[0081] The ANI of shared genes between two strains is known to be a robust means of comparing genetic kinship between strains, and an ANI value of approximately 95% is known to correspond to the 70% DNA-DNA hybridization standard for defining species. See, for example, Konstantinidis and Tiedje, Proc Natl Acad Sci USA, 102(7):2567-72 (2005); and Goris et al., Int Syst Evol Microbiol. 57(Pt 1):81-91 (2007). The ANI between two bacterial genomes is calculated from pairwise comparisons of all sequences shared between any two strains and can be determined using, for example, any of the various publicly available ANI tools, including, but not limited to, OrthoANI using usearch (Yoon et al. Antonie van Leeuwenhoek 110:1281-1286 (2017)); ANI Calculator, JSpecies (Richter and Rossello-Mora, Proc Natl Acad Sci USA 106:19126-19131 (2009)); and JSpeciesWS (Richter et al., Bioinformatics 32:929-931 (2016)). Other methods for determining the ANI of two genomes are known in the art. See, for example, Konstantinidis, K.T. and Tiedje, J.M., Proc. Natl. Acad. Sci. USA, 102:2567-2572 (2005); and Varghese et al., Nucleic Acids Research, 43(14):6761-6771 (2015). In certain embodiments, the ANI between two bacterial genomes can be calculated, for example, by averaging the base match of orthologous genes identified as bidirectional best hits (BBHs).The protein-coding genes of the first genome (genome A) and the second genome (genome B) are compared at the nucleotide level using a similarity search tool, such as NSimScan (Novichkov et al., Bioinformatics 32(15):2380-23811(2016)). The results are then filtered to retain only the BBHs that show at least 70% sequence agreement over at least 70% of the shorter sequence length for each BBH pair. The ANI of genome A to genome B is defined as the sum of the percentage agreements multiplied by the alignment lengths of all BBHs, divided by the sum of the lengths of the BBH genes. These calculation techniques and ANI calculation techniques are known in the field.

[0082] According to the present invention, the B. longum transitional strain deposited with CNCM under deposit number CNCM I-5942 represents the reference genome on which the test genome is compared.

[0083] In some embodiments, the transitional strain of B. longum of the present invention is isolated from a human.

[0084] In some other embodiments, the transitional strain of B. longum is not of the subspecies B. longum subspecies longum or B. longum subspecies infantis.

[0085] Preferably, the transitional strain of B. longum is provided as a probiotic. Preferably, the transitional strain of B. longum is provided in a composition.

[0086] antibiotic resistance Preferably, this B. longum transitional strain does not possess transmissible antibiotic resistance to one or more antibiotics, preferably one or more relevant antibiotics as defined by the European Food Safety Authority (EFSA) (see European Food Safety Authority. 2012. Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance. EFSA J 10:2740).

[0087] Antibiotic resistance refers to the ability of microorganisms to withstand antibiotic treatment. Overuse or inappropriate use of antibiotics is associated with the emergence and spread of antibiotic-resistant microorganisms, rendering treatments ineffective and posing a significant risk to public health. Furthermore, widespread use of antibiotics means that it is becoming increasingly difficult to provide bacterial strains that do not exhibit transmissible resistance to one or more EFSA-related antibiotics.

[0088] It is known that a single gene can confer antibiotic resistance to a particular antibiotic, and that bacteria can transmit genes through horizontal gene transfer via conjugation, transduction, or transformation. Therefore, it is known that antibiotic resistance can be transmitted among bacteria, including those in the gut microbiome, via horizontal gene transfer.

[0089] Therefore, the fact that the B. longum transitional strain of the present invention does not possess transmissible resistance to one or more antibiotics is advantageous because it reduces the risk of antibiotic resistance being transmitted to other components of the microbiome when the B. longum transitional strain of the present invention is used as a probiotic.

[0090] Antibiotic resistance is well known and can be evaluated using any suitable assay known in the art. For example, phenotypic and / or genetic methods may be used. Phenotypic methods typically involve measuring the growth of test bacteria in the presence of the antibiotic under consideration at an appropriate concentration. Furthermore, many genes mediating antibiotic resistance are known. Therefore, genetic methods for evaluating antibiotic resistance include confirming the presence of one or more antibiotic resistance genes in the genome of the test bacteria (e.g., by PCR, DNA microarrays, whole-genome sequencing and metagenomics, and matrix-assisted laser desorption / ionization time-of-flight mass spectrometry). Preferably, phenotypic antibiotic testing can be carried out in accordance with EFSA recommendations (EFSA J 16,e05206,doi:10.2903 / j.efsa.2018.5206(2018)), for example, according to the formal method ISO 10932. Exemplary methods for evaluating antibiotic resistance are detailed in this embodiment.

[0091] The antibiotic resistance present in Bifidobacterium and the genes responsible for it are known in the art (see, for example, Duranti et al.; Appl Environ Microbiol. 2017 Feb 1; 83(3): e02894-16). Therefore, those skilled in the art can evaluate whether a test Bifidobacterium is resistant to one or more antibiotics.

[0092] Preferably, the longum transitional strain is free from resistance to at least one, at least two, at least three, at least four, at least five, at least six, or at least seven EFSA-related antibiotics.

[0093] Preferably, the transitional strain of B. longum is resistant to both tetracycline and erythromycin.

[0094] Preferably, the transitional strain of B. longum is resistant to tetracycline, erythromycin, clindamycin, and ampicillin.

[0095] Preferably, the transitional strain of B. longum is resistant to tetracycline, erythromycin, clindamycin, ampicillin, gentamicin, streptomycin, chloramphenicol, and vancomycin.

[0096] Tetracycline resistance may be conferred by the tet(W) or tet(Q) gene encoding a ribosomal protection protein. Preferably, the transitional strain of B. longum of the present invention may lack the tet(W) gene. Preferably, the transitional strain of B. longum of the present invention may lack the tet(W) gene encoding a polypeptide represented as SEQ ID NO: 1 or a variant that shares at least 80% sequence identity with SEQ ID NO: 1. Preferably, the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with SEQ ID NO: 1.

[0097] Sequence ID 1 MKIINIGILAHVDAGKTTTLTESLLYASGAISEPGSVEKGTTRTDTMLLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVS LSPEIVLEENTDIEAWDAVIENNDKLLEKYIAGEPISREKLVREEQRRVQDASLFPVYYGSAKKGLGIQPLMDAVTGLFQPIGEQGSAALCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAYPGEIVILPSD SVRLNDVLGDPTRLPRKRWREDPLPMLRTSIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVVSALLSEKYKLETVVKEPTVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLPLGSGVQYKSRVSLGYLNQSFQNAVRD GIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFTLYAPREYLSRAYHDAPKYCATIETVQVKKDEVVFTGEIPARCIQAYRTDLAFYTNGQSVCLTELKGYQAAVGKPVIQPRRPNSRLDKVRHMFSKIT

[0098] Preferably, the transitional strain of B. longum of the present invention may not have a tet(Q) gene. Preferably, the transitional strain of B. longum of the present invention may not have a tet(Q) gene encoding a polypeptide shown as SEQ ID NO: 2 or a variant that shares at least 80% sequence identity with SEQ ID NO: 2. Preferably, the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with SEQ ID NO: 2.

[0099] Sequence ID 2 MRFDNASNVVYYCLIQMNIINLGILAHIDAGKTSVTENLLFASGATEKCGRVDNGDTITDSMDIEKRRGITVRASTTSIIWNGVKCNIIDTPGHMDFIAEVERTFKMLDGAVLILSAKEGIQAQTKLLFNTLQKLQIPTIIFINKIDRAGVNLERLYLDIKTNL SQDVLCMQTVVDGSVYPVCSQTYIKEEYKEFVCDHDDNILERYLADSEIPPTDYWNTIIALVAKAKVYPVLHGSAMFNIGINELMDAITSFILPPASVSDRLSAYLYKIEHDPKGHKRSFLKIIDGSLRLRDVVRINDSEKSIKIKNLKTIYQGREINVDEVGA NDIAIVEDMEDFRIGDYLGAEPCLIQGLSHQHPALKSSVRPDKPEERSKVISALNTLWIEDPSLSFSINSYSDELEISLYGLTQKEIIQTLLEERFSVKVHFDEIKTIYKERPIKKVNKIIQIEVPPNPYWATIGLTLEPLPLGAGLQIESDISYGYLNHSFQN AVFEGIRMSCQSGLHGWEVTDLKVTFTQAEYYSPVSTPADFRQLTPYVFRLALQQSGVDILEPMLYFELQIPQEASSKAITDLQKMMSEIEDISCNNEWCHIKGKVPLNTSKDYASEVSSYTKGLGIFMVKPCGYQITKDGYSDNIRMNEKDKLLFMFQKSMSLK

[0100] Resistance to erythromycin may be conferred by the erm(49) gene encoding rRNA methylase. Preferably, the transitional strain of B. longum of the present invention may lack the erm(49) gene. Preferably, the transitional strain of B. longum of the present invention may lack the erm(49) gene encoding a polypeptide represented as SEQ ID NO: 3 or a variant that shares at least 80% sequence identity with SEQ ID NO: 3. Preferably, the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with SEQ ID NO: 3.

[0101] Sequence ID 3 MRNIKDTQNFLHSKELVRHLIGICNIKLDDVVIEIGPGKGIITNELAHKARKVVAIEFDEELYEKLKNKFQSNNKVDIIYGDILNYTPRIPSYCVFSNIPFNITSEILNKFLSDKKNEKMFLIMQYEPFIKYAGNPYGAETLRSMLYKPFFD MDLKYRFDPSDFKAPQARIVLASFERKQFPDVKKEEEKLYKDFLAYIYTNKGETFFAKIKTLFSSNQIKRVWGQIKIDKTTKISEVPYESILKVFKLFFLYGTDANKQLVVNSFNNMNKQNNKLQKNHRNNSKAKSWNSNRKRKPYHRNNV

[0102] Resistance to erythromycin and clindamycin may be conferred by the erm(X) gene encoding a ribosomal protective protein. Preferably, the transitional strain of B. longum of the present invention may not have the erm(X) gene. Preferably, the transitional strain of B. longum of the present invention may not have the erm(X) gene encoding a protein containing SEQ ID NO: 4 or a variant that shares at least 80% sequence identity with SEQ ID NO: 4. Preferably, the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with SEQ ID NO: 4.

[0103] Sequence ID 4 MSAYGHGRHENGQNFLTNHKIINSIIDLVKQTSGPIIEIGPGSGALTHPMAHLGRAITAVEVDAKLAAKLTQETSSAAVEVVHDDFLNFRLPATPCVIVGNIPFHLTTAILRKLLHAPAWTDAVLLMQWEVARRRAGVGAST MMTAQWSPWFTFHLGSRVPRTAFRPQPNVDGGILVIRRVGDPKIPIEQRKAFQAMVHTVFTARGRGIGEILRRAGLFSSRSETQSWLRSRGIDPATLPPRLHTNDWIDLFQVTGSSLPHHRPISPSGSSQRPPQQKNRSRRR

[0104] Streptomycin resistance can be conferred by mutations in the rpSL gene encoding the ribosomal S12 protein. More specifically, a mutation involving the substitution of an A residue to a G residue at nucleotide position 128 has been shown to provide streptomycin resistance (see Kiwaki & Sato; Int J Food Microbiol. 2009 Sep 15;134(3):211-5). Preferably, the B. longum transitional strain of the present invention may have an A residue at position 128 of the rpSL gene. Preferably, the B. longum transitional strain of the present invention does not contain the G128A mutation in the rpSL gene. An exemplary rpSL gene sequence containing A at position 128 is shown as Sequence ID No. 5.

[0105] Sequence ID 5 TTGCCTACTATTGAACAGCTCGTCCGTAAGGGACGTCAGGCAAAGCCGAAGAAGTCCAAGACTTTGGCCCTGAAGGGCAGCCCGCTGCGTCGCGGCGTGTGCACCCGTGTCTACACCACCACCCCGAAGAAGCCGAACTCGGCTCTGCGTAAGGTCGCTCGTGTGCGCCTGTCCTCGGGCATCGAA GTCACCGCCTACATTCCGGGCGAGGGCCACAACCTGCAGGAGCACTCCATCGTGCTCGTGCGCGGCGGCCGTGTGAAGGATCTCCCGGGTGTGCGTTACCACATCGTGCGTGGCGCGCTCGATACCCAGGGTGTCAAGGACCGTAAGCAGGGTCGTTCCCTGTATGGAGCAAAGAAGGCGAAGTAA

[0106] Resistance to chloramphenicol may be conferred by the crmX gene encoding a ribosomal protective protein. Preferably, the transitional B. longum strain of the present invention may lack the crmX gene. Preferably, the transitional B. longum strain of the present invention may lack the crmX gene encoding a polypeptide containing SEQ ID NO: 6 or a variant that shares at least 80% sequence identity with SEQ ID NO: 6. Preferably, the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity with SEQ ID NO: 6.

[0107] Sequence ID 6 MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAAFARRWPRLTLIIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLVPANQKGRALSILLSGTTIATVVGVPAGALLSTALGWRTTFWAIAILCIPAAVGVIRGVTTNNVGRSETSATSPRLR VELSQLATPRLILAMALGALNNGGTFAAFTFLAPIVTETAGLAEAWVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLVLVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGALGLATGLGLLAPVWVASVLTAIALVIMLLTRRALTKTAAEAN

[0108] Glycan substrate / carbohydrate-related enzyme (CAZyme) The B. longum transitional strain of the present invention encodes a specific profile of carbohydrate-related enzymes (CAZyme).

[0109] Carbohydrate-related enzymes (CAZymes) are involved in the synthesis and degradation of complex carbohydrates, oligosaccharides, and polysaccharides. Typically, carbohydrate-related enzymes account for 1–5% of an organism's genes. Complex carbohydrates, oligosaccharides, and polysaccharides play crucial roles in many biological functions, such as as components of structure and energy storage, and in numerous intracellular and intercellular events. The CAZy classification is a sequence-based family classification system that correlates with the structure and molecular mechanism of CAZymes (www.CAZy.org).

[0110] CAZyme contains glycoside hydrolyase (GH), glycosyltransferase (GT), polysaccharide lyase (PL), carbohydrate esterase (CE), and the carbohydrate-binding module family (CBM).

[0111] GH catalyzes the hydrolysis of glycosidic bonds between two or more carbohydrates or between a carbohydrate and a non-carbohydrate moiety. In most cases, the hydrolysis of glycosidic bonds is catalyzed by two amino acid residues of the enzyme: a common acid (proton donor) and a nucleophile / base. Depending on the spatial arrangement of these catalytic residues, hydrolysis occurs via either overall retention or overall inversion of the anomeric configuration.

[0112] The GH classification system is provided by the CAZy classification. In this specification, GH is divided into several families based on molecular function (e.g., GH1, GH2, GH3, GH4, etc.). These families are then further divided into subfamilies based on subgroups that share a more recent ancestor and are typically more homogeneous in molecular function, as seen in families (e.g., GH13_1, GH13_2, GH13_3, GH13_4, etc.).

[0113] Preferably, the B. longum transitional strain of the present invention encodes a glycosyl hydrolase family 43_17 (GH43_17) enzyme. GH43_17 possesses both α-L-arabinofuranosidase (EC3.2.1.55) activity and endo-β-1,4-xylanase (EC3.2.1.8) activity and has the ability to degrade complex carbohydrates such as arabinan, arabinogalactan, and arabinoxylan. Preferably, the GH43_17 gene contains SEQ ID NO: 7 or a sequence having at least 60% sequence identity to SEQ ID NO: 7. Preferably, the GH43_17 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 7.

[0114] Sequence ID 7 ATGAAACGAACTGACATCCACCTGCGCGATCCGTTCGTCCTGCCTCACGACGGTGTCTATTACCTGTATGGCACCCGCGCTGATAACGTGTGGGGCGCGATGGATGGTTTTGATTGCTACACCAGCCGCGACCTTGACAATTGGGAGGGTCCGTTCGAGGTGTTCCACAAGCCGGATGAATTCACGGCCGACCGTGCTTACTGGGCGCCCGAATGCTACGAGCGAGACGGTGTATTCCACCTGATTGCCACGCTCGGCGAGCCGGACGGGCGCAAAAGCGTGCACATGCTACGCGCTGATAGTCCGCTTGATCCGTTCGAATATGTCTGCCGGCTGACCGATCCGAATCAGTCCTGCATTGACGGAACTCTGCATGGTGAAGGTACCGATATGTGGCTTGTCTACTCGCATTCCTTGGAGGATGTGCCCGCCGGAGACATGGATGCCGTACGTCTGTCCTCCGACCTGACTCGGACGGTGGGGGAGAGCATGACATTGTTCCAGGCCTCGGATGCGCCGTGGGCGGTGCCGGTGCCGTTCGCGAAAGCGGAATTCGGCATCGACGAGGACGCCTACTTCTCCGATGGTCCCTGCCTGTGCAGGCTTTCCAACGGACGGCTGGCGATGCTGTGGTCGAGCTGGTCGACGGAAGGCGGATATGCAGTCGGCCAGGCCATCAGCGAATCAGGGTCGATTGCTGGGCCTTGGACGCAATGCCCCGAGCCTCTGCTTAGCCACGGCGGCCACGGCATGCTGTTCAACGGTCTCGATGGCGTGCTGCGTTACGCGGTCCACTCGCCCAACGACCCCGGCCAGGAACGGCCTACGTTTTTGTGCGTCGAAGAACAAGACGGGCTGCTGACGATTACGGAATAG

[0115] Preferably, the GH43_17 gene may encode the protein shown as SEQ ID NO: 8, or a sequence having at least 80% sequence identity to SEQ ID NO: 8. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 8.

[0116] Sequence ID 8 MKRTDIHLRDPFVLPHDGVYYLYGTRADNVWGAMDGFDCYTSRDLDNWEGPFEVFHKPDEFTADRAYWAPECYERDGVFHLIATLGEPDGRKSVHMLRADSPLDPFEYVCRLTDPNQSCIDGTLHGEGTDMWLVYSHSLEDVPAG DMDAVRLSSDLTRTVGESMTLFQASDAPWAVPVPFAKAEFGIDEDAYFSDGPCLCRLSNGRLAMLWSWSTEGGYAVGQAISESGSIAGPWTQCPEPLLSHGGGHGMLFNGLDGVLRYAVHSPNDPGQERPTFLCVEEQDGLLTITE

[0117] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 43_22 (GH43_22) gene. Preferably, the GH43_22 gene contains SEQ ID NO: 9 and / or SEQ ID NO: 10, or contains a sequence having at least 60% sequence identity with SEQ ID NO: 9 or SEQ ID NO: 10. Preferably, the B. longum transitional strain of the present invention contains a GH43_22 gene having at least 60% sequence identity with SEQ ID NO: 9 and a GH43_22 gene having at least 60% sequence identity with SEQ ID NO: 10. Preferably, the GH43_22 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 9 or SEQ ID NO: 10.

[0118] Sequence ID 9

[0119] Sequence ID 10

[0120] Preferably, the GH43_22 gene may encode a protein represented as SEQ ID NO: 11 or SEQ ID NO: 12, or a sequence having at least 80% sequence identity with SEQ ID NO: 11 or SEQ ID NO: 12. Preferably, the B. longum transitional strain includes a GH43_22 gene encoding a protein represented as SEQ ID NO: 11, or a sequence having at least 80% sequence identity with SEQ ID NO: 11m, and a GH43_22 gene encoding a protein represented as SEQ ID NO: 12, or a sequence having at least 80% sequence identity with SEQ ID NO: 12. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 11 or SEQ ID NO: 12.

[0121] Sequence ID 11

[0122] Sequence ID 12

[0123] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 43_27 (GH43_27) gene. Preferably, the GH43_27 gene contains a sequence having at least 60% sequence identity to SEQ ID NO: 13, or a sequence having at least 60% sequence identity to SEQ ID NO: 13. Preferably, the GH43_27 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 13.

[0124] Sequence ID 13

[0125] Preferably, the GH43_27 gene may encode the protein shown as SEQ ID NO: 14, or a sequence having at least 80% sequence identity to SEQ ID NO: 14. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 14.

[0126] Sequence ID 14

[0127] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 43_29 (GH43_29) gene. Preferably, the GH43_29 gene contains SEQ ID NO: 15 or a sequence having at least 60% sequence identity with SEQ ID NO: 15. Preferably, the GH43_29 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 15.

[0128] Sequence ID 15

[0129] Preferably, the GH43_29 gene may encode the protein shown as SEQ ID NO: 16, or a sequence having at least 80% sequence identity to SEQ ID NO: 16. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 16.

[0130] Sequence ID 16

[0131] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 121 (GH121) gene. Preferably, the GH121 gene contains SEQ ID NO: 17 or a sequence having at least 60% sequence identity to SEQ ID NO: 17. Preferably, the GH121 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 17.

[0132] Sequence ID 17 CGCCACCGCAGAACAGGTCGCCGAGCAGGTGACCAAGCTCGAGGACGGCCAGAAGGCACTCGTTGCGCTCGCCACCGACGTGGAGAAGTCCACGTTGCAGGCGGCCATCGATGCGGCCAAAGCCGAGGCCGCTTCCGGCAAGTACACGGATAAGAGTGTCGAGGCCTTGAACAAGG CCATCGAGGCTGCGGAAGGTGTGCTCAAGGTCGGTGAGGTCGGTGAGGTCACTCAGGCCGCCGTCCAGGAAGCGTCCGCTTCGCTGAACAAGGCCGTCAAGGCCTTGGAAGAGAAGCCCGCCGCCGAAACGGTGAAGAAGGAGTCCCTCGAGGCTTCCATCGAGCAGGCCAAGAAGG CTGACAAGTCGAAGTACACCGAGGAGGCATGGCAGGCTCTGCAGAGCCAGATTGCCGCCGCTCAGAAGGTGTACGACGACAAGGATGCCAAGCAGGCCGATGTCGATGCCGCACAGGATGCCCTTGACAAGGCATTTTGGGCCACCAAGGTTGAGCAGAAGCCCGGCTCCCAGCAG CCTGGTTGACCGACACTGATAAGGATGATAAGGACAACAAGGGTGATCGTGCCTCCGACTGGTGCCGCGGTTTCCGTAGTTGCTGCGGCTGCCGTGCTGCTCACCGCCGCAGGCGTGACCATCCTGAAGCGTCGCCAGTCCGGCGACCACGGTTCGGCTCGCCACTCGGCCTGA

[0133] Preferably, the GH121 gene may encode the protein shown as SEQ ID NO: 18, or a sequence having at least 80% sequence identity to SEQ ID NO: 18. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 18.

[0134] Sequence ID 18

[0135] Preferably, the B. longum transitional strain comprises the GH43_17 gene and one or more genes selected from the GH43_22, GH43_27, GH43_29, and GH121 genes as defined herein.

[0136] Preferably, the B. longum transitional strain includes the GH43_17 gene, GH43_22 gene, GH43_27 gene, GH43_29 gene, and GH121 gene as defined herein.

[0137] Preferably, one or more of the arabinane-degrading GHs described herein include a signal peptide. A “signal peptide” can refer to a short amino acid sequence, typically located at the N-terminus of a polypeptide, that enables the polypeptide to be secreted extracellularly from a non-microbial cell (abacterial cell). While not wishing to be constrained by theory, this may advantageously allow the B. longum transitional strain of the present invention to act as a primary degrader of high molecular weight arabinane complex structures, which are normally present in food. Preferably, a “primary degrader” can refer to a bacterium capable of depolymerizing certain polysaccharides into monosaccharides, disaccharides, and oligosaccharides. Such bacterium can take in these monosaccharides, disaccharides, and oligosaccharides and ferment them into acidic end products, such as acetic acid or lactic acid. Preferably, the GH43_22 enzyme, GH43_27 enzyme, GH43_29 enzyme, GH_121 enzyme, GH43_24 enzyme, and / or GH30_5 enzyme may include a signal peptide. Preferably, each of the GH43_22 enzyme, GH43_27 enzyme, GH43_29 enzyme, GH_121 enzyme, GH43_24 enzyme, and GH30_5 enzyme may contain a signal peptide.

[0138] Preferably, the B. longum transitional strain of the present invention contains a glycosyl hydrolase family gene that encodes a CAZyme targeting arabinogalactan.

[0139] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 43_24 (GH43_24) gene. Preferably, the GH43_24 gene contains SEQ ID NO: 19 or a sequence having at least 60% sequence identity with SEQ ID NO: 19. Preferably, the GH43_24 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 19.

[0140] Sequence ID 19

[0141] Preferably, the GH43_24 gene may encode the protein shown as SEQ ID NO: 20, or a sequence having at least 80% sequence identity to SEQ ID NO: 20. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 20.

[0142] Sequence ID 20

[0143] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 127 (GH127) gene. Preferably, the GH127 gene contains SEQ ID NO: 21 or a sequence having at least 60% sequence identity to SEQ ID NO: 21. Preferably, the GH127 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 21.

[0144] Sequence ID 21

[0145] Preferably, the GH127 gene may encode the protein shown as SEQ ID NO: 22, or a sequence having at least 80% sequence identity to SEQ ID NO: 22. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 22.

[0146] Sequence ID 22 MNVTITSPFWKRRRDQIVESVIPYQWGVMNDEIDTTVPDDPAGNQLADSKSHAVANLKVAAGELDDEFHGMVFQDSDVYKWLEEAAYALAYHPDPELKALCDRTVDLIARAQQPDGYLDTPYQIKSGVWADRPRFSLIQQSHEMYVMGHYIEAAVAYHQVTGNE QALEVAKKMADCLDANFGPEEGKIHGADGHPEIELALAKLYEETGEKRYLTLSQYLIDVRGQDPQFYTKQLKALNGDNIFPDLGFYKPTYFQAAEPVRDQQTADGHAVRVGYLCTGVAHVGRLLGDRGLIDTAKRFWTNIVARRMYVTGAIGSTHVGESFTYDYD LPNDTMYGETCASVAMSMFAQQMLDLEPKGEYADVLEKELFNGSIAGISLDGKQYYYVNALETTPDGLDNPDRHHVLSHRVDWFGCACCPANIARLIASVDRYIYTERDGGKTVLSHQFIANTAEFASGLTVEQRSNFPWDGHVEYTVSLPASATDSSVRFGLR IPGWSRGSYTLTVNGKPAVGSLEDGFVYLVVNAGDTLEIALELDMSVKFVRANSRVRSDAGQVAVMRGPLVYCAEQVDNPGDLWNYRLADGVTGADAAVAFQADLLGGVDTVDLPAVREHADEDDAPLYVDADEPRAGEPATLRLVPYYSWANREIGEMRVFQRR

[0147] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 30_5 (GH30_5) gene. Preferably, the GH30_5 gene contains SEQ ID NO: 23 or a sequence having at least 60% sequence identity to SEQ ID NO: 23. Preferably, the GH30_5 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 23.

[0148] Sequence ID 23

[0149] Preferably, the GH30_5 gene may encode the protein shown as SEQ ID NO: 24, or a sequence having at least 80% sequence identity to SEQ ID NO: 24. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 24.

[0150] Sequence ID 24

[0151] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 43_32 (GH42_32) gene. Preferably, the GH42_32 gene contains SEQ ID NO: 25 or a sequence having at least 60% sequence identity to SEQ ID NO: 25. Preferably, the GH42_32 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 25.

[0152] Sequence ID 25

[0153] Preferably, the GH42_32 gene may encode the protein shown as SEQ ID NO: 26, or a sequence having at least 80% sequence identity to SEQ ID NO: 26. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 26.

[0154] Sequence ID 26 MTATISNGVSASYSPAEDELGAADPTALLAESGDLKPLAERTYTNPVPYADGKSHTAPDPFVLKYRDLYYCYATDEHGILVSTSPDMVHWTSHGFCYTEAGRRNFWAPSVILINGVFHMYFSNMPAEETDTHTEIMRVAVSEDPLGPFEKKAELFNTFAIDSQVVYGDDGQLYLLYAD NQVTGLSDDRPGTSVMIDRLVTPYSRENKPRPLIVPTMDEEIFARNRFGDGRDWHTVEGATYFAYRDRAFITYSANAYEHEDYFVGYSYAQLPNKQADAHIDQLDWTKQLNENRFDPLLIRSPKVEGTGHNSIVKAPNAVDDWIVYHGRNADDELYVGTEQRVMRIDPLYYAEGGLDT PGPTAAAQSAPLYGTVHDDFADGLNAGWSVISGAAHTESDVDGHALVADESSVFIAVSGKSSATQVIDVWAKAPVTPLGARFGIVVRYQDANNLTKLEVDAGRQVISVVDVIGGVASERVTNADLHDFDSHAWHEYRLERRYCRLEIRIDGRFAASCTISDKPGRAGLFSLRTGAAFS AYAATEHVNLWGAGLRDLGRELHADRRLVIDGGVRSSGVCPVTLELAYPLVSNRFVLDFAGQTSRGQALLSLGEYRLSGTASSVEFMRNGKSLPSTPEPARLRVFEDNVRRDRSGRAVLTIRIEALNGTMRLHLRGKTWQVPFADNAARARITLDRASLTGYERTSLESSIEERSASGN

[0155] Preferably, the B. longum transitional strain contains one or more genes selected from the GH43_24 gene, GH127 gene, GH30_5 gene, and GH43_32 gene as defined herein.

[0156] Preferably, the B. longum transitional strain comprises the GH43_17 gene and one or more genes selected from the GH43_24, GH127, GH30_5, and GH43_32 genes as defined herein.

[0157] Preferably, the B. longum transitional strain includes the GH43_17 gene, GH43_24 gene, GH127 gene, GH30_5 gene, and GH43_32 gene as defined herein.

[0158] Preferably, the B. longum transitional strain includes the GH43_17 gene, GH43_22 gene, GH43_27 gene, GH43_29 gene, GH121 gene, GH43_24 gene, GH127 gene, GH30_5 gene, and GH43_32 gene as defined herein.

[0159] Preferably, the transitional strains of B. longum include GH43_17, GH43_22, GH43_27, GH43_29, GH121, GH43_24, GH127, GH30_5, and GH43_32 as defined herein.

[0160] GH43_17 gene cluster Preferably, the B. longum transitional strain may contain one or more genes encoding family 31 glucosidase (GH31), ABC transporters, Lac-I type regulators, MFS transporters, and / or AraC family transcriptional regulators.

[0161] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 31 (GH31) gene. Preferably, the GH31 gene contains sequence number 27, or a sequence having at least 60% sequence identity to sequence number 27. Preferably, the GH31 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to sequence number 27.

[0162] Sequence ID 27

[0163] Preferably, the GH31 gene may encode the protein shown as SEQ ID NO: 28, or a sequence having at least 80% sequence identity to SEQ ID NO: 28. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 28.

[0164] Sequence ID 28 MTTSFTIDGNALIWTGDGETLRIEPWEENSVRVRATRNRGFGPVDWALLEPKNESGRVADIAVGEDGEHASLTNGSITVKADSNHAPLLSAGYETFRCDLSFWNAEGELLFREYPQGGSLLLKARDYTPVSGESFAVTTSFSADPKERLYGMGEYQQDVLDLKGSTFELAH RNSQASVPFVVSSKGYGFLWHNPAIGRATFGRNRTEWAAQSTDQIDYWVTAGDSYAQIESQYADATGHAPVMPEWGMGFWQCKLRYWNQEQLLDVARGFKSRNIPLDLIVIDFFHWPHLGDYKFEDEFWPDPEAMVAELNSMGVKLMVSVWPQVSVSSENFVEMKRNNYLVS AEAGLNLDMMFEEPCVNYDPTNPGARKFVWDKCKANYWDKGVRAFWLDEAEPEYGVYDFRNYRYHMGSDLNVGNVYPQAYNRGFYEGQIEAGMEGEIVNLTRCAWAGSQRYGSLVWSGDVGSTFADLKSQITCAIHMGMAGIPWFTTDMGGFHDGVIDSDSFKELLARWCAF SCFLPVMRNHGDRSLGESTGKQTITKATGEHRSPSGADNEPWSYGPEMESIFRKYIAVREVMRPYTRELFQSAHEQGQPLVRGLFYEFPTDEHVADIADEYLYGPDILVAPVVEAGAASRSVYLPGDETTTWTDLRDGAVYAGGQSIESSAAIDTVPAFARDGRDHGLIGLL

[0165] Preferably, the B. longum transitional strain of the present invention contains one or more ABC transporter genes. Preferably, the ABC transporter genes contain sequence numbers 29 to 31, or sequences having at least 60% sequence identity with sequence numbers 29 to 31. Preferably, the ABC transporter genes contain sequences having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with sequence numbers 29 to 31. Preferably, the B. longum transitional strain of the present invention contains a gene having at least 60% sequence identity with sequence number 29, a gene having at least 60% sequence identity with sequence number 30, and a gene having at least 60% sequence identity with sequence number 31.

[0166] Sequence ID 29 ATGACGCATCGTAGCACCTGGTGGAAAACCGCTCTCGGCATCATATTGACGCTCATCATGATGTTTCCTGTCTACTGGATGATCAACATCTCGTTCACTGGTAAGGCATCCATTCGTTCCGGCGACCTGTGGCCCAAGGATTTCACCTTTGACAACTACGCCCGCGTAATCGCGACCAAATGCCCTATCTGGGCACTTCCATC CTCGTAGCGGTATGCTGCGTGATTCTAACGCTGGTCATCGCACTGCCTGCCGCCTAGCACTGGCTTTGCTGCGCTGCAGCAGCGGCGCGCTCAGCTTCCTGCTCATCGTGGCTCAGATGATTCCCGCCGTCGTGATGTCGCTCGGCTTCTACGAGATTTATAACAACATTGGTCTGCTCGATACGTTGCCCGGCCTGAT CTCGCCGACTCGACCATTGCGGTGCCGTTCGCGGGTCATGCTCCTGACTTCTTCATGGCCGGCATCCCGCGGTCCCTGCTTGAGGCCGCCGAAGTGGATGGAGCCTCACGTACCCGTCGCTTTCTTCCATTGTCATCCCGTTATCGCGCAATTCGATCGTGACCGTCTCCCTGTTCGCTTTCCTATGGTCTGGAGCGACTTC CTGTTCGCTTCCACCCTTGACTCCGGCGGCGGCAAGATGCGCCCGATCACTATGGGTCTGTACAACTATATCGGTGCGCAGACCCAGGAATGGGGGCCGATGGCCACCGCAGTGCTTGCATCCATTCCCGCGACCATCCTGCTTGTCTTCGCCCAGAAGTACGTCGCCGCAGGCGTGACCGCCGGTGCTGTTAAGGACTAA

[0167] sequence no. 30 ATGACAGCCTCAACAAGAGCCCGTTCGCCGGGCAAAGTCCGGCACTCCGGTCCGGGCCAAACTGGCCATCGCCGGATTCATTGCCCCACTGATTATCTACTTGGTAATCTTTACGCGTTCCGCTCATCCAGAACGTGTCCAATGAGCCTGCACGATACACGCGACGAACCTTCGTTACCGGAGATGCGCTGTTCGTGGGTCTCGACATCTCAAAGGAAGTCATTCCT CCGTGGAGTTCTGGCCGGTTGTGGGGCAGACCTTCGTGTTCGTGGTCGTCTCGCTGATATTCCAATATGTAATCGGCTTGGCCCTGGCGGTGTTCTTCAACGATAACTTCAAGCTCTCGGTGTGCTGCGCGGCATCATGCTGGTTCCGTGGCTGTTGCCGCTGATTGTTTCTGGAACCGTCTGGCAGTGGATGGACCCTGACTCCGGCATCCTCAACATGTTCCTCGG CTGTTTGACATCGAACCCATCTGGTGGCTCCAGGCGATAACTCGCTGTGGGCCGTCATCATCGCCAACATCTGGCTGGGAATCCCCTTCAACCTCGTGATCCTGTATTCCGGCCTACAGAACATCAGCGGCGACCTGTATGAAGCCGCCTCCCTCGATGGCTGCAACGCCTGGCAGCGCTTCTGGAAGATCACCTTCCCTCTCTGAAGCCCGTCACTTCGATCACCCTGT TGCTCGGCTTCGTCTATACATTGAAGGTCGTTGACGTGATCTGGATGATGTCCCAGGGAACCGGCACCTCGCGTACCCTCGCCACCTGGGCCTTATTCGATGGCATTTGGCAAGGGAACTTCCAATGACTATCAAATACTCGGAGGCTTCGGTGCTCGCACGATTCTCATCATCGTGGCGTTGATTTTCGGACTGATTTACCTGCGGGTCCAGAAGACCCAGGAAACCTGCTAA

[0168] sequence number 31

[0169] Preferably, the ABC transporter gene may encode a protein represented as SEQ ID NOs. 32 to 34, or a polypeptide having at least 80% sequence identity to SEQ ID NOs. 32 to 34. Preferably, this gene may encode a polypeptide having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NOs. 32. Preferably, this gene may encode a polypeptide having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NOs. 33. Preferably, this gene may encode a polypeptide having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NOs. 34.

[0170] Sequence ID 32 MTHRSTWWKTALGIILTLIMMFPVYWMINISFTGKASIRSGDLWPKDFFTFDNYARVIADQMPYLGTSILVAVCCVILTLVIALPAAYALALLRCPGSGALSFLLIVAQMIPAVVMSLGFYEIYNNIGLLDTLPGL ILADSTIAVPFAVMLLTSFMAGIPRSLLEAAEVDGASRTRRFFSIVIPLSRNSIVTVSLFAFLWSWSDFLFASTLDSGGGKMRPITMGLYNYIGAQTQEWGPMMATAVLASIPATILLVFAQKYVAAGVTAGAVKD

[0171] Sequence ID 33 MTASTTSPVRRAKSGTPVRAKLAIAGFIAPLIIYLVIFYAFPLIQNVSMSLHRYTRRTFVTGDALFVGLDIYKEVISSVEFWPVVGQTFVFVVVSLIFQYVIGLALAVFFNDNFKLSGVLRGIMLVPWLLPLIVSGTVWQWMMDPDSGILNMFL GLFDIEPIWWLQADNSLWAVIIANIWLGIPFNLVILYSGLQNISGDLYEAASLDGCNAWQRFWKITFPLLKPVTSITLLLGFVYTLKVVDVIWMMSQGTGTSRTLATWAYSMAFGKGTSMTIKYSEASVLGTILIIVALIFGLIYLRVQKTQETC

[0172] Sequence ID 34 MKSNTALKITAALCSCAMLVGVSACGSSNSTTDDKVIEWWDDWTRHEDGSEFDKLVKACAPEGYTIERQAIATSDLLNNLTTAIKEDNGPDVAVIDNPMIPSAVDAGLVAGSDETGLDVSAWDENLEAPGVVDGQAYGVPLGGSNTLGLMYNPTIIEAAGVDVSTITDWDSLNAAIKKVVDAGYKGITFSGISGEE GVFQFLPWFWGAGGDLSKLDSQAQKDAEDLLSGWISKGWAPKSATTNTQSASWDLFLAGDYGFAEIGTWMQSEADEAGAKLIPIPAKDGGVATVPTGGEFAMVAYHKKDAESHYKLANQVIECLSEDETLLKVSNALSNLAAKKAVRAEQLAASDGLAQWKESIENAAGRTSDLGLKYEEASASISESLLAALNAA

[0173] Preferably, the B. longum transitional strain of the present invention contains a Lac-I type regulatory factor gene. Preferably, the Lac-I type regulatory factor gene contains SEQ ID NO: 35 or a sequence having at least 60% sequence identity with SEQ ID NO: 35. Preferably, the Lac-I type regulatory factor gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 35.

[0174] Sequence ID 35

[0175] Preferably, the Lac-I type regulatory factor gene may encode a protein represented as SEQ ID NO: 36, or a sequence having at least 80% sequence identity to SEQ ID NO: 36. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 36.

[0176] Sequence ID 36 MVTINDVAREAGVSKTTVSFVLSGSRPVAAATEQRIREAMDRLGYTVNHAARSLSTSKTMTIAVVTSNRQDAYFDIARGTYINGLSRAAAETGYDMLITNDPDGSATENACQSHKADGLVFLDVRQNDPRVPIAAESGIPTVSLGVPVNPMNLDVVDTDFTDMAAST MRTLHDAGHRRVSVITLSSRVIAEQLNDTARFLEIERSGERLGMHATIRHCSTRPGIIDTDIARILDGRGEDTAFVIHNESAVLVFRRAVEHRGLRIPEDISVIAINEKQMSDALYLPYSAYENDVELVTQSAVNTLVDRIEHPELTPTRTLIKASYIDRDSVANI

[0177] Preferably, the B. longum transitional strain of the present invention contains an MFS (facilitator superfamily) gene. Preferably, the MFS gene contains SEQ ID NO: 37 or a sequence having at least 60% sequence identity to SEQ ID NO: 37. Preferably, the MFS gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 37.

[0178] Sequence ID 37

[0179] Preferably, the MFS gene may encode the protein shown as SEQ ID NO: 38, or a sequence having at least 80% sequence identity to SEQ ID NO: 38. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 38.

[0180] Sequence ID 38 MAEFHYAIGHFHCAGHRIGCSGIPGQLALQRADDCFGITLTALVGAWLTGKLASILSRKTVALIGAGGMLLFGLLPYFVHSSLAAVIAFSALMGVCLGFINNVLPTLISVHYEGDERQSIMGQQVAVASIGAMVFMTVAGKLATAQWYHAYLIYLFAAVVLVVCAFTLPTKNGETDEAGRIQGTGPSASIR EVMTGKLWFLVVAGFFFLLANNAYSNNLSLLVEQRGLGDAGTAGLISTIGQFGGLLAGLCVGLMVRFVKNHLLMVGFIVEGLSLLLLGCSASLPLLIIGSFFAGAGLSIYYAQAPFLVTVIEKPYLIPLGIAAMTTANALGGFASPVLVNAINGLFGSHAAGAMFIGAAIALAGAVALGVSGFQKKCLESAK

[0181] Preferably, the B. longum transitional strain of the present invention contains an AraC family transcription factor gene. Preferably, the AraC gene contains SEQ ID NO: 39 or a sequence having at least 60% sequence identity to SEQ ID NO: 39. Preferably, the AraC gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 39.

[0182] Sequence ID 39 ATGGAGCGCGATGCTTTCCGGCTGCCGGGCCTCACCGCCGGCGATGACAACCAGTATGCCGATCACACGCTCACCGGCATGGCAGCCGATGCGGCGAACGTCATAGCCGCAGGCGGTCCCGCCCCGCTGACTAGCTTCGGCACTGTCGCTCAAGCCGCCCATCTCAATCCAGATGACGGCTTCGGCATCATTGGCCATGATCTTGCACACCCATCGCACCTACACCGGCATGACTATATGGAAATCACGCACGCCATCGCCGGTACGGTACTGGTCTGGGTCGAAGGAGAGACCAACGTGCTGACACAGGGCGGCACCATACTCATCAAGCCTGGAGCCCGTCATCTCATCTCCCCCATCATCGAATACGGGCAAACACCACACGAGGCGGACATCCTGATTAAACCCGAGCTCATCAGGCAATGCCGCATTCCGATTCTGGAAGCAGCCGGCGCCGACCGGATGTTCATTAGCTGGCTTGACGATGACCGGCAGACCCACTGCCTGCTGGCAGCCGGCAAGCACCACGCCGGCGAGGCCGCTATCAGCCGCATGTTCATCGCCTACTGCATCAACGCAACCTACAGGCCAGACTTCACCGTCATCGGCAACCTGCTCGAGCTGTTCCACGAAACGTCCCGAGTCTTGGAACACCAGCCACGTACCGATCCGCTGATCGCCGCCATCATCGAAACCATCACGGCAGATCCCGCCACGGCCCACAACCAGGCCATAGCGGACACACTTGGATACAGCGTGGGATATCTGTCCCGGTACGCGCGCAAGCACAGCGGGCACACACTCGGCCAACTCATCAACGAGGAAAGGCTCCGACTCGGCGCCGAACTGCTCGTCACCACCGACGACACCATTGCCGAAATCACCCGAACCATTGGCTACGAAAGTCCAGCCTATTTCCATAAACTCTTCCGCAGCCGCTACCTCATTACCCCCGACCGCTACCGCAACGACTTCCGTATCGCATTACGTTGCGGATGA

[0183] Preferably, the AraC gene may encode the protein shown as SEQ ID NO: 40, or a sequence having at least 80% sequence identity to SEQ ID NO: 40. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 40.

[0184] Sequence ID 40 MERDAFRLPGLTAGDDNQYADHTLTGMAADAANVIAAGGPAPLTSFGTVAQAAHLNPDDGFGIIGHDLAHPSHLHRHDYMEITHAIAGTVLVWVEGETNVLTQGGTILIKPGARHLISPIIEYGQTPHEADILIKPELIRQCRIPILEAAGADRMFISWLDDDRQT HCLLAAGKHHAGEAAISRMFIAYCINATYRPDFTVIGNLLELFHETSRVLEHQPRTDPLIAAIIETITADPATAHNQAIADTLGYSVGYLSRYARKHSGHTLGQLINEERLRLGAELLVTTDDTIAEITRTIGYESPAYFHKLFRSRYLITPDRYRNDFRIALRCG

[0185] Preferably, the B. longum transitional strain contains MFS transporter genes and AraC family transcription factor genes.

[0186] Preferably, the B. longum transitional strain contains the GH43_17 gene, the MFS transporter gene, and the AraC family transcription factor gene. Preferably, the GH43_17 gene, the MFS transporter gene, and the AraC family transcription factor gene are included in a gene cluster.

[0187] As used herein, "gene cluster" may refer to a group of genes located adjacent to each other within a chromosome.

[0188] Preferably, the B. longum transitional strain contains each of the following: the GH31 gene, the ABC transporter gene, the Lac-I type regulatory factor gene, the MFS transporter gene, and / or the AraC family transcription factor gene.

[0189] Preferably, the B. longum transitional strain contains the GH43_17 gene, MFS transporter gene, AraC gene, GH31 gene, ABC transporter gene, and Lac-I type regulatory factor gene. Preferably, the GH43_17 gene, MFS transporter gene, AraC family transcription factor gene, GH31 gene, ABC transporter gene, and Lac-I type regulatory factor gene are included in the above aa gene cluster.

[0190] Preferably, the B. longum transitional strain further comprises a xylulose kinase gene and / or a xylulose isomerase gene. Preferably, the xylulose kinase gene and / or xylulose isomerase gene are included in the gene cluster defined above.

[0191] Preferably, the xylulose kinase gene contains SEQ ID NO: 41 or a sequence having at least 60% sequence identity with SEQ ID NO: 41. Preferably, the xylulose kinase gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 41.

[0192] Sequence ID 41

[0193] Preferably, the xylulose kinase gene may encode the protein shown as SEQ ID NO: 42, or a sequence having at least 80% sequence identity to SEQ ID NO: 42. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 42.

[0194] Sequence ID 42 MTRVLVAGVDTSTQSTKVRITDAATGEQVRFGQAKHPDGTSVNPEFWWEAFTKAAEQAGGLDDVAALAVGGQQHGMVILDKQGNVIRDAMLWNDTSSAPQAAALIDKLGATPAEGDEPDDVTARGK QRWVKAVGSSPVASYTLTKVAWVAENEPENAKKIAAVCLPHDWLSWRIAGYGPVAEGEDAHLEALFTDRSDASGTIYYDAAHDEYRRDLIAMVLTPAEGEEAAKAHADAIVLPTVLPGHEAAAVKAD PAIAGKDVEGGCIIGPGGGDNAMASLGLGMAVGDVSVSLGTSGVAAAIAENPVYDLTGAISGFADCTGHYLPLACTINGSRILDAGRAALGVDYDELAELAFKAEPGAGGITLVPYFDGERTPNRP DATASLTGLTLHNTTKENLAAFVEGLLCSQRDCLELIRSLGAENRILLIGGGAKSVAIRTLAPSILGMDVTRPATDEYVAIGAARQAAWVLSGEAEPLTWQLTIEGVETGEPTEAVYEAYAKARG

[0195] Preferably, the xylose isomerase gene contains SEQ ID NO: 43 or a sequence having at least 60% sequence identity with SEQ ID NO: 43. Preferably, the xylose isomerase gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity with SEQ ID NO: 43.

[0196] Sequence ID 43

[0197] Preferably, the xylose isomerase gene may encode the protein shown as SEQ ID NO: 44, or a sequence having at least 80% sequence identity to SEQ ID NO: 44. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 44.

[0198] Sequence ID 44 MGLWDVDKIEYVGRAKGPKEDFAFHYYDADKVVAGKKMKDWLRFGVAWWHTFNQELVDPFGTGTAHRPYYKYTDPMDQALAKVDYAFELFQKLGVEYFCFHDRDIAPEGDTL RETNANLDKVVDKIDENMKSTGVKLLWNTSSLFTNPRFVSGAATSPFADIYAYAGGQLKKSLEIGKRLGAENYVFWGGREGYENLWNTEMKRETDHIAKFFHMCADYAKEIG FEAQFLIEPKPKEPTLHQYDFDAATAIEFLRNHDLTDVFKLNLEGNHANLAGHTYQHEIRVARESGFLGSLDANQGDKLIGWDMDEFPTDLYETVAVMWEVLQAGSIGPHGG LNFDAKPRRTSFYEEDLFRSHIAGMDAYAAGLLVADKMNQDGFIQNLQAERYSSYDSGIGKDIDEGNVTLADLEAYSLDKPQSELIAATKSDHLESVKATINNYIIDALAEVE

[0199] Human milk oligosaccharides (HMOs) Preferably, this B. longum transitional strain preferentially utilizes 3-fucosyl lactose (3-FL) compared to other B. longum transitional strains, as demonstrated by better growth, for example, as shown in the examples of the present invention.

[0200] Preferably, the transitional strain of B. longum may have a growth rate of at least 0.6 k when cultured in the presence of 3-FL. Preferably, the transitional strain of B. longum may have a growth rate of at least 0.7 k, at least 0.8 k, or at least 0.9 k when cultured in the presence of 3-FL. The growth rate can be calculated by culturing the bacteria in a given substrate or mixture of substrates for a certain period of time and modeling the growth curve using a logistic growth model to obtain the relative growth rate k. An exemplary method for calculating the growth rate is provided in this embodiment. While we do not wish to be bound by theory, preferential growth in 3-FL is considered advantageous because the level of 3-FL increases in human breast milk during the weaning period. Preferential growth in 3-FL suggests that the transitional strain of B. longum of the present invention may be particularly well-suited for survival and growth in the microbiome during the weaning period.

[0201] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 25 (GH25) gene. Preferably, the GH25 gene contains SEQ ID NO: 45 or a sequence having at least 60% sequence identity to SEQ ID NO: 45. Preferably, the GH25 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 45.

[0202] Sequence ID 45

[0203] Preferably, the GH25 gene may encode the protein represented as SEQ ID NO: 46, or a sequence having at least 80% sequence identity to SEQ ID NO: 46. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 46.

[0204] Sequence ID 46 MSNPTNDGINLNYLANVRPSSRQLVWQRMEMYAFIHFGMNTMTDREWGLGHEDPALFDPQNVDVEQWMDALVAGGMTGVILTCKHHDGFCLWPSRYTQHTVAASPWRDGKGDLVREVSE SARRHGLKFGVYLSPWDRTEESYGKGKAYDDFYVGQLTELLTQYGPIFSVWLDGANGEGKNGKTQYYDWDRYYNVIRSLQPNAVISVCGPDVRWAGNEAGHVRDNEWSVVPRRLRSAELT MENSQQEDDASFASTVRSQDDDLGSREAVSGYGDDVCWYPAEVDTSIRPGWFYHKYEDDKVMSADQLFDLWLSAVGGNSSLLLNIPPSPEGLFAEPDVESLKGLGSRINEFRKALASSC CEVKTSSADETAMRLLDGNQDTYWSPDANDVAPAVTLTFPQLTTINAVVVEEAIEYGQRIEHMRVTGVLSDGTECVLGQFGTVGYRRILRFDDVEVSSVTLHVDDSRFTPMISRAAAVRI

[0205] Preferably, the B. longum transitional strain of the present invention contains the glycosyl hydrolase family 95 (GH95) gene. Preferably, the GH95 gene contains SEQ ID NO: 47 or a sequence having at least 60% sequence identity to SEQ ID NO: 47. Preferably, the GH95 gene contains a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 47.

[0206] Sequence ID 47

[0207] Preferably, the GH95 gene may encode the protein represented as SEQ ID NO: 48, or a sequence having at least 80% sequence identity to SEQ ID NO: 48. Preferably, this protein may contain a sequence having at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity to SEQ ID NO: 48.

[0208] Sequence ID 48 MKLTFDGISSCWEEGIPLGNGRMGAVLCSEPETDVLYLNDDTLWSGYPHAETSPVTPEIVAKARQASLQDDYTAATRIIKEATLQEKDEQIYEPFGTARIQYSTPADGRESMKRQLDLARALAGETFQMGDANVHVDAWCSEPDDLLVYRMSSDAPVDVNISVAGTFLKQSRASLETVSDGHRATLVVMGRMPGL NIGLLPHPSEHPWEDEQDGTGMAYAGAFSLTVTGGDINVDDNSLQCSHITGLSLRFRSMSGFKGSDQQPERSMTVIADHLEKTIDEWSTDLQTMLDRHIADYRRYFDRVAIHLGSAHDDDTELPFSAILRSDENKEPHRLEMLAEAMFDFGRYMLISSSRPHTQPANLQGIWNHKDFPNWYSAYTTNINVEMNYWM TGPCALKELIEPLVSMNEELLAPGHDAADRILGCRGSAVFHNVDLWRRALPANGDPMWAFWPFGQAWMCRNLFDEYLFNQDASYLARIWPIMRDNARFCMDFLSETEHGLAPSPATSPENCFLVNGEPVSVAQSSENATAIVRNLLDDLIQASHDLENLDEEDRNLVREAESVRSQLAETRLGADGRVLEWNDEFI ESDPQHRHLSHLYELHPGAGITSKTPRLEEAARKSLEVRGDDGSGWSIVWRMIMWARLRDAEHAKRIIGMFLRPVDANAETNLLGGGVYDSGLCAHPPFQIDGNLGFPAALSEMLVQSHDGWIRVLPALPEDWHEGSFHALRARGGIQVDATWTDQTVEYTLRCSKPTEITLNVLGTDMGRVALSPDKPFKGTIRR

[0209] Preferably, the B. longum transitional strain of the present invention may contain the GH25 gene and the GH95 gene as defined herein.

[0210] Embodiment The present invention provides embodiments that comply with the following numbered clauses.

[0211] 1. A Bifidobacterium longum transitional microbial strain deposited with the Collection nationale de cultures de micro-organismes (CNCM) under deposit number CNCM I-5942, or a B. longum transitional strain possessing the distinguishing characteristics of the B. longum transitional strain deposited under deposit number CNCM I-5942.

[0212] 2. A transitional B. longum microbial strain having at least 99% mean base identity (ANI) to the B. longum strain deposited with CNCM under depositary number CNCM I-5942.

[0213] 3. B. longum transition strains as described in Clause 1, having at least 98.1% ANI compared to B. longum transition strains deposited under deposit number CNCM I-5942.

[0214] 4. The transitional B. longum strain described in any one of clauses 1 to 3, wherein the transitional B. longum strain is resistant to both tetracycline and erythromycin.

[0215] 5. The transitional B. longum strain described in any one of clauses 1 to 4, wherein the transitional B. longum strain is resistant to tetracycline, erythromycin, clindamycin, and ampicillin.

[0216] 6. The B. longum transitional strain described in any one of clauses 1 to 5, wherein the B. longum transitional strain is resistant to tetracycline, erythromycin, clindamycin, ampicillin, gentamicin, streptomycin, chloramphenicol, and vancomycin.

[0217] 7. (i) The lack of resistance to tetracycline is due to the absence of a tetracycline resistance gene, preferably the tetW gene encoding a protein having at least 80% sequence identity to SEQ ID NO: 1 and / or the tetQ gene encoding a protein having at least 80% sequence identity to SEQ ID NO: 2. (ii) The lack of resistance to erythromycin is due to the absence of an erythromycin resistance gene, preferably the Erm49 gene which encodes a protein having at least 80% sequence identity with SEQ ID NO: 3. (iii) The lack of resistance to erythromycin and / or clindamycin is due to the absence of the corresponding resistance gene, preferably the Erm(X) gene which encodes a protein having at least 80% sequence identity with SEQ ID NO: 4, and / or (iv) A transitional B. longum strain according to any one of clauses 1 to 6, wherein the lack of resistance to chloramphenicol is due to the absence of a chloramphenicol resistance gene, preferably a CrmX gene encoding a protein having at least 80% sequence identity with SEQ ID NO: 6.

[0218] 8. The B. longum transitional strain according to any one of the clauses 1 to 7, wherein the B. longum transitional strain comprises the glycosyl hydrolase family 43_17 (GH43_17) gene, and preferably the GH43_17 gene comprises SEQ ID NO: 7 or a sequence having at least 60% sequence identity with SEQ ID NO: 7.

[0219] 9. A B. longum transitional strain according to any one of the clauses 1 to 8, further comprising an MFS (major facilitator superfamily) gene, preferably wherein the MFS gene comprises SEQ ID NO: 37 or a sequence having at least 60% sequence identity with SEQ ID NO: 37.

[0220] 10. A B. longum transitional strain according to any one of the clauses 1 to 9, further comprising the AraC gene, preferably the AraC gene comprising SEQ ID NO: 39 or a sequence having at least 60% sequence identity with SEQ ID NO: 39.

[0221] 11. The B. longum transitional strain described in Clause 10, wherein the GH43_17 gene, the MFS gene, and the AraC gene are included in the gene cluster.

[0222] 12. The B. longum transitional strain according to any one of the B. longum transitional strains further comprising one or more of the GH31 gene and the LacI gene, preferably further comprising a xylulose kinase gene and a xylulose isomerase gene.

[0223] 13. The B. longum transitional strain according to Clause 12, wherein the GH43_17 gene, the MFS gene, the AraC gene, the GH31 gene, and the LacI gene are included in the gene cluster, preferably the GH43_17 gene, the MFS gene, the AraC gene, the GH31 gene, the LacI gene, the xylulose kinase gene, and the xylulose isomerase gene are included in the gene cluster.

[0224] 14. A B. longum transitional strain as described in any one of clauses 1 to 13, further comprising one or more genes encoding one or more glycoside hydrolases selected from GH43_17, GH43_22, GH43_27, GH43_29, GH121, GH43_24, GH127, GH30_5, GH43_32, and GH30.

[0225] 15. A transitional strain of B. longum described in any one of clauses 1 to 14, further comprising the GH29 gene and the GH95 gene.

[0226] 16. The B. longum transition strain described in any one of clauses 1 to 15, wherein the B. longum transition strain preferentially utilizes 3-fucosyl lactose (3-FL).

[0227] 17. The B. longum transitional strain according to any one of the clauses 1 to 16, wherein the B. longum transitional strain has a growth rate of at least 0.6 k when cultured in the presence of 3-FL.

[0228] 18. A composition comprising the transitional strain of B. longum described in any one of Clauses 1 to 17, wherein the composition is a probiotic composition.

[0229] 19. A composition comprising a B. longum transitional strain as described in any one of clauses 1 to 18, and at least one further probiotic and / or prebiotic.

[0230] 20. Use of the B. longum transitional strain or composition described in any one of claims 1 to 19 as a nutritional supplement, wherein the B. longum transitional strain or composition is administered to a subject in combination with a fiber-containing diet or fiber-containing food.

[0231] 21. Use of B. longum transitional strain or composition as described in any one of Clauses 1 to 19 to promote and / or support the metabolism of fiber-containing foods or dietary fiber by the subject.

[0232] 22. A method for promoting and / or supporting the metabolism of a fiber-containing diet or fiber-containing food by a subject, comprising administering to the subject a transitional strain or composition of B. longum described in any one of the clauses 1 to 19.

[0233] 23. Use of B. longum transition strain or composition as described in any one of Clauses 1 to 19 to promote and / or assist the transition from milk-based food to solid food in infants and / or toddlers.

[0234] 24. A method for promoting and / or assisting the transition from milk-based food to solid food in infants and / or toddlers, comprising administering to the infant and / or toddler a B. longum transition strain or composition described in any one of Clauses 1 to 19.

[0235] 25. The use described in Clause 20, 21, or 23, or the method described in Clause 22 or 24, wherein the transitional B. longum strain is administered in combination with a prebiotic.

[0236] 26. The composition according to Clause 19 or the use or method according to Clause 25, wherein the prebiotic is fiber and / or human milk oligosaccharide (HMO), preferably the HMO is 3-FL. [Examples]

[0237] The present invention will be further illustrated with reference to the following examples. It will be understood that the claimed invention is not intended to be limited by these examples.

[0238] Example 1 - Isolation and phylogenetic identity of strain NCC5025 The transitional strain of B. longum, NCC5025, was isolated at Nestle Research from the feces of weaned infants aged 6–12 months. NCC5025 was obtained from fecal samples by culturing on Eugon tomato agar, then preliminaryly identified using MALDI-ToF MS (Biotyper, Bruker Scientific Instruments, Billerica, USA), and confirmed by sequencing. The isolate was deposited as NCC5025 in the Nestle Culture Collection (Nestle Research, Lausanne, Switzerland) and further deposited as CNCM I-5942 in the "Collection Nationale de Culture Microorganismes" (CNCM, Paris, France). PacBio sequencing of NCC5025 was performed according to the supplier's recommendations. The sequencing data were further assembled using the Hierarchical Genome Assembly Process (HGAP4) de novo assembly analysis application provided by the SMRT Link portal (Pacific Biosciences, Menlo Park, USA). The resulting sequences were compared to publicly available B. longum samples using mean nucleotide identicality (ANI) calculated with OrthoANIu v1.2 (Yoon et al., 2017). The generated matrix for pairwise genome similarity was further used to construct a UPGMA phylogenetic tree using BioNumerics software (v8.0, bioMerieux SA, Marcy l'Etoile, France). The analysis revealed that NCC5025 belongs to the transitional group of B. longum, as it clustered with other strains of this newly described putative subspecies (Vatanen et al.; Cell; 2022 Nov 10; 185(23): 4280-4297. e12).Phylogenetically, NCC5025 lies between strains isolated in China (e.g., JDM301;CMCCP001) and strains isolated in Bangladesh (NCC5000-NCC5004), sharing a mean base pair (ANI) of 98.4% with the latter group of strains (see Figure 1).

[0239] Example 2 - Profiling of antibiotic resistance In accordance with EFSA recommendations (EFSA J 16,e05206,doi:10.2903 / j.efsa.2018.5206(2018)), phenotypic antibiotic testing of transitional strains of B. longum was performed according to the official method ISO 10932. As required by ISO method 10932, B. longum ATCC15707 was used as an internal control. The minimum inhibitory concentration (MIC) obtained for this control strain was within the established range for this strain (see the annex to the ISO method). The obtained MICs were compared to EFSA applicable thresholds (EFSA Journal 2012 Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance) to assess susceptibility or resistance phenotypes to a range of relevant antibiotics. Table 1 shows the MICs obtained for B. longum transition strains NCC5000, NCC5001, NCC5002, NCC5003, NCC5004, and NCC5025.

[0240] The results indicated that most strains appeared to be resistant to several antibiotics considered important for EFSA. B. longum transitional strains NCC5000 and NCC5001 appeared to be resistant to erythromycin and clindamycin. NCC5003 appeared to be resistant to tetracycline, erythromycin, and clindamycin. NCC5004 appeared to be resistant to tetracycline, erythromycin, clindamycin, and ampicillin. Similarly, B. longum transitional strain NCC5002 showed resistance to tetracycline.

[0241] B. longum transitional strain NCC5025 was the only strain that was susceptible to all antibiotics considered associated by EFSA, namely gentamicin, streptomycin, tetracycline, erythromycin, clindamycin, ampicillin, and vancomycin.

[0242] [Table 1]

[0243] Example 3 - Profiling of carbohydrate-related enzyme (CaZy) The dbCAN3 tool (Yin et al., 2012; Zhang et al., 2018) and the databases HMMdb (v10) and DIAMOND (v 2.0.14) were used to annotate transitional strains of B. longum for CAZyme. Query sequences with coverage greater than 0.50 and an e-value less than 1e-15 were annotated using HMMER according to the dbCAN CAZyme domain HMM database. DIAMOND was also used to annotate query sequences that hit the CAZy database (Lombard et al., 2014) (http: / / www.cazy.org / ) based on identity greater than 0.90 and an e-value less than 1e-100. In cases where the CAZyme annotation of query sequences did not match between the HMMER and DIAMOND tools, the HMMER annotation was used preferentially. Only the CAZyme family and subfamilies encoding glycoside hydrolases (GH) and polysaccharide lyases (PL) were used for the comparative analysis of the B. longham clade.

[0244] All genes predicted as CAZyme by dbCAN3 were further analyzed for their estimated extracellular activity. For this purpose, signal peptides were predicted using DeepSig (Savojardo et al; Bioinformatics, 34(10), 2018, 1690-1696), a deep convolutional neural network trained with the widely known SignalP (v4.0) (Petersen et al.; Nat Methods; 2011 Sep 29; 8(10): 785-6), and tested on UniproKB. This network incorporates the N-terminus of the input sequence with a threshold of 21 residues. This input is then transferred to a feature extraction module, which then outputs a binary output (yes / no) for signal peptide prediction.

[0245] Analysis revealed that NCC5025 possesses a unique enzyme setup compared to other genomes within the B. longum transitional clade. Specifically, NCC5025 is the only strain possessing glycosylhydrolase (GH) family 43 subfamily 17 (GH43_17) that encodes enzymes with both α-L-arabinofuranosidase (EC3.2.1.55) activity and endo-β-1,4-xylanase (EC3.2.1.8) activity, and the ability to degrade complex carbohydrates such as arabinan, arabinogalactan, and arabinoxylan. To date, the only enzyme activity of GH43_17 that has been evaluated is from Bacteroides intestinalis (Pereira et al.; Nat Commun. 2021 Jan; 12(1): 459.) and Caldicellulosiruptor owensensis (Helbert et al; 2019; 116(13); 6063-6068).

[0246] Overall, among the B. longum transitional strains, NCC5025 possesses a unique CAZyme profile. The genome of NCC5025 encodes five different arabinan-targeting CAZymes (GH43_22, GH43_27, GH43_29, GH121, and GH43_17, unique to this strain), while UCD399 and BSM11-5 encode four, and other B. longum transitional genomes encode three or fewer of these CAZymes (Figure 2). Furthermore, four of the five arabinan-degrading CAZymes present in NCC5025 possess signal peptides, which generally give the bacterium an advantage as a primary degrader of the complex structure of arabinan, which is present in the diet at high molecular weight (Figure 2).

[0247] The B. longum transitional strain NCC5025 also encodes five different CAZymes (GH43_24, GH127, GH30_5, GH43_32, and GH43_17) that target arabinogalactan, two of which possess signal peptides. Furthermore, NCC5025, like NCC5000 and UCD399, contains three genes encoding the inulin-degrading CAZyme (GH32). Other B. longum transitional strains possess two or fewer GH32-coding genes, which results in a lower efficiency of their utilization of environmental inulin (Figure 2).

[0248] The B. longum transitional strain NCC5025 also contains several enzymes involved in the degradation and metabolism of human milk oligosaccharides (HMOs). NCC5025 contains the enzymes GH20 (lacto-N-biosidase) and GH112 (lacto-N-biose phosphorylase) and several types of GH42 (β-galactosidase), which are involved in the degradation and metabolism of lacto-N-tetraose (LNT) and its subcomponents. The NCC5025 strain also possesses GH29 and GH95 (fucosidases) which encode genes involved in the degradation and metabolism of fucosylated human milk oligosaccharides, such as 2'FL, 3'FL, or diFL. In summary, the B. longum transitional strain NCC5025 can function as a primary degrader of arabinan, arabinogalactan, and inulin, thanks to its unique CAZyme repertoire, including the exclusive presence of GH43_17. Carbohydrate blends containing arabinan in combination with arabinogalactan, inulin, or fucosylated HMOs can give NCC5025 an advantage in growing and producing beneficial metabolites.

[0249] Example 4 - GH43_17 coding gene cluster of NCC5025 By aligning all available genomes of the B. longum transitional strain using BioNumerics software (v8.0, bioMerieux SA, Marcy l'Etoile, France), we identified that the GH43_17 gene of NCC5025 is located in a gene region unique to this strain. This unique region contains the family 31 glucosidase (GH31; NCC5025_001581), followed by ABC transporters (NCC5025_001580-001578), Lac-I type regulators (NCC5025_001577), the GH43_17 enzyme (NCC5025_001576), the MFS transporter (NCC5025_001575), and the AraC family transcription regulator (NCC5025_001574) (see Figure 3 and Table 2).

[0250] [Table 2]

[0251] Further BLASTn analysis of all genes contained in this region using BioNumerics software (v8.0, bioMerieux SA, Marcy l'Etoile, France) revealed that the Lac-I type regulator (CDS_000417), GH43_17 enzyme (CDS_000418), MFS transporter (CDS_000419), and AraC family transcription regulator (CDS_000420) do not have homologs in other strains of the Bl subspecies Juvenis. Three closely related isolates, JDM301, BXY01, and CMCC P001, showed homologs with relatively low similarity (up to 80% coverage / 60% identity) to the genes encoding family 31 glucosidase (GH31;CDS000413) and ABC transporters (CDS_000414~00416).

[0252] Example 5 - NCC5025 exhibits a high growth rate in 3-FL. Transitional strains of B. longum were obtained from the Nestle Culture Collection and reactivated from lyophilized stocks using two consecutive culture cycles (16 hours, 37°C, anaerobic environment) in 0.05% cysteine-supplemented MRS (MRSc) medium. The reactivated cultures were then centrifuged, washed, and resuspended in 1:1 volume of PBS. The washed cells were inoculated into a carbon-source-free MRS-based medium (MRSc-C) (10 g / L bacto proteose peptone n°3, 5 g / L bacto yeast extract, 1 g / L Tween 80, 2 g / L diammonium hydrogen citrate, 5 g / L sodium acetate, 0.1 g / L magnesium sulfate, 0.05 g / L manganese sulfate, 2 g / L disodium phosphate, 0.5 g / L cysteine) with 3-FL added at a final concentration of 0.5% as the sole carbon source. Next, growth was carried out in a 96-well microplate with each well having a volume of 200 μL. Incubation was performed under anaerobic conditions for 46 hours, during which the optical density was measured at 580 nm using a spectrophotometer. Then, the growth curve was modeled using a logistic growth model to obtain the relative growth rate k for each manifold.

[0253] Among all B. longum transitional strains tested, NCC5025 exhibited the highest growth rate against 3FL, suggesting that this strain is best suited to this substrate (see Figure 4). 3-FL has been shown to be the human milk oligosaccharide that shows the greatest increase in human breast milk during the transition period between milk-based and solid foods (Plows, JF, et al., Longitudinal Changes in Human Milk Oligosaccharides (HMOs) Over the Course of 24 Months of Lactation. J Nutr, 2021. 151(4):p.876-882). Therefore, these results demonstrate the advantage of NCC5025 for application during this period.

[0254] Example 6 - Growth of NCC5025 in high molecular weight dietary fiber The inventors tested whether strain NCC 5025 has the ability to grow on the associated high molecular weight fibers. For the purpose of the test, 5 g / L% arabinan (arabinan derived from Megazyme sugar beet pulp) or inulin (Beneo's Orafti HSI) was added to the above-mentioned sugar-free MRSc medium, and selected transitional B. longum strains (NCC5002, NCC5004, and NCC5025, respectively) were grown. The growth assay was performed for 50 hours using a BioLector XT microbioreactor system (m2p-labs GmbH, Baesweiler, Germany) with a 48-well flower plate inserted into an anaerobic chamber (2 mL volume per well, stirred at 600 rpm, CO2 atmosphere, 37°C). Growth was tracked over time by continuous measurement of scattered light at 620 nm.

[0255] Surprisingly, the results demonstrated that among the tested strains, the B. longum transitional strain NCC5025 exhibited outstanding growth ability with inulin (average size DP6-8, Tsatsaragkou et al.; Foods 2021, 10(5), 951) and high molecular weight arabinan. Compared to the other B. longum transitional strains NCC5002 and NCC5004, B. longum transitional strain NCC5025 grew faster (faster doubling time) and had a higher final yield. With high molecular weight arabinan, only strain NCC5025 grew among all the tested strains (see Figure 5).

[0256] conclusion The data provided demonstrates the following: a) The B. longum transition strain NCC5025 is clearly distinct from the previously isolated B. juwenis strain and shares 98.4% ANI with a strain previously isolated from Bangladeshi infants (Vatanen et al. 2022; as above); b) NCC5025 is currently the only B. longum transitional strain that is considered to be free of antibiotic resistance to the set of antibiotics considered associated by EFSA; c) B. longum NCC5025 has a unique carbohydrate-related enzyme (CaZy) profile, including the presence of 17 enzymes from the GH43 subfamily that have not been evaluated in B. longum species to date. d) B. Longum transitional strain NCC5025 proliferates particularly well in 3-FL; e) The transitional strain NCC5025 of B. longum proliferates well with a set of dietary fibers (e.g., inulin and arabinan).

[0257] Overall, the data suggest that this strain is particularly well-adapted to the weaning period and may perform better than other B. longum transitional strains in this environment. Similarly, our data suggest that this strain may also perform better than other B. longum transitional strains in diets containing dietary fiber (e.g., in adulthood).

[0258] Although the present invention has been described using examples, it should be understood that modifications and alterations can be made without departing from the scope of the invention as defined in the claims. Furthermore, where known equivalents exist for certain features, such equivalents are incorporated as if they were specifically referred to herein.

Claims

1. A Bifidobacterium longum transitional microbial strain deposited with the Collection nationale de cultures de micro-organismes (CNCM) under deposit number CNCM I-5942, or a Bifidobacterium longum transitional strain having the distinguishing characteristics of the aforementioned B. longum transitional strain deposited under deposit number CNCM I-5942.

2. A B. longum transitional microbial strain having at least 99% mean base identity (ANI) to the B. longum strain deposited with CNCM under deposit number CNCM I-5942.

3. The B. longum transition strain according to claim 1, having at least 98.1% ANI compared to the B. longum transition strain deposited under deposit number CNCM I-5942.

4. The B. longum transitional strain according to any one of claims 1 to 3, wherein the B. longum transitional strain is not resistant to any of tetracycline, erythromycin, clindamycin, and ampicillin, and preferably, the B. longum transitional strain is not resistant to any of tetracycline, erythromycin, clindamycin, ampicillin, gentamicin, streptomycin, chloramphenicol, and vancomycin.

5. The B. longum transitional strain according to any one of claims 1 to 4, wherein the B. longum transitional strain comprises the glycosylhydrolase family 43_17 (GH43_17) gene, and preferably the GH43_17 gene comprises SEQ ID NO: 7 or a sequence having at least 60% sequence identity with SEQ ID NO:

7.

6. A B. longum transitional strain according to any one of claims 1 to 5, further comprising the MFS (major facilitator superfamily) gene and / or the AraC gene, preferably the MFS gene comprising SEQ ID NO: 37 or a sequence having at least 60% sequence identity with SEQ ID NO: 39, preferably the AraC gene comprising SEQ ID NO: 39 or a sequence having at least 60% sequence identity with SEQ ID NO: 39, and preferably the GH43_17 gene, the MFS gene, and the AraC gene being included in a gene cluster.

7. The B. longum transitional strain according to claim 6, wherein the B. longum transitional strain further comprises one or more of the GH31 gene and the LacI gene, preferably further comprising the xylulose kinase gene and the xylulose isomerase gene, and even more preferably the GH43_17 gene, the MFS gene, the AraC gene, the GH31 gene, the LacI gene, the xylulose kinase gene, and the xylulose isomerase gene are included in a gene cluster.

8. The B. longum transitional strain according to any one of claims 1 to 7, further comprising one or more genes encoding one or more glycoside hydrolases selected from GH43_17, GH43_22, GH43_27, GH43_29, GH121, GH43_24, GH127, GH30_5, GH43_32, and GH30.

9. The B. longum transitional strain according to any one of claims 1 to 8, wherein the B. longum transitional strain preferentially utilizes 3-fucosyl lactose (3-FL), and preferably has a growth rate of at least 0.6 k when cultured in the presence of 3-FL.

10. A probiotic composition comprising the B. longum transitional strain according to any one of claims 1 to 9.

11. A composition comprising the B. longum transitional strain described in any one of claims 1 to 10, and at least one further probiotic and / or prebiotic.

12. Use of B. longum transitional strain or composition as described in any one of claims 1 to 11 as a nutritional supplement, preferably wherein the B. longum transitional strain or composition is administered to a subject in combination with a fiber-containing diet or fiber-containing food.

13. Use of the B. longum transitional strain or composition according to any one of claims 1 to 9 to promote and / or support the metabolism of fiber-containing foods or dietary fiber by a subject.

14. Use of the B. longum transitional strain or composition according to any one of claims 1 to 9 to promote and / or support the transition from milk-based foods to solid foods in infants and / or toddlers.

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