Probiotic compositions and uses thereof

Abstract

Provided herein is a non-therapeutic method of replenishing a microbiome of an infant or a breastfeeding mother of the infant, a composition comprising a consortium of isolated bacteria representing a number of bacterial clades found to be absent or present in differentially lower abundance in infants delivered by C- section. Compositions for replenishing a microbiome of a healthy infant born by Caesarean Section are also described.

Description

[0001] TITLE

[0002] Probiotic compositions and uses thereof

[0003] Technical Field

[0004] The present disclosure relates to probiotic compositions and uses thereof for infants. In particular, the disclosure provides probiotic compositions for replenishment of a gut microbiome of an infant with an altered gut microbiome or a breastfeeding mother of an infant. In some embodiments, the infant was born by Caesarean Section. In some embodiments, the infant was born to a mother who took antibiotics during the third trimester of pregnancy. In some embodiments, the infant was exposed to antibiotics in early-life.

[0005] Technical Background

[0006] The intestinal microbiome in early life plays a major role in infant health and development, impacting the maturation of the immune system, protecting against pathogens and influencing the long-term metabolic welfare of the host. The acquisition of microbial strains from mother to infant may occur through multiple different pathways, including the birth canal (and the proximity of the birth canal to the anus), contact between mother and infant during parental care and through breast milk. Breast milk is a natural prebiotic source that provides the optimal active ingredients for the growth of beneficial microbial species in the infants' intestines. The microbiome of vaginally born, exclusively breastfed infants at term, with no previous exposure to antibiotics either directly or indirectly from the mother, could be considered the ‘gold standard’. In contrast, antibiotic exposure, C-section birth or formula feeding are known to be associated with altered gut microbiome compared with ‘gold standard’ babies, and this may be associated with poorer health status. In particular, infants born by C-section in most cases have a significantly different early gut microbiota compared to infants born vaginally, including the lack or low abundance of the beneficial species (i.e., genus Bacteroides and Bifidobacterium) and enrichment of opportunistic pathogens (e.g., Klebsiella and Streptococcus).

[0007] Antibiotic treatment throughout pregnancy accounts for up to 80% of prescribed medications during pregnancy. It is estimated that one in five pregnant women in Europe is prescribed at least one course of antibiotics during pregnancy. Considering that it is now accepted that an optimal establishment of the gut microbiome in infants is highly desirable for the normal development of a human, the risk is that antibiotic usage during pregnancy may have undesirable effects on the maternal vaginal, gut and milk microbiome, with knock-on negative impact on the early infant gut microbiome.

[0008] Methods of supplementing the microbiome of caesarean section (CS) born infants is described in CN111187736, US2009162323, WO2017 / 043962, CN108079024, US2023364164, Biasucci et al (Early Human Development, Shannon, IR. Vol. 86, No. 1. 1 July 2010), and Korpela et al. (Microbiome, Biomed Central Ltd, London, UK, Vol. 6, No. 1 , 16 October 2018).

[0009] Despite this, the need for new nutritional interventions, focusing on microbial therapeutics and supplements, has not been fully explored. The present disclosure addresses these needs and provides additional benefits as well.

[0010] Summary of the Disclosure

[0011] The disclosure finds basis in the identification by the Applicant of specific clades of bacteria that are missing (or present in differentially lower abundance) in infants born by Caesarean Section compared with infants born vaginally, compositions comprising a consortium of bacteria that are representative of at least two (and generally a plurality) of these clades, and the use of the compositions to replenish the gut microbiome of such infants. A combination of advanced bioinformatic analysis (culture-independent and culture-rich metagenomic sequencing, strain level metagenomic sequencing) and culturomics (isolation and whole genome sequencing) was employed to identify thirty-nine clades of bacteria including two clades of Bacteroides thetaiotaomicron, three clades of Bacteroides uniformis, one clade of Bifidobacterium adolescentis, six clades of Bifidobacterium bifidum, seven clades of Bifidobacterium breve, one clade of Bifidobacterium dentium, six clades of Bifidobacterium longum subspecies longum, four clades of Bifidobacterium longum subspecies infantis, one clade of Lacticaseibacillus rhamnosus, five clades of Phocaeicola dorei, two clades of Phocaeicola vulgatus, and one clade of Streptococcus lutetiensis. Each clade is characterised by one or more of (a) 16S ribosomal RNA sequence information, (b) a gene sequence that is unique to the clade, or (c) whole genome sequence homology with a reference strain of the clade. The clades are represented by eighty-two isolates which have been cultured and sequenced (whole genome sequencing).

[0012] The disclosure describes compositions comprising a consortium of bacteria representing one, two or more of these clades, and the use of these compositions to replenish the gut microbiome of target infants. In some embodiments, the target infants have an altered gut microbiome. In some embodiments, the target infants were born by C-section. In some embodiments, the target infants were born to mothers who took antibiotics during the third trimester of their pregnancy. In some embodiments, the target infants were exposed to antibiotics in early-life. The compositions may be, for example, an infant formula or early years infant food, a pharmaceutical, a dietary supplement, or a food product. The composition may be administered or formulated for the infant or a breastfeeding mother. Replenishment of the infant gut microbiome improves the infant’s health status and / or improves later life outcomes of the infant.

[0013] In one aspect, there is provided a composition comprising a consortium of isolated bacteria comprising an isolated bacterium from one, two or more clade groupings selected from: (a) a clade of Bacteroides thetaiotaomicron comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 646 and 661 or by comprising a gene sequence of SEQUENCE ID NO: 1 or 2;

[0014] (b) a clade of Bacteroides uniformis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 654, 655 or 659 or by comprising a gene sequence selected from: SEQUENCE ID NO: 3 or 4 to 32, 33-53

[0015] (c) a clade of Bifidobacterium adolescentis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 652 or by comprising a gene sequence selected from SEQUENCE ID NO: 54 to 176;

[0016] (d) a clade of Bifidobacterium bifidum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 630, 637, 638, 641 , 643, 644 or by comprising a gene sequence selected from SEQUENCE ID NO: 177 to 182, 183 to 184, or 185 to 202;

[0017] (e) a clade of Bifidobacterium breve comprising a 16S rRNA sequence selected from ID NO: 632, 626, 627, 629, 647, 648 or 658 or by comprising a gene sequence selected from SEQUENCE ID NO: 203 to 210, 211 to 220, or 221 ;

[0018] (f) a clade of Bifidobacterium dentium comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 640 or by comprising a gene sequence selected from SEQUENCE ID NO: 222 to 288;

[0019] (g) a clade of Bifidobacterium longum subsp. longum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 624, 625, 628, 631 , 642, or 653 or by comprising a gene sequence selected from SEQUENCE ID NO: 289 to 292, 293 to 295, 296, 297 to 300, or 301 to 351 ; (h) a clade of Bifidobacterium longum subspecies infantis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 633, 657, 639, 656, or by comprising a gene sequence selected from SEQUENCE ID NO: 352 to 360, 361 , 362 to 363, or 364 to 367;

[0020] (i) a clade of Lacticaseibacillus rhamnosus comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 634;

[0021] (j) a clade of Phocaeicola dorei comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 635, 645, 650, 651 or 660 or by comprising a gene sequence selected from SEQUENCE ID NO: 368 to 458, 459 to 531 , 532 to 597, 598 and 599;

[0022] (k) a clade of Phocaeicola vulgatus comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 636 and 649 or by comprising a gene sequence selected from SEQUENCE ID NO: 600 or 601 , and 602 to 621 ; and

[0023] (l) a clade of Streptococcus lutetiensis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 662 or by comprising a gene sequence of SEQUENCE ID NO: 622 or 623.

[0024] The twelve groups of clades (a) to (I) above represent thirty-nine clades of bacteria (Clades 1-39 - See Table 3). The bacteria of each clade are absent or present in differentially lower abundance in infants born by Caesarean Section compared with vaginally born infants, and therefore find utility in replenishment of the microbiome of infants having a dysregulated microbiome, such as infants born by Caesarean Section and infants born to mothers on antibiotic therapy during the third trimester of pregnancy.

[0025] As used herein, the term “clade” refers to a group of strains of a specific species that fall within a percent sequence identity of the genome sequence of the reference strain of the clade. In some embodiments, the percent sequence identity is 98%, 99% or more to the genome sequence of a reference strain of the clade. In some embodiments, the percent sequence identity is at least 98% of the genome sequence of a reference strain of the clade. In some embodiments, the percent sequence identity is at least 99% of the genome sequence of a reference strain of the clade.

[0026] In any embodiment, the isolated bacterium is culturable.

[0027] In any embodiment, the isolated bacterium is derived from the human gastrointestinal tract, human faeces or breast milk.

[0028] In any embodiment, the human is an infant.

[0029] In any embodiment, the bacterium of the disclosure may be viable or non-viable, and may comprise a strain extract (i.e. bacterial cell lysate) or supernatant derived from the strain. The extract or supernatant may be in any physical form, for example, liquid or dried.

[0030] In any embodiment, the consortium of bacteria comprises an isolated bacterium from a plurality of clades, for example at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38 or 39 clades of groups (a) to (I).

[0031] In any embodiment, the consortium of bacteria comprises at least 102, 103, 104, 105, 106, 107’ 108’ 109, 1010or 1011, or 1012CFU (colony-forming units) of bacteria.

[0032] In any embodiment, the composition is a pharmaceutical composition and comprises a pharmaceutically acceptable excipient. The composition may be provided in a unit dose form suitable for oral administration, e.g. a tablet, pill, capsule, powder, gummy, gel, paste or beverage. In any embodiment, the composition is a nutritional or dietary supplement.

[0033] In any embodiment, the composition is food or beverage.

[0034] In any embodiment, the composition is an infant food product or infant formula.

[0035] In any embodiment, the composition comprises a prebiotic, for example, a soluble dietary fibre such as inulin.

[0036] In any embodiment, the composition is a unit dose composition.

[0037] The composition may be solid or liquid. The composition may comprise a carrier for oral delivery. The carrier may be in the form of tablet, oil drops, capsule, powder, granules, microparticles or nanoparticles. The carrier may be configured for targeted release in the intestine (i.e. configured for gastric transit and ileal release). The carrier may be configured for controlled release in the intestine (i.e. configured for gastric transit and ileal release).

[0038] In some embodiments, the composition has been pasteurized or heat-treated. In some embodiments, the composition is lyophilized or freeze-dried or spray-dried.

[0039] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (a).

[0040] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (b).

[0041] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (c).

[0042] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (d). In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (e).

[0043] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (f).

[0044] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (g).

[0045] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (h).

[0046] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (i).

[0047] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (j).

[0048] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (k).

[0049] In any embodiment, the consortium of bacteria comprises a bacterium from clade grouping (I).

[0050] In any embodiment, the consortium of bacteria comprises a bacterium from at least two of the clade groupings (a) to (I).

[0051] In any embodiment, the consortium of bacteria comprises a bacterium from all of the clade groupings (a) to (I).

[0052] In any embodiment, the consortium of bacteria comprises: a Bacteroides from clade groupings (a) or (b); a Bifidobacterium from any of clade groupings (c) to (h); a Phocoaeicola from clade groupings (j) or (k); optionally, a Lacticaseibacillus rhamnosus of clade groupings (i); and optionally, a Streptococcus lutetiensis of clade groupings (I).

[0053] In any embodiment, the consortium of bacteria comprises a Bacteroides thetaiotaomicron from clade grouping (a) or a Bacteroides uniformis from clade groupings (b).

[0054] In any embodiment, the consortium of bacteria comprises a Phocaeicola bacterium from clade groupings (j) or (k).

[0055] In any embodiment, the consortium of bacteria comprises a Lacticaseibacillus rhamnosus bacterium of clade grouping (i) or a Streptococcus lutetiensis bacterium of clade grouping (I).

[0056] In any embodiment, the consortium of bacteria comprises at least 102CFU of bacteria selected from two or more clade groupings (a) to (I).

[0057] In any embodiment, the consortium of bacteria comprises or consists essentially of bacteria selected from the group:

[0058] Bacteroides thetaiotaomicron MSB062, MSB164, and MSB165;

[0059] Bacteroides uniformis MSB121 , MSB084, MSB130, MSB156, MSB157;

[0060] Bifidobacterium adolescentis MSB113;

[0061] Bifidobacterium bifidum MSB016, MSB017, MSB019, MSB031 , MSB033, MSB034, MSB039, MSB040, MSB050, MSB038, MSB052, and MSB053;

[0062] Bifidobacterium breve MSB008, MSB020, MSB021 , MSB009, MSB012, MSB014, MSB015, MSB072, MSB073, MSB074 and MSB141 ;

[0063] Bifidobacterium dentium MSB037;

[0064] Bifidobacterium longum subspecies longum MSB001 , MSB002, MSB003, MSB005, MSB006, MSB007, MSB010, MSB011 , MSB013, MSB018, MSB051 and MSB114, Bifidobacterium longum subspecies infantis MSB022, MSB023, MSB030, MSB171 , MSB133, MSB035, MSB036, MSB131 , MSB167, MSB168, MSB169 and MSB170;

[0065] Lacticaseibacillus rhamnosus MSB024, MSB025, MSB032, MSB042, MSB115;

[0066] Phocaeicola dorei MSB026, MSB027, MSB056, MSB085, MSB108, MSB110, MSB112, MSB154, MSB159, MSB160, and MSB162. Phocoeicola vulgatus MSB028, MSB029, MSB079 and MSB161 ; and / or Streptococcus lutetiensis MSB190, MSB193, MSB194, MSB195 and MSB196.

[0067] In any embodiment, the consortium of bacteria comprises substantially all of a strain of Bacteroides thetaiotaomicron selected from MSB062, MSB164, and MSB165; a strain of Bacteroides uniformis selected from MSB121 , MSB084, MSB130, MSB156, MSB157; a strain of Bifidobacterium adolescentis MSB113; a strain of Bifidobacterium bifidum selected from MSB016, MSB017, MSB019, MSB031 , MSB033, MSB034, MSB039, MSB040, MSB050, MSB038, MSB052, and MSB053; a strain of Bifidobacterium breve selected from MSB008, MSB020, MSB021 , MSB009, MSB012, MSB014, MSB015, MSB072, MSB073, MSB074 and MSB141 ; a strain of Bifidobacterium dentium MSB037; a strain of Bifidobacterium longum subspecies longum selected from MSB001 , MSB002, MSB003, MSB005, MSB006, MSB007, MSB010, MSB011 , MSB013, MSB018, MSB051 and MSB114, a strain of Bifidobacterium longum subspecies infantis selected from MSB022, MSB023, MSB030, MSB171 , MSB133, MSB035, MSB036, MSB131 , MSB167, MSB168, MSB169 and MSB170; a strain of Lacticaseibacillus rhamnosus selected from MSB024, MSB025, MSB032, MSB042, MSB115; a strain of Phocaeicola dorei selected from MSB026, MSB027, MSB056, MSB085, MSB108, MSB110, MSB112, MSB154, MSB159, MSB160, and MSB162; and a strain of Phocaeicola vulgatus selected from MSB028, MSB029, MSB079 and MSB161 ; and a strain of Streptococcus lutetiensis selected from MSB190, MSB193, MSB194, MSB195 and MSB196.

[0068] In any embodiment, the consortium of bacteria comprises: a Bacteroides of clade groupings (a) or (b); a Bifidobacterium of any of clade groupings (c) to (h); a Phocaeicola of clade groupings (j) or (k); optionally, a Lacticaseibacillus rhamnosus of clade grouping (i); and optionally, a Streptococcus lutetiensis of clade grouping (I).

[0069] In any aspect, the disclosure provides a method of replenishing (or supplementing) a microbiome of a subject having an altered microbiome comprising administering to the infant or a breastfeeding mother of an infant a composition of the disclosure.

[0070] In any embodiment, the infant having an altered microbiome is selected from (a) an infant born by Caesarean Section, (b) an infant born to a mother exposed to antibiotics during pregnancy (e.g. during a third trimester of pregnancy), or (c) an infant exposed to antibiotics in early life.

[0071] In any embodiment, the infant is exposed to antibiotics directly.

[0072] In some embodiments, the infant is not exposed to antibiotics directly.

[0073] In some embodiments, the infant is exposed to antibiotics indirectly through the mother.

[0074] In some embodiments, the infant is a mammal. The disclosure encompasses compositions comprising isolated strains of bacteria and variants thereof, for example as described below. The term “variant” as applied below should be understood to mean a bacterium of the same strain and clade as the reference bacterium and that additionally is almost genetically identical to the reference bacterium. Thus, for example, the term “variant” as applied to Bifidobacterium bifidum MSB017 means strains of Bifidobacterium bifidum having a genome sequence that is at least 99.7114 % identical to the genome sequence of MSB017. Examples of such variants are the isolates MSB016 and MSB019.

[0075] In any embodiment, the strain of Bacteroides thetaiotaomicron of clade grouping (a) is characterised by a 16S ribosomal RNA sequence of SEQUENCE ID NO: 646 or SEQUENCE ID NO: 661.

[0076] In any embodiment, the strain of Bacteroides thetaiotaomicron of group (a) is selected from:

[0077] Bacteroides thetaiotaomicron MSB062 having a genome sequence of SEQUENCE ID NO: 721 ; a variant of Bacteroides thetaiotaomicron MSB062 having a genome characterised by at least 99.022 % sequence identity with SEQUENCE ID No: 721 ;

[0078] Bacteroides thetaiotaomicron MSB164 having a genome sequence comprising the contigs of SEQUENCE ID NO: 842 or 843; and a variant of Bacteroides thetaiotaomicron MSB164 having a genome characterised by at least 99.7122 % sequence identity with MSB164.

[0079] In any embodiment, the strain of Bacteroides uniformis of clade grouping (b) is characterised by a 16S ribosomal RNA sequence selected from: SEQUENCE ID NO: 654, 655 and 659.

[0080] In any embodiment, the strain of Bacteroides uniformis of clade grouping (b) is selected from:

[0081] Bacteroides uniformis MSB121 having a genome sequence of SEQUENCE ID NO: 749; a variant of Bacteroides uniformis MSB121 having a genome characterised by at least 99.5922 % sequence identity with SEQUENCE ID No: 749 (e.g. MSB084); Bacteroides uniformis MSB130 having a genome sequence of SEQUENCE ID NO: 750; and a variant of Bacteroides uniformis MSB130 having a genome characterised by at least 98.8959 % sequence identity with SEQUENCE ID No: 750.

[0082] Bacteroides uniformis MSB156 having a genome sequence comprising the contigs of SEQUENCE ID NO: 837 to 840; and a variant of Bacteroides uniformis MSB156 having a genome characterised by at least 99.1941 % sequence identity with the genome sequence of MSB156.

[0083] In any embodiment, the strain of Bifidobacterium adolescentis of clade grouping (c) is characterised by a 16S ribosomal RNA sequence of SEQUENCE ID NO: 652.

[0084] In any embodiment, the strain of Bifidobacterium adolescentis is selected from: Bifidobacterium adolescentis MSB113 having a genome sequence comprising the contigs of SEQUENCE ID NO: 746 and 747; and a variant of Bifidobacterium adolescentis MSB113 having a genome characterised by at least 97.921 % sequence identity with the genome sequence of MSB113.

[0085] In any embodiment, the strain of Bifidobacterium bifidum of clade grouping (d) is characterised by a 16S ribosomal RNA sequence selected from: SEQUENCE ID NO: 630, 637, 638, 641 , 643 and 644.

[0086] In any embodiment, the strain of Bifidobacterium bifidum of clade grouping (d) is selected from:

[0087] Bifidobacterium bifidum MSB017 having a genome sequence of SEQUENCE ID NO: 680; a variant of Bifidobacterium bifidum MSB017 having a genome characterised by at least 99.7114 % sequence identity with SEQUENCE ID No: 680 (e.g. MSB016 and MSB019); Bifidobacterium bifidum MSB031 having a genome sequence comprising the contigs of SEQUENCE ID NO: 706 and 707; and a variant of Bifidobacterium bifidum MSB031 having a genome characterised by at least 98.9041 % sequence identity with the genome sequence of MSB031 ;

[0088] Bifidobacterium bifidum MSB033 having a genome sequence of SEQUENCE ID NQ:708; a variant of Bifidobacterium bifidum MSB033 having a genome characterised by at least 99.9934 % sequence identity with SEQUENCE ID No: 708 (e.g MSB034, MSB039, MSB040, MSB050);

[0089] Bifidobacterium bifidum MSB038 having a genome sequence comprising the contigs of SEQUENCE ID NO: 711 and 712; a variant of Bifidobacterium bifidum MSB038 having a genome characterised by at least 99.5025 % sequence identity with the genome sequence of MSB038;

[0090] Bifidobacterium bifidum MSB052 having a genome sequence of SEQUENCE ID NO: 717; a variant of Bifidobacterium bifidum MSB052 having a genome characterised by 100 % sequence identity with SEQUENCE ID No: 717;

[0091] Bifidobacterium bifidum MSB053 having a genome sequence of SEQUENCE ID NO: 718; and a variant of Bifidobacterium bifidum MSB053 having a genome characterised by 100 % sequence identity with SEQUENCE ID No: 718; and

[0092] In any embodiment, the strain of Bifidobacterium breve of clade grouping (e) is characterised by a 16S ribosomal RNA sequence selected from: SEQUENCE ID NO: 632, 626, 627, 629, 647, 648, and 658.

[0093] In any embodiment, the strain of Bifidobacterium breve of clade grouping (e) is selected from:

[0094] Bifidobacterium breve MSB021 having a genome sequence of SEQUENCE ID NO: 686; a variant of Bifidobacterium breve MSB021 having a genome characterised by at least 98.0878 % sequence identity with SEQUENCE ID No: 686 (e.g. MSB008 and MSB020);

[0095] Bifidobacterium breve MSB009 having a genome sequence of SEQUENCE ID NO: 670; and a variant of Bifidobacterium breve MSB009 having a genome characterised by at least 98.5507 % sequence identity with SEQUENCE ID NO: 670.

[0096] Bifidobacterium breve MSB012 having a genome sequence of SEQUENCE ID NO: 671 ; a variant of Bifidobacterium breve MSB012 having a genome characterised by at least 98.7375 % sequence identity with SEQUENCE ID No: 671 ;

[0097] Bifidobacterium breve MSB015 having a genome sequence comprising the contigs of SEQUENCE ID NO: 678 and 679; a variant of Bifidobacterium breve MSB015 having a genome characterised by at least 98.9883 % sequence identity with the genome sequence of MSB015;

[0098] Bifidobacterium breve MSB073 having a genome sequence of SEQUENCE ID NO: 722; a variant of Bifidobacterium breve MSB073 having a genome characterised by at least 99.0299 % sequence identity with SEQUENCE ID No: 722 (e.g. MSB072); Bifidobacterium breve MSB074 having a genome sequence of SEQUENCE ID NO: 723; a variant of Bifidobacterium breve MSB074 having a genome characterised by at least 98.8045 % sequence identity with SEQUENCE ID No:723;

[0099] Bifidobacterium breve MSB141 having a genome sequence comprising the contigs of SEQUENCE ID NO: 822 to 836; and a variant of Bifidobacterium breve MSB141 having a genome characterised by at least 98.8747 % sequence identity with the genome sequence of MSB141.

[0100] In any embodiment, the strain of Bifidobacterium dentium of clade grouping (f) is characterised by a 16S ribosomal RNA sequence of SEQUENCE ID NO: 640.

[0101] In any embodiment, the strain of Bifidobacterium dentium is selected from: Bifidobacterium dentium MSB037 having a genome sequence of SEQUENCE ID NO: 710; and a variant of Bifidobacterium dentium MSB037 having a genome characterised by at least 99.2815 % sequence identity with SEQUENCE ID No: 710.

[0102] In any embodiment, the strain of Bifidobacterium longum subspecies longum of clade grouping (g) is characterised by a 16S ribosomal RNA sequence selected from: SEQUENCE ID NO: 624, 625, 628, 631 , 642, and 653.

[0103] In any embodiment, the strain of Bifidobacterium longum subspecies longum of clade grouping (g) is selected from:

[0104] Bifidobacterium longum subspecies longum MSB005 having a genome sequence comprising the contigs of SEQUENCE ID NO: 663 to 666; a variant of Bifidobacterium longum subspecies longum MSB005 having a genome characterised by at least 97.2955 % sequence identity with the genome of MSB005 (e.g. MSB001 , MSB002, MSB003 or MSB006);

[0105] Bifidobacterium longum subspecies longum MSB007 having a genome sequence comprising the contigs of SEQUENCE ID NO: 667 to 669; and a variant of Bifidobacterium longum subspecies longum MSB007 having a genome characterised by at least 98.5411 % sequence identity with the genome of MSB007;

[0106] Bifidobacterium longum subspecies longum MSB013 having a genome sequence comprising the contigs of SEQUENCE ID NO: 672 to 677; a variant of Bifidobacterium longum subspecies longum MSB013 having a genome characterised by at least 97.3753 % sequence identity with the genome of MSB013 (e.g. MSB011 or MSB010);

[0107] Bifidobacterium longum subspecies longum MSB018 having a genome sequence comprising the contigs of SEQUENCE ID NO: 681 to 685; a variant of Bifidobacterium breve MSB018 having a genome characterised by at least 99.8781 % sequence identity with the genome sequence of MSB018;

[0108] Bifidobacterium longum subspecies longum MSB051 having a genome sequence comprising the contigs of SEQUENCE ID NO: 713 to 716; a variant of Bifidobacterium longum subspecies longum MSB051 having a genome characterised by at least 99.827 % sequence identity with the genome sequence of MSB051 ;

[0109] Bifidobacterium longum subspecies longum MSB114 having a genome sequence of SEQUENCE ID NO: 748; and a variant of Bifidobacterium longum subspecies longum MSB114 having a genome characterised by at least 98.6731 % sequence identity with SEQUENCE ID No: 748.

[0110] In any embodiment, the strain of Bifidobacterium longum subspecies infantis of clade grouping (h) is characterised by a 16S ribosomal RNA sequence selected from: SEQUENCE ID NO: 633, 639, 656 and 657.

[0111] In any embodiment, the strain of Bifidobacterium longum subspecies infantis of clade grouping (h) is selected from:

[0112] Bifidobacterium longum subspecies infantis MSB023 having a genome sequence comprising the contigs of SEQUENCE ID NO: 687 to 694; a variant of Bifidobacterium longum subspecies infantis MSB023 having a genome characterised by at least 99.7311 % sequence identity with the genome sequence of MSB023 (e.g. MSB022);

[0113] Bifidobacterium longum subspecies infantis MSB133 having a genome sequence comprising the contigs of SEQUENCE ID NO: 786 to 821 ; and a variant of Bifidobacterium longum subspecies infantis MSB133 having a genome characterised by at least 98.9053 % sequence identity with the genome sequence of MSB133 (e.g. MSB030 and MSB171 );

[0114] Bifidobacterium longum subspecies infantis MSB036 having a genome sequence of SEQUENCE ID NO: 709; a variant of Bifidobacterium longum subspecies infantis MSB036 having a genome characterised by at least 99.886 % sequence identity with SEQUENCE ID No: 709 (e.g. MSB035);

[0115] Bifidobacterium longum subspecies infantis MSB131 having a genome sequence comprising the contigs of SEQUENCE ID NO: 751 to 785; and a variant of Bifidobacterium longum subspecies infantis MSB131 having a genome characterised by at least 99.59 % sequence identity with the genome sequence of MSB131 (e.g. MSB167, MSB168, MSB169, or MSB170).

[0116] In any embodiment, the strain of Lacticaseibacillus rhamnosus is selected from: Lacticaseibacillus rhamnosus MSB024 having a genome sequence of SEQUENCE ID NO: 695; and a variant of Lacticaseibacillus rhamnosus MSB024 having a genome characterised by at least 98.6196 % sequence identity with SEQUENCE ID No: 695 (e.g.

[0117] MSB025, MSB032, MSB042, or MSB115).

[0118] In any embodiment, the strain of Phocaeicola dorei of clade grouping (j) is characterised by a 16S ribosomal RNA sequence selected from: SEQUENCE ID NO: 635, 645, 650, 651 , and 660.

[0119] In any embodiment, the strain of Phocaeicola dorei of clade grouping (j) is selected from:

[0120] Phocaeicola dorei MSB026 having a genome sequence comprising the contigs of SEQUENCE ID NO: 696 to 701 ; a variant of Phocaeicola dorei MSB026 having a genome characterised by at least 99.1888 % sequence identity with the genome sequence of MSB026;

[0121] Phocaeicola dorei MSB056 having a genome sequence comprising the contigs of SEQUENCE ID NO: 719 to 720; and a variant of Phocaeicola dorei MSB056 having a genome characterised by at least 99.9357 % sequence identity with the genome sequence of MSB056 (e.g.

[0122] MSB027);

[0123] Phocaeicola dorei MSB085 having a genome sequence comprising the contigs of SEQUENCE ID NO: 727 to 743; a variant of Phocaeicola dorei MSB085 having a genome characterised by at least 99.1042 % sequence identity with the genome sequence of MSB085;

[0124] Phocaeicola dorei MSB108 having a genome sequence comprising the contigs of SEQUENCE ID NO: 744 and 745; a variant of Phocaeicola dorei MSB108 having a genome characterised by at least 98.8494 % sequence identity with the genome sequence of MSB108 (e.g. MSB110 or MSB112);

[0125] Phocaeicola dorei MSB162 having a genome sequence of SEQUENCE ID NO: 841 ; and a variant of Phocaeicola dorei MSB 162 having a genome characterised by at least 99.316 % sequence identity with SEQUENCE ID NO: 841 (e.g. MSB154, MSB159, or MSB160).

[0126] In any embodiment, the strain of Phocaeicola vulgatus of clade grouping (k) is characterised by a 16S ribosomal RNA sequence SEQUENCE ID NO: 636 or 649.

[0127] In any embodiment, the strain of Phocaeicola vulgatus of clade grouping (k) is selected from:

[0128] Phocaeicola vulgatus MSB028 having a genome sequence comprising the contigs of SEQUENCE ID NO: 702 to 705; a variant of Phocaeicola vulgatus MSB028 having a genome characterised by at least 99.3315 % sequence identity with the genome sequence of MSB028 (e.g. MSB029); and

[0129] Phocaeicola vulgatus MSB079 having a genome sequence comprising the contigs of SEQUENCE ID NO: 724 to 726; and a variant of Phocaeicola vulgatus MSB079 having a genome characterised by at least 98.2156 % sequence identity with the genome of MSB079 (e.g. MSB161);

[0130] In any embodiment, the strain of Streptococcus lutetiensis of clade grouping (I) is characterised by a 16S ribosomal RNA sequence SEQUENCE ID NO: 662.

[0131] In any embodiment, the strain of Streptococcus lutetiensis is selected from: Streptococcus lutetiensis MSB195 having a strain sequence comprising the contigs of SEQUENCE ID NO: 844 to 867; and a variant of Streptococcus lutetiensis MSB195 characterised by at least 99.8855 % sequence identity with the genome sequence of MSB195 (e.g. MSB190, MSB193, MSB194 or MSB196).

[0132] In any embodiment, the composition further comprises a cryoprotectant.

[0133] In any embodiment, the composition comprises a pharmaceutical composition, a food composition, a beverage, a dietary supplement, a probiotic, a prebiotic, a postbiotic, or a nutritional supplement composition.

[0134] In any embodiment, the composition is formulated as a solution, oil drop, suspension, emulsion, tablet, pill, capsule, powder, or sustained-release formulation.

[0135] In any embodiment, the composition further comprises a pharmaceutically acceptable excipient.

[0136] In any embodiment, the composition is at least 102to 1012or 104to 1010or 106to 108CFU of bacteria.

[0137] In any embodiment, the bacteria in the composition are fully or partially lysed.

[0138] Also described is an isolated bacterium as described herein.

[0139] Also described is a deposited isolated bacterium as described herein.

[0140] Also provided is a kit comprising an isolated bacterium or composition of the disclosure.

[0141] Also provided is a method of producing a cell extract, comprising lysing one or more isolated bacteria of the disclosure, and separating the cell extract from lysed cell material. Also provided is a method of producing a supernatant, comprising culturing one or more isolated bacteria of the disclosure, and separating the supernatant from the one or more isolated bacteria.

[0142] Also provided is a method of replenishing (or supplementing) a microbiome of a subject, for example, an infant (for example, a healthy infant) born by Caesarean Section (or born to a mother who took antibiotics during the third term of her pregnancy) comprising administering to the subject, or a breastfeeding mother of the subject, an isolated bacterium or composition as described herein.

[0143] In any embodiment, the method comprises: assaying a biological sample obtained from the subject or a breastfeeding mother of the subject to profile a microbiome of the subject to provide microbiome data; identifying from the microbiome data a target clade of bacteria that is absent or present in low abundance in the sample; and formulating a composition for the subject that comprises a bacterium of the target clade of bacteria that is identified as being absent or present in reduced numbers in the sample,

[0144] In any embodiment, the target clade of bacteria is selected from:

[0145] (a) a clade of Bacteroides thetaiotaomicron comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 646 and 661 or by comprising a gene sequence of SEQUENCE ID NO: 1 or 2;

[0146] (b) a clade of Bacteroides uniformis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 654, 655 or 659 or by comprising a gene sequence selected from: SEQUENCE ID NO: 3 or 4 to 32, 33-53.

[0147] (c) a clade of Bifidobacterium adolescentis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 652 or by comprising a gene sequence selected from SEQUENCE ID NO: 54 to 176;

[0148] (d) a clade of Bifidobacterium bifidum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 630, 637, 638, 641 , 643, 644 or by comprising a gene sequence selected from SEQUENCE ID NO: 177 to 182, 183 to 184, or 185 to 202;

[0149] (e) a clade of Bifidobacterium breve comprising a 16S rRNA sequence selected from ID NO: 632, 626, 627, 629, 647, 648 or 658 or by comprising a gene sequence selected from SEQUENCE ID NO: 203 to 210, 211 to 220, or 221 ;

[0150] (f) a clade of Bifidobacterium dentium comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 640 or by comprising a gene sequence selected from SEQUENCE ID NO: 222 to 288;

[0151] (g) a clade of Bifidobacterium longum subsp. longum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 624, 625, 628, 631 , 642, or 653 or by comprising a gene sequence selected from SEQUENCE ID NO: 289 to 292, 293 to 295, 296, 297 to 300, or 301 to 351 ;

[0152] (h) a clade of Bifidobacterium longum subspecies infantis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 633, 657, 639, 656, or by comprising a gene sequence selected from SEQUENCE ID NO: 352 to 360, 361 , 362 to 363, or 364 to 367; (i) a clade of Lacticaseibacillus rhamnosus comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 634;

[0153] (j) a clade of Phocaeicola dorei comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 635, 645, 650, 651 or 660 or by comprising a gene sequence selected from SEQUENCE ID NO: 368 to 458, 459 to 531 , 532 to 597, 598 and 599;

[0154] (k) a clade of Phocaeicola vulgatus comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 636 and 649 or by comprising a gene sequence selected from SEQUENCE ID NO: 600 or 601 , and 602 to 621 ; and

[0155] (l) a clade of Streptococcus lutetiensis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 662 or by comprising a gene sequence of SEQUENCE ID NO: 622 or 623.

[0156] In any embodiment, the method comprises identifying from the microbiome data a plurality of target clades of bacteria that are absent or present in reduced abundance in the sample, and formulating a composition for the subject that comprises a bacterium of each target clade of bacteria that is identified as being absent or present in reduced abundance in the sample.

[0157] In any embodiment, the subject is an infant.

[0158] In any embodiment, the biological sample is selected from: a sample obtained from the gut of the infant or the breast-feeding mother of the subject; a faeces sample from the infant or the breast-feeding mother of the infant; and a sample of breast milk from the breast-feeding mother of the infant. Other aspects and preferred embodiments of the disclosure are defined and described in the other claims set out below.

[0159] Detailed Description

[0160] All publications, patents, patent applications and other references mentioned herein are hereby incorporated by reference in their entireties for all purposes as if each individual publication, patent or patent application were specifically and individually indicated to be incorporated by reference and the content thereof recited in full.

[0161] Definitions and

[0162] Where used herein and unless specifically indicated otherwise, the following terms are intended to have the following meanings in addition to any broader (or narrower) meanings the terms might enjoy in the art:

[0163] Unless otherwise required by context, the use herein of the singular is to be read to include the plural and vice versa. The term "a" or "an" used in relation to an entity is to be read to refer to one or more of that entity. As such, the terms "a" (or "an"), "one or more," and "at least one" are used interchangeably herein.

[0164] As used herein, the term "comprise," or variations thereof such as "comprises" or "comprising," are to be read to indicate the inclusion of any recited integer (e.g. a feature, element, characteristic, property, method / process step or limitation) or group of integers (e.g. features, element, characteristics, properties, method / process steps or limitations) but not the exclusion of any other integer or group of integers. Thus, as used herein the term "comprising" is inclusive or open- ended and does not exclude additional, unrecited integers or method / process steps.

[0165] As used herein, the term “replenish” as applied to the microbiome of a subject (e.g. an infant) means supplementing the microbiome of the subject to introduce bacterial strains that are usually present in healthy, vaginally born, infants. The applicant has identified thirty-nine clades of gut-derived bacteria that are absent, or present in differentially lower abundance, in infants born by Caesarean Section, and one object of the invention is to replenish the microbiome in these infants with at least two, and preferably a selection, of the thirty-nine clades of gut-derived bacteria. Thus, the disclosure describes infant foods or supplements that are enriched in these gut-derived bacteria, and also foods and supplements for breastfeeding mothers.

[0166] As used herein, the term “clade” refers to a grouping of bacterial strains that includes a common ancestor and all the descendants of that ancestor. As used herein, the term clade is used to define a group of strains of a specific species that fall within a percent sequence identity of the genome sequence of the reference strain of the clade. In some embodiments, the percent sequence identity is 98%, 99% or more to the genome sequence of a reference strain of the clade. In some embodiments, the percent sequence identity is at least 98% of the genome sequence of a reference strain of the clade. In some embodiments, the percent sequence identity is at least 99% of the genome sequence of a reference strain of the clade. For example, a clade may be defined as a set of bacteria from the same species as a chosen reference strain that is culturable and proprietary, and which have an ANI to the reference strain below a threshold defined using the Youden’s index, and which have a set of genes unique to this clade when applicable. To calculate a cut-off threshold to define clades around each reference strain, a method in line with Valles-Colomer et al. (2022) was employed. Briefly, the method is based on comparison of inter-individual (i.e. , from different pairs or individuals / datasets) and intra-pair (i.e., from the same mother / infant pair in the MIMIC cohort) phylogenetic distances using the MIMIC WGS and MAGs from shotgun data. The intra-pair and interindividual phylogenetic distance distributions can be used to identify the threshold that maximizes the Youden's Index. Once the threshold was obtained using the Younden’s index, a subset of genomes lower than the threshold for each MIMIC WGS strain (i.e., the reference strain) was selected. To obtain the full monophyletic clade corresponding to all these genomes, the most recent common ancestor (MRCA) in the tree using the R function “findMRCA” from the package “phylotools” was selected. The maximum Average Nucleotide Identity (ANI) from this reference strain for which a strain is included in this clade was calculated using fastANI v1 .34 (https: / / github.com / ParBLiSS / FastANI). It means that any strain with an ANI lower than this number is a member of the clade. Additionally, a set of genes that are unique for each clade based on the pangenome is defined herein.

[0167] As used herein, the term “contigs” as applied to a whole genome sequence (WGS) refers to the genomic sequences that together represent the whole genome sequence (e.g. a set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a whole genome sequence). As an example, the whole genome sequence (WGS) of MSB085 is represented by the contigs of SEQUENCE ID NO’S: 727 to 743.

[0168] As used herein, the term “disease” is used to define any abnormal condition that impairs physiological function and is associated with specific symptoms. The term is used broadly to encompass any disorder, illness, abnormality, pathology, sickness, condition or syndrome in which physiological function is impaired irrespective of the nature of the aetiology (or indeed whether the aetiological basis for the disease is established). It therefore encompasses conditions arising from infection, trauma, injury, surgery, radiological ablation, poisoning or nutritional deficiencies.

[0169] As used herein, the term "treatment" or "treating" refers to an intervention (e.g. the administration of an agent to a subject) which cures, ameliorates or lessens the symptoms of a disease or removes (or lessens the impact of) its cause(s). In this case, the term is used synonymously with the term “therapy”.

[0170] Additionally, the terms "treatment" or "treating" refers to an intervention (e.g. the administration of an agent to a subject) which prevents or delays the onset or progression of a disease or reduces (or eradicates) its incidence within a treated population. In this case, the term treatment is used synonymously with the term “prophylaxis”.

[0171] As used herein, an effective amount or a therapeutically effective amount of an agent (i.e. bacterium or composition of the disclosure) defines an amount that can be administered to a subject without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit / risk ratio, but one that is sufficient to provide the desired effect, e.g. the treatment or prophylaxis manifested by a permanent or temporary improvement in the subject's condition. The amount will vary from subject to subject, depending on the age and general condition of the individual, mode of administration and other factors. Thus, while it is not possible to specify an exact effective amount, those skilled in the art will be able to determine an appropriate "effective" amount in any individual case using routine experimentation and background general knowledge. A therapeutic result in this context includes eradication or lessening of symptoms, reduced pain or discomfort, prolonged survival, improved mobility and other markers of clinical improvement. A therapeutic result need not be a complete cure.

[0172] In the context of treatment and effective amounts as defined above, the term subject (which is to be read to include "individual", "animal", "patient" or "mammal" where context permits) defines any subject, particularly a mammalian subject, for whom treatment is indicated. Mammalian subjects include, but are not limited to, humans, domestic animals, farm animals, zoo animals, sport animals, pet animals such as dogs, cats, guinea pigs, rabbits, rats, mice, horses, cattle, cows; primates such as apes, monkeys, orangutans, and chimpanzees; canids such as dogs and wolves; felids such as cats, lions, and tigers; equids such as horses, donkeys, and zebras; food animals such as cows, pigs, and sheep; ungulates such as deer and giraffes; and rodents such as mice, rats, hamsters and guinea pigs. In preferred embodiments, the subject is a human, for example, an infant, adolescent or adult. Strains

[0173] The following strains were deposited on 10 December 2024 at Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) of Inhiffenstrasse 7B, 38124 Brauschweig, Germany by University College Cork, College Road, Cork, Ireland and assigned the following accession numbers:

[0174] DSMZ 35276 Bifidobacterium longum subsp. longum MSB005

[0175] DSMZ 35277 Bifidobacterium longum subsp. longum MSB011

[0176] DSMZ 35278 Bifidobacterium breve MSB012

[0177] DSMZ 35279 Bifidobacterium longum subsp. iongum MSB018

[0178] DSMZ 35280 Bifidobacterium breve MSB021

[0179] DSMZ 35281 Bifidobacterium longum subsp. infantis MSB023

[0180] DSMZ 35282 Lacticaseibacillus rhamnosus MSB024

[0181] DSMZ 35283 Bifidobacterium longum subsp. infantis MSB036

[0182] DSMZ 35284 Bifidobacterium longum subsp. longum MSB051

[0183] DSMZ 35285 Bifidobacterium bifidum MSB053

[0184] DSMZ 35286 Bifidobacterium breve MSB074

[0185] DSMZ 35287 Bifidobacterium longum subsp. Infantis MSB133

[0186] The following strains were deposited on 12 December 2024 at Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) of Inhiffenstrasse 7B, 38124 Brauschweig, Germany by University College Cork, College Road, Cork, Ireland and assigned the following accession numbers:

[0187] DSMZ 35288 Bifidobacterium longum subsp. longum MSB007

[0188] DSMZ 35289 Bifidobacterium breve MSB009

[0189] DSMZ 35290 Bifidobacterium breve MSB015 DSMZ 35291 Bifidobacterium bifidum MSB017

[0190] DSMZ 35292 Phocaeicola dorei MSB026

[0191] DSMZ 35293 Phocaeicola vulgatus MSB028

[0192] DSMZ 35294 Bifidobacterium bifidum MSB031

[0193] DSMZ 35295 Bifidobacterium bifidum MSB033

[0194] DSMZ 35296 Bifidobacterium dentium MSB037

[0195] DSMZ 35297 Bifidobacterium bifidum MSB038

[0196] DSMZ 35298 Bifidobacterium bifidum MSB052

[0197] DSMZ 35299 Phocaeicola dorei MSB056

[0198] DSMZ 35300 Bacteroides thetaiotaomicron MSB062

[0199] DSMZ 35301 Bifidobacterium breve MSB073

[0200] DSMZ 35302 Phocaeicola dorei MSB 108

[0201] DSMZ 35303 Bifidobacterium adolescentis MSB113

[0202] DSMZ 35304 Bifidobacterium iongum subsp. iongum MSB114

[0203] DSMZ 35305 Bacteroides uniformis MSB121

[0204] DSMZ 35306 Bacteroides uniformis MSB130

[0205] DSMZ 35307 Bifidobacterium longum subsp. infantis MSB131

[0206] DSMZ 35308 Bifidobacterium breve MSB141

[0207] DSMZ 35309 Bacteroides uniformis MSB156

[0208] DSMZ 35310 Phocaeicola vulgatus MSB161

[0209] DSMZ 35311 Phocaeicola dorei MSB 162

[0210] DSMZ 35312 Bacteroides thetaiotaomicron MSB164

[0211] DSMZ 35313 Streptococcus lutetiensis MSB 195 The following strain was deposited on 25 February 2025 at Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) of Inhiffenstrasse 7B, 38124 Brauschweig, Germany by University College Cork, College Road, Cork, Ireland and assigned the following accession number:

[0212] DSMZ 35365 Phocaeicola dorei MSB085

[0213] Compositions and Foods

[0214] The invention also relates to a composition comprising a bacterium or a consortium of bacteria of the disclosure, or a supernatant or cell extract obtained therefrom, as described above. The composition may be a pharmaceutical composition, or a food composition, a beverage, or a dietary or nutritional supplement composition. The term “food” refers to a man-made food product including beverages, food additives and food supplements. Examples of foods include dairy products such as milk, yoghurt, cheese, cheese food, dairy powders, probiotic formulations, infant formula powders, follow-on milk formula, food for special medicinal purposes, meat products, soups, vegetable products, fruit juices, fruit products, breads, confectionary, cakes, sports supplements, nutritional supplements and the like. The food may be an infant food, for example, an infant formula or an infant follow-on food. In one embodiment, the composition includes a probiotic material. In one embodiment, the composition comprises a prebiotic material.

[0215] “Probiotic” refers to live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. They are described in Hill et al. (Nat. Rev. Gastroenterol. Hepatol. 2014:11 , 506-514).

[0216] “Prebiotic” refers to a material or composition that is selectively utilized by host microorganisms conferring a health benefit (Gibson et al. 2017, Nat. Rev. Gastroenterol. Hepatol. 14, 491-502). Examples include oligosaccharides, dietary fibres, or mixtures thereof. Exemplary prebiotics are described in WO2011 / 039176, pg 12-15. The invention also relates to pharmaceutical compositions which comprise pharmaceutical carriers. As used herein, the term “pharmaceutical composition” refers to a therapeutically effective amount of the strain of the invention, and a pharmaceutically acceptable carrier. In a specific embodiment, the term "pharmaceutically acceptable" means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. In the case of the present invention, the term “therapeutically effective amount” should be taken to mean an amount of therapeutic which results in a clinically significant increase in proliferation of target cells, for example, gut epithelial cells or skin epithelial cells.

[0217] As used herein, the term “adjuvant” means an agent that enhances the recipient’s immune response to an immunogenic peptide or protein. Details of suitable adjuvant compositions are well known to those skilled in the art.

[0218] As used herein, the term "pharmaceutically acceptable carrier" refers to a diluent, adjuvant, excipient, or vehicle with which the Therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, water, ethanol and the like.

[0219] The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, oil drops, suspensions, emulsions, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in "Remington's Pharmaceutical Sciences" by E. W. Martin. Such compositions will contain a therapeutically effective amount of the therapeutic, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.

[0220] In a preferred embodiment, the composition is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anaesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water-free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical-grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.

[0221] Pharmaceutical compositions formulated or configured for oral administration and gastric transit are known in the art and include those described below:

[0222] • Sathish et al. (Int. J. Pharm. Sci.2013; 258-269);

[0223] • Kushal et al. (Int. Res. J. Pharm. 2013, 4(3));

[0224] • Philip et al. (Oman Med J. 2010, 25(2));

[0225] • Polymers for controlled drug delivery - Peter Tarcha (CRC Press, 21 November 1990); • Pharmaceutical coating technology - Michael Aulton et al. (Taylor & Francis 27 October 1995);

[0226] • http: / / www.slideshare.net / Balimusale / oral-controlled-drug-delivery-system;

[0227] • European Patent No: 2418968 (Teagasc); and

[0228] • European Patent No: 2097072 (RCSI).

[0229] • Brayden et al. (European Journal of Pharmaceutical Sciences 79 (2015), 102-111.

[0230] • Tambuwala et al. (Journal of Controlled Release 217 (2015) 221-227.

[0231] • Zhang et al. Evaluation of alginate-whey protein microcapsules for intestinal delivery of lipophilic compounds in pigs (J. Sci. Food Agric. (2015).

[0232] • Lamprecht et al. (Journal of Controlled Release 104 (2005) 337-346.

[0233] • Hua et al. (Nanomedicine: Nanotechnology, Biology and Medicine 11 (2015) 1117-1132.

[0234] • Drug Delivery: Fundamentals and Applications (Chapter 7, Oral Drug Delivery, Hillary and Brayden)

[0235] As used herein, the term “food” refers to a man-made food product including beverages, food additives and food supplements. Examples of foods include dairy products such as milk, yoghurt, cheese, cheese food, dairy powders, probiotic formulations, infant formula powders, follow-on milk formula, food for special medicinal purposes, meat products, soups, vegetable products, fruit juices, fruit products, breads, confectionary, cakes, sports supplements, nutritional supplements and the like.

[0236] It is preferable that the strain or composition is administered at least once per week over a treatment period of at least 4 weeks, and preferably for at least a 5, 6, 7, 8, 9, 10, 11 , 12, 14, 16, 18 or 20 week period. Preferably, the strain or composition is administered several times a week, and ideally once a day. Compositions of the invention generally comprise between 102and 1012CFU of the strain of the invention per gram of dry weight of the composition, or per unit dose. In one embodiment, the composition comprises 102and 1012CFU, or 103and 1012CFU, or 106and 1010CFU of the strain of the invention per gram of dry weight of the composition, or per unit dose. A daily dose generally comprises between 102and 1012CFU of the strain. In one embodiment, the daily dose comprises 102and 1012CFU, or 103and 1012CFU, or 106and 1010CFU of the strain.

[0237] Exemplification

[0238] The invention will now be described with reference to specific Examples. These are merely exemplary and for illustrative purposes only: they are not intended to be limiting in any way to the scope of the monopoly claimed or to the invention described. These examples constitute the best mode currently contemplated for practicing the invention.

[0239] A: Identification of Missing Clades of Bacteria in the Microbiome of C-section- delivered infants

[0240] A list of species that are missing or differentially less abundant in C-section- delivered infants (as opposed to vaginally delivered infants) was defined. Strains of these species were isolated using culturomics techniques. Whole genome sequencing of some of these strains, and shotgun metagenomics, was performed on a subset of the MIMIC cohort (795 unique samples corresponding to 100 mother / infant pairs across 1 , 4, 8, 24, 52, 78, 104 weeks of age), the methods of which was also described previously. From the shotgun data, 7434 Metagenome Assembled Genomes (MAGs) of good quality (completeness >50 % and contamination <10 %) were generated; the assembly method was also described previously.

[0241] Method for culturomics

[0242] The infant fecal samples and maternal breast milk samples were collected at the Cork University Maternity Hospital or at the participants’ homes at 1 , 4, 8, 24, 52, 78, 104 weeks after delivery. The maternal fecal samples were collected on the day of delivery or after 1 week of delivery. The mothers of all infants were not exposed to antibiotic treatment during third trimester of pregnancy and gave birth at full-term longer than 37 gestational weeks, and the infants were grouped according to their delivery mode (i.e. , five born vaginally and five born by C-section). One aliquot of infant fecal sample and breast milk samples were transferred to an anaerobic chamber for culturing within 24 h after collection. The rest of the samples were stocked at -80 °C for DNA extraction. All cultured samples were processed in the anaerobic chamber. A total of 14 media were used to culture the widest possible range of the infant gut microbiota based on previous studies, including four non- selective media and 10 specific-species selective media (Table 1 ). All the media or the components were commercially available. The non-selective media included: Brain heart infusion agar (BHI) with 0.5 g / l L-cysteine hydrochloride hydrate, Tryptic soy agar (TAS) + 0.5 g / l L-cysteine hydrochloride hydrate, Gut microbiota medium agar (GMM), YCFA8 + 2 g / l each of glucose, maltose and cellobiose. The selective media included: BHIS for Bacteroides spp., Bifidobacterium selective agar (BSM), Colombia agar (COL), Fastidious anaerobic agar with horse blood (FAA) (Fisher Scientific), Kanamycin esculin azide agar (KEA), Lactobacillus selective agar (LBS), MacConkey agar (MAC), Man, Rogosa and Sharpe agar (MRS) + 0.5 g / l L-cysteine hydrochloride hydrate, Reinforced clostridial agar (RCA), and Tryptic soy yeast extract agar (TSY). All media were prepared according to the manufacturer’s instructions. The fresh fecal samples collected from infants were vortexed to dissolve in reduced sterile maximum recovery diluent (MRD) (0.1 g stool per ml), serially diluted, and cultured as described below. All 14 media were placed in the anaerobic cabinet 24 h before use to reduce aerobic condition. The amount of 100 pl of 10A-5 and 10A-6 dilutions of fecal samples from the first three sampling time points (weeks 1 , 4, 8, 24, 52, 78, 104 of age), and 10A-6 and 10A-8 dilutions for samples collected at week 24 were plated on the reduced 100-mm agar plates given the increasing richness of microbiota as infants became older. After incubation at 37 °C for seven days in an anaerobic chamber (5% H2, 10% CO2, 85% NO2), all colonies that grew on each medium were collected by adding reduced sterile MRD and scraping the surface of plates with sterile spreaders. Both dilutions of each medium were combined and stored in 25% glycerol (further referred to as stocked colonies) at -80 °C for DNA extraction.

[0243] Considering the low abundance of microbiota in the breast milk samples, the fresh breast milk samples were first cultured in broth of BHIS, BSM, MRS, and RCA for 2 days to enrich the milk-associated bacteria. MRS and RCA were supplemented with mupirocin (100 pg / ml) as separate media types (MRS+Mup, RCA+Mup) to select the specific targeted species of Bifidobacterium', and MRS was additionally supplemented with vancomycin (10 pg / ml, MRS+Van) to select Lactobacillus species. Afterwards, the enriched broths were serially diluted, and then an amount of 100 pl of 10A-4 and 10A-5 dilutions for BHIS and MRS broth, 10A-3 and 10A-4 dilutions for BSM and RCA, and 10A-2 and 10A-3 dilutions for antibiotics- supplementary broths was plated on the corresponding agar plates. After incubation for seven days, all colonies from the seven types of media were collected and stocked following the protocol for the fecal samples.

[0244] Table 1. Culture media used in the isolation and culturing of isolates.

[0245] Media Targeted taxa Company Supplement / Reference

[0246] Brain heart infusion agar, BHI Non-selection BD 0.5 g / L L-cysteine hydrochloride hydrate

[0247] Tryptic soy agar, TSA Non-selection BD 0.5 g / L L-cysteine hydrochloride hydrate

[0248] YCFA Non-selection N Browne, et al.

[0249] Gut microbiota medium agar, GMM Non-selection N Goodman, et al.

[0250] BHIS Bacteroides BD Bacic and Smith

[0251] Bifidobacterium selective agar, BSM Bifidobacterium Sigma BSM Supplement (Sigma, 83055)

[0252] Lactobacillus selective agar, LBS Lactobacillus BD None

[0253] De Man, Rogosa and Sharpe agar, MRS Bifidobacterium', BD 0.5 g / L L-cysteine hydrochloride hydrate

[0254] Lactobacillus

[0255] Reinforced clostridial agar, RCA Clostridium Merck None

[0256] Bifidobacterium

[0257] MacConkey, MAC Escherichia Merck None

[0258] Pesudomonas

[0259] Klebsiella

[0260] Fastidious anaerobic agar with horse blood, FAA Veillionella Fisher None

[0261] Propionibacterium Scientific

[0262] Tryptic soy yeast extract agar, TSY Streptococcus Merck ATCC Medium: 1887

[0263] Kanamycin esculin azide agar, KEA Streptococcus Merck None

[0264] Colombia agar, COL Clostridium Sigma None Method for each species

[0265] We gathered all the publicly available isolate genomes of the same species from NCBI (September 2023). We also gathered the MAGs and WGS of the same species from MIMIC. We annotated all the genomes using PROKKA v1 .14.5 and used the “.gff” (annotation) files to perform a pangenome using ROARY v3.13.0. We reconstructed a phylogenetic tree from the pangenome using the aligned core genome and FASTTREE v2.1.10 using the GTR model. We subsequently visualized the tree using R v4.2.0 and the package “ggtree”. We calculated the phylogenetic distance distribution between genomes. To calculate a cut-off threshold to define patentable clades around each MIMIC reference strain (i.e. , WGS), we used a method in line with Valles-Colomer et al. (2022). Briefly, the method is based on comparison of inter-individual (i.e., from different pairs or individuals / datasets) and intra-pair (i.e., from the same mother / infant pair in the MIMIC cohort) phylogenetic distances using the MIMIC WGS and MAGs. For highly prevalent species (at least 50 same-individual comparisons available), the intra-pair and interindividual phylogenetic distance distributions can be used to identify the threshold that maximizes the Youden's Index. For less prevalent species (less than 50 same-individual comparisons available) in which specific thresholds based on comparison of phylogenetic distances cannot be reliably computed, we set as threshold the median of the inter-individual phylogenetic distance percentiles that we obtained for the highly prevalent species. We did not encounter this case here, but displayed a threshold of 3% percentile as a comparison standard. Once the threshold was obtained using the Youden’s index, we selected a subset of genomes lower than the threshold for each MIMIC WGS strain (i.e., the reference strain). To obtain the full monophyletic clade corresponding to all these genomes, we found the most recent common ancestor (MRCA) in the tree using the R function “findMRCA” from the package “phylotools”. Then, for each clade, we defined a reference genome corresponding to a MIMIC WGS sequence (i.e., for which we have an isolate). We calculated the maximum Average Nucleotide Identity (ANI) from this reference strain for which a strain is included in this clade using fastANI It means that any strain with an ANI higher than this number is a member of the clade. Additionally, we defined a set of genes that are unique for each clade based on the pangenome.

[0266] When the phylogenetic tree was plotted for each species, metadata were added to the trees generated from the clade analysis (i.e., trees obtained from pan-genome analysis and clades obtained using the Youden index) and each figure displays the following for each species, from the inner circle to the outer circle (see figure 1 below):

[0267] -Delivery mode (middle legend “Type”)

[0268] -Visit (from visit 3, noted V3, to visit 9, noted V9) (upper legend “value”) -Type (infant or mother or commercial or unknown source) (lower legend “Type”) The visits correspond to the following days before (i.e., for mothers) or after birth (Table 2): Table 2 Results

[0269] The Clades identified by the Applicant are described in Table 3 below:

[0270] Table 3

[0271] * MSB isolate underlined in “Isolate” column corresponds with genome in Genome column (e.g. SEQ ID NO: 749 represents the genome of the isolate MSB121 (Clade 3 - Bacteroides uniformis). Where more than one sequence ID is provided for the genome of any strain, the sequences are contigs, that are representative of the whole genome sequence. Thus, for clade 10 (Bifidobacterium bifidum), the representative strain MSB038 has a genome represented by the contigs of SEQ ID NO: 711 and 712.

[0272] Bacteroides thetalotaomlcron has 2 unmixed clades (no C-Section genomes) Bacteroides uniformis has 3 clades

[0273] -2 unmixed (no C-Section genomes) -1 mixed with V3 and V7 C-Section (i.e. , very early and late visits) Bifidobacterium adolescentis has only 1 mixed clade, with mostly V7, V8, V9 C- Section genomes (i.e., late visits) but also one V3 (i.e., early visit). Bifidobacterium bifidum has 6 clades:

[0274] -5 are unmixed

[0275] -1 clade (defined by MSB031 ) is very mixed with early and late C-Section genomes (i.e., from V3 to V9).

[0276] Bifidobacterium breve has 7 clades, zero of them matching known commercial strains:

[0277] -3 are unmixed

[0278] -1 (defined by MSB014) is mixed with 2 early C-Section genomes

[0279] -3 mixed with early and late visits

[0280] Bifidobacterium dentium has one clade with only C-Section genomes Bifidobacterium longum subspecies longum has 6 clades, with zero clades matching known commercial strains:

[0281] -3 unmixed clades (represented by MSB007, MSB114, and MSB018)

[0282] -2 mixed clades (e.g., including MSB005 and MSB011 ). In the clade including MSB005, C-Section genomes mainly come from late visits (>V6). In the clade including MSB011 , C-Section genomes also come from early visits (<V6) but also from mothers.

[0283] -1 clade with only C-Section (MSB051) Bifidobacterium longum subspecies infantis has 4 clades, with 1 clade matching known commercial strains:

[0284] -1 is unmixed (e.g., the one including MSB035)

[0285] -2 are mixed with one C-Section genome from late time point (V6 or V7) (e.g., clades including MSB131 and MSB133).

[0286] -1 is mixed (e.g., the one including MSB030)

[0287] Lacticaseibacillus rhamnosus has 1 clade mixed with early and late C-Section visits genomes.

[0288] Phocaeicola dorei has 5 clades:

[0289] -3 are unmixed -2 (MSB159 and MSB112) are mixed with only one late C-Section visit genomes (> or equal to V7)

[0290] Phocaeicola vulgatus has 2 clades (2 of which are largely overlapping):

[0291] -1 is unmixed (MSB028)

[0292] -1 are mixed with late visits (> or equal to V7) or mother strains from early time points

[0293] Streptococcus I utetiensis has 1 unmixed clade

[0294] The term “mixed” as applied to a clade means that it contains strains or MAGs from vaginally and CS-born babies in the clade, whereas the term “unmixed” means that the clade does not contain any CS strains.

[0295] Snippy and InStrain analysis of MiMIC patent strains

[0296] Snippy is a tool that identifies single nucleotide polymorphisms (SNPs) between two reference genomes (Seeman, 2014 GitHub repository. https: / / github.com / tseemann / snippy.). Hereafter, the term SNP will encompass both snps and indels.

[0297] Snippy was carried out on MiMIC patent clades. Snippy comparisons were made only between strains in the same clade. Snippy was used to count the number of SNPs between two strains. We used a threshold of 20 SNPs between strains to determine that they could be classified as the same strain, as suggested in the literature (Pightling et al., 2018 Front Microbiol. 2018 Jul 10;9:1482. doi: 10.3389 / fmicb.2018.01482. PMID: 30042741 ; PMCID: PMC6048267).

[0298] InStrain is a tool that can determine the presence of an organism at the strain-level in a metagenomic sample (Olm et al., 2021 Nat Biotechnol 39, 727-736 (2021).). In the present study it was used to determine the presence of a strain in shotgun sequenced human stool samples, specifically infant siblings, to demonstrate horizontal transmission. Methods: The following software modules were loaded using bash on MobaXterm: Snippy version 4.6.0, bowtie2 version 2.5.3, samtools version 1.20.0, InStrain version 1.9.

[0299] The input data for Snippy was two whole-genome sequenced (WGS) strains, in .fasta format, for pairwise comparison. For InStrain analysis, shotgun reads were aligned to an indexed strain, in .fasta format, using the tool Bowtie2. InStrain was then used to analyse the alignment using the InStrain profile command from the InStrain package. To compare how alike the InStrain profiles were, the command InStrain compare was used.

[0300] A detailed description of InStrain outputs can be found at InStrain — inStrain 1 .0.0 documentation.

[0301] Naming custom for samples is participant number_sample type_mother / infant_visit. For example, 050_ST_l_V8 means participant number 050, stool sample, infant, visit 8. ‘ST’ denotes stool, ‘BM’ denotes breastmilk; T denotes infant, ‘M’ denotes mother.

[0302] Results:

[0303] Candidates for persistence, vertical transfer and horizontal transfer:

[0304] Persistence in this context means the strain is detectable across multiple timepoints in the infant gut.

[0305] Vertical transfer means the acquisition of a strain by the infant from its mother. Horizontal transmission means the strain is transferred between individuals who are not parent-offspring.

[0306] Summary of candidates for these three mechanisms is given in Table 4.

[0307]

[0308] Table 4 Evidence for persistent strains and vertically and horizontally transmitted strains.

[0309] Using InStrain for Assessing Horizontally Transferred Strains

[0310] Rationale: Clade 3 contains two B. uniformis strains: MSB084 and MSB121 (DSM 35305). MSB084 was isolated from infant 050 and MSB121 (DSM 35305) was isolated from infant 303. These infants are siblings; therefore, these two strains are deemed to be the same strain since Snippy detected only nine SNPs between them. Hence, it was investigated whether this strain was horizontally transmitted between the siblings.

[0311] InStrain Method: MSB084 was tested for its presence in all participant 050 samples and all participant 303 samples. The same was then carried out for MSB121 (DSM 35305). Once the InStrain profile was generated for each strain-shotgun sample pair, profiles with >90% breadth and >5x coverage were compared against each other to see if the mapped profiles were similar.

[0312] Results: The InStrain profile results are given in Tables 5A to 5D.

[0313] Table 5A

[0314] Table 5B

[0315] Table 5C

[0316] Table 5D

[0317] Table 5. (A) MSB121 (DSM 35305) InStrain profiles mapped against participant 050. (B) MSB121 (DSM 35305) mapped against participant 303. (C) MSB084 InStrain profiles InStrain profiles mapped against participant 050. (D) MSB084 InStrain profiles mapped against participant 303.

[0318] InStrain Interpretation: Firstly, the InStrain profiles for both MSB084 and MSB121 (DSM 35305) were almost identical. This supports the notion that these are the same strain, and they are treated hereafter as one strain. The InStrain profile results indicated that the strain MSB121 (DSM 35305) and MSB084 was present in the timepoints V7 and V9 (coverage >8, breadth > 99.5%) of both infants and in additional timepoint V8 (coverage >14.81 , breadth = 99.957%) in infant 303. These results are evidence that the strain was horizontally transmitted. Furthermore, the presence of only nine SNPs between the two strains additionally supports their classification as the same strain. Exemplary Compositions

[0319] A number of consortia of bacteria were assembled according to Table 6 below. Each MSB strain was cultured, purified and then freeze-dried using standard techniques. The consortia were prepared using freeze-dried cultures and each consortium contained approximately 106CFU per g.

[0320] Table 6

[0321] B1 : Infant Formula

[0322] A standard infant formula was made up comprising (per 100 kcal) 2g of protein, 5g of fat, 10g of carbohydrate, 0.45g of iron, and vitamins and minerals. The formula was fortified with one of the consortia of bacteria of Table 6 at a rate of at least 102CFU I daily dose.

[0323] Sequence Listing

[0324] The instant application contains a Sequence Listing which has been submitted herewith and is hereby incorporated by reference in its entirety. Said .xml copy, created on September 19, 2025, is named P14871 PC00, and is 131 ,975,727 bytes in size. Equivalents

[0325] The foregoing description details presently preferred embodiments of the present invention. Numerous modifications and variations in practice thereof are expected to occur to those skilled in the art upon consideration of these descriptions. Those modifications and variations are intended to be encompassed within the claims appended hereto.

Claims

1. CLAIMS:

1. A composition comprising a consortium of bacteria comprising an isolated bacterium from each of two or more clades selected from:(f) a clade of Bifidobacterium dentium comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 640 or by comprising a gene sequence selected from SEQUENCE ID NO: 222 to 288;(I) a clade of Streptococcus lutetiensis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 662 or by comprising a gene sequence of SEQUENCE ID NO: 622 or 623;(a) a clade of Bacteroides thetaiotaomicron comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 646 and 661 or by comprising a gene sequence of SEQUENCE ID NO: 1 or 2;(b) a clade of Bacteroides uniformis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 654, 655 or 659 or by comprising a gene sequence selected from: SEQUENCE ID NO: 3 or 4 to 32, 33 to 53;(c) a clade of Bifidobacterium adolescentis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 652 or by comprising a gene sequence selected from SEQUENCE ID NO: 54 to 176;(d) a clade of Bifidobacterium bifidum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 630, 637, 638, 641 , 643, 644 or by comprising a gene sequence selected from SEQUENCE ID NO: 177 to 182, 183 to 184, or 185 to 202;(e) a clade of Bifidobacterium breve comprising a 16S rRNA sequence selected from ID NO: 632, 626, 627, 629, 647, 648 or 658 or by comprising a gene sequence selected from SEQUENCE ID NO: 203 to 210, 211 to 220, or 221 ;(g) a clade of Bifidobacterium longum subsp. longum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 624, 625, 628, 631 , 642, or 653 or by comprising a gene sequence selected from SEQUENCE ID NO: 289 to 292, 293 to 295, 296, 297 to 300, or 301 to 351 ;(h) a clade of Bifidobacterium longum subspecies infantis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 633, 657, 639, 656, or by comprising a gene sequence selected from SEQUENCE ID NO: 352 to 360, 361 , 362 to 363, or 364 to 367;(i) a clade of Lacticaseibacillus rhamnosus comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 634;(j) a clade of Phocaeicola dorei comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 635, 645, 650, 651 or 660 or by comprising a gene sequence selected from SEQUENCE ID NO: 368 to 458, 459 to 531 , 532 to 597, 598 and 599; and(k) a clade of Phocaeicola vulgatus comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 636 and 649 or by comprising a gene sequence selected from SEQUENCE ID NO: 600 or 601 , and 602 to 621.

2. A composition according to Claim 1 , wherein the isolated bacterium from the two or more clades comprises a bacterium from clade (f).

3. A composition according to Claim 1 , wherein the isolated bacterium from the two or more clades comprise a bacterium from clade (f) and a bacterium from clade (I).

4. A composition according to Claim 1 , wherein the isolated bacterium from clade(f) comprises Bifidobacterium dentium MSB037 as deposited with the DSMZ under the Accession No.35296.

5. A composition according to Claim 3 or 4, wherein the isolated bacterium from clade (I) comprises Streptococcus lutetiensis MSB195 as deposited with the DSMZ under the Accession No.35313.

6. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (e) and a bacterium selected from clades (a) to(d) and (f) to (I).

7. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (f) and a bacterium selected from clades (a) to(e) and (g) to (I).

8. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (g) and a bacterium selected from clades (a) to(f) and (h) to (I).

9. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (h) and a bacterium selected from clades (a) to(g) and (i) to (I).

10. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (i) and a bacterium selected from clades (a) to(h) and (j) to (I).11 . A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (j) and a bacterium selected from clades (a) to (i) and (k) to (I).

12. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (k) and a bacterium selected from clades (a) to 0) and (I).

13. A composition according to Claim 1 , in which the consortium of bacteria comprises a bacterium from clade (I) and a bacterium selected from clades (a) to(k).

14. A composition according to any preceding Claim, in which the consortium of bacteria comprises a bacterium from substantially all of the clades of groups (a) to(l).

15. A composition according to any of claims 1-14, wherein the composition comprises a food composition, a beverage, a dietary supplement, a probiotic, a prebiotic, a postbiotic, or nutritional supplement composition.

16. The composition of any one of claims 1-15, wherein the composition is pasteurized or heat treated.

17. The composition of any of claims 1-16, wherein the composition is lyophilized, freeze-dried or spray-dried.

18. A composition according to any of Claims 1 to 17, in which the consortium of bacteria comprises at least 102colony-forming units (CFU) of bacteria.

19. A pharmaceutical composition comprising a composition according to any of Claims 1 to 18 combined with a pharmaceutically acceptable excipient.

20. A non-therapeutic method of replenishing a microbiome of a subject wherein the subject is an infant with an altered gut microbiome or a breastfeeding mother, the method.comprising administering to the subject a composition according to any of Claims 1 to 19.21 . The method of claim 20, wherein the infant with an altered gut microbiome was born by Caesarean section.

22. The method of claim 20 or claim 21 , wherein the infant with an altered gut microbiome was born to a mother treated with antibiotics during the third trimester of pregnancy.

23. The method of any one of claims 20-22, wherein the infant with an altered gut microbiome was exposed to antibiotics in early life.

24. A method of producing a cell extract, comprising lysing the bacteria of the composition of any one of claims 1-18 and separating the cell extract from lysed cell material.

25. A method of producing a supernatant, comprising culturing the bacteria of the composition of any of claims 1-18 and separating the supernatant from the bacterium.

26. A method formulating a composition according to any of Claims 1 to 18 for a subject, comprising the steps of: assaying a biological sample obtained from the subject or a breastfeeding mother of the subject to profile a microbiome of the subject to provide microbiome data; identifying from the microbiome data a target clade of bacteria that is absent or present in low abundance in the sample; andformulating a composition for the subject that comprises a bacterium of the target clade of bacteria that is identified as being absent or present in reduced numbers in the sample, wherein the target clade of bacteria is selected from:(f) a clade of Bifidobacterium dentium comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 640 or by comprising a gene sequence selected from SEQUENCE ID NO: 222 to 288;(I) a clade of Streptococcus lutetiensis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 662 or by comprising a gene sequence of SEQUENCE ID NO: 622 or 623;(a) a clade of Bacteroides thetaiotaomicron comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 646 and 661 or by comprising a gene sequence of SEQUENCE ID NO: 1 or 2;(b) a clade of Bacteroides uniformis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 654, 655 or 659 or by comprising a gene sequence selected from: SEQUENCE ID NO: 3 or 4 to 32, 33 to 53.(c) a clade of Bifidobacterium adolescentis comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 652 or by comprising a gene sequence selected from SEQUENCE ID NO: 54 to 176;(d) a clade of Bifidobacterium bifidum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 630, 637, 638, 641 , 643, 644 or by comprising a gene sequence selected from SEQUENCE ID NO: 177 to 182, 183 to 184, or 185 to 202;(e) a clade of Bifidobacterium breve comprising a 16S rRNA sequence selected from ID NO: 632, 626, 627, 629, 647, 648 or 658 or by comprising a gene sequence selected from SEQUENCE ID NO: 203 to 210, 211 to 220, or 221 ;(g) a clade of Bifidobacterium longum subsp. longum comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 624, 625, 628, 631 , 642, or 653 or by comprising a gene sequence selected from SEQUENCE ID NO: 289 to 292, 293 to 295, 296, 297 to 300, or 301 to 351 ;(h) a clade of Bifidobacterium longum subspecies infantis comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 633, 657, 639, 656, or by comprising a gene sequence selected from SEQUENCE ID NO: 352 to 360, 361 , 362 to 363, or 364 to 367;(i) a clade of Lacticaseibacillus rhamnosus comprising a 16S rRNA sequence selected from SEQUENCE ID NO: 634;(j) a clade of Phocaeicola dorei comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 635, 645, 650, 651 or 660 or by comprising a gene sequence selected from SEQUENCE ID NO: 368 to 458, 459 to 531 , 532 to 597, 598 and 599; and(k) a clade of Phocaeicola vulgatus comprising a 16S rRNA sequence selected from SEQUENCE ID NO’s: 636 and 649 or by comprising a gene sequence selected from SEQUENCE ID NO: 600 or 601 , and 602 to 621.

27. A method according to Claim 26, comprising identifying from the microbiome data a plurality of target clades of bacteria that are absent or present in reduced abundance in the sample, and formulating a composition for the subject thatcomprises a bacterium of each target clade of bacteria that is identified as being absent or present in reduced abundance in the sample.

28. A method according to Claim 26 or 27, in which the subject is an infant, and in which the biological sample is selected from: a sample obtained from the gut of the infant or the breastfeeding mother of the subject; a faeces sample from the infant or the breastfeeding mother of the infant; and a sample of breast milk from the breastfeeding mother of the infant.

29. A composition comprising an isolated strain of Bifidobacterium longum subsp. longum selected from:Bifidobacterium longum subsp. longum MSB005 as deposited with theDSMZ under the Accession No.35276;Bifidobacterium longum subsp. longum MSB011 as deposited with theDSMZ under the Accession No.35277;Bifidobacterium longum subsp. longum MSB018 as deposited with theDSMZ under the Accession No.35279;Bifidobacterium longum subsp. longum MSB051 as deposited with theDSMZ under the Accession No.35284;Bifidobacterium longum subsp. longum MSB007 as deposited with theDSMZ under the Accession No.35288; andBifidobacterium longum subsp. longum MSB114 as deposited with the DSMZ under the Accession No.35304.

30. A composition comprising an isolated strain of Bifidobacterium longum subsp. infantis selected from:Bifidobacterium longum subsp. infantis MSB023 as deposited with the DSMZ under the Accession No.35281 ;Bifidobacterium longum subsp. infantis MSB036 as deposited with the DSMZ under the Accession No.35283;Bifidobacterium longum subsp. infantis MSB133 as deposited with the DSMZ under the Accession No.35287; andBifidobacterium longum subsp. infantis MSB131 as deposited with the DSMZ under the Accession No.35307.31 . A composition comprising an isolated strain of Bifidobacterium breve selected from:Bifidobacterium breve MSB012 as deposited with the DSMZ under the Accession No.35278;Bifidobacterium breve MSB021 as deposited with the DSMZ under the Accession No.35280;Bifidobacterium breve MSB074 as deposited with the DSMZ under the Accession No.35286;Bifidobacterium breve MSB009 as deposited with the DSMZ under the Accession No.35289;Bifidobacterium breve MSB015 as deposited with the DSMZ under the Accession No.35290;Bifidobacterium breve MSB073 as deposited with the DSMZ under theAccession No.35301 ; andBifidobacterium breve MSB141 as deposited with the DSMZ under the Accession No.35308.

32. A composition comprising an isolated strain of Bifidobacterium bidifum selected from:Bifidobacterium bidifum MSB017 as deposited with the DSMZ under the Accession No.35291 ;Bifidobacterium bidifum MSB031 as deposited with the DSMZ under the Accession No.35294;Bifidobacterium bidifum MSB033 as deposited with the DSMZ under the Accession No.35295;Bifidobacterium bidifum MSB038 as deposited with the DSMZ under the Accession No.35297;Bifidobacterium breve MSB052 as deposited with the DSMZ under the Accession No.35298;Bifidobacterium breve MSB073 as deposited with the DSMZ under the Accession No.35301 ; andBifidobacterium breve MSB141 as deposited with the DSMZ under the Accession No.35308.

33. A composition comprising an isolated strain of Bifidobacterium dentium MSB037as deposited with the DSMZ under the Accession No.35296.

34. A composition comprising an isolated strain of Streptococcus lutetiensis MSB195 as deposited with the DSMZ under the Accession No.35313.

35. A composition according to any of Claims 29 to 34 for use as a medicament.

36. A composition according to any of Claims 29 to 34 which is a pharmaceutical composition and comprises a pharmaceutically acceptable excipient.

37. A composition according to any of Claims 29 to 34, for use in a method of replenishing a microbiome of a subject wherein the subject is an infant with an altered gut microbiome or a breastfeeding mother, the method comprising administering the composition to the subject.