Novel biomarkers in canine samples

Abstract

A method of detecting one or more bacteria in a canine sample is described. The detection of the one or more bacteria can be used to determine or monitor the health of a canine, more specifically the gut health of a canine. Also disclosed herein is one or more bacteria for use as a biomarker to determine or monitor the health of a canine, more specifically the gut health of a canine. The one or more bacteria may have a sequence with at least 85% sequence identity, or at least 95% sequence identity, or 100% sequence identity with a sequence defined in SEQ ID NO 1-92.

Description

[0001] NOVEL BIOMARKERS IN CANINE SAMPLES

[0002] CROSS-REFERENCES TO RELATED APPLICATIONS

[0003] This application claims the benefit of priority to GB Patent Application No. 2415507.9, filed October 21, 2024, the content of which is incorporated herein by reference in its entirety, and to which priority is claimed.

[0004] SEQUENCE LISTING

[0005] The present specification makes reference to a Sequence Listing (submitted as an .xml file named 0692690769SL). The XML file was generated on October 20, 2025, and is 174,376,060 bytes in size. The entire contents of the Sequence Listing are hereby incorporated by reference.

[0006] BACKGROUND

[0007] Composed primarily of bacteria and archaea, the gastrointestinal microbiome contributes to essential host metabolic function, immune system education and pathogen protection (Pilla & Suchodolski, 2020). Either directly or indirectly, a healthy and resilient gut microbiome is central to countless physiological processes (Barko et al., 2018). Consequently, the role of the microbiome in both human and animal health, as well as in the etiology and progression of various diseases has become increasingly apparent (Ma et al., 2023). Recently, evident correlations have emerged between gut microbial dysbiosis and a number of acute and chronic canine GI disorders such as chronic enteropathy (CE) (Jergens & Heilmann, 2022; Pilla & Suchodolski, 2020). With probiotic candidates, fecal microbiota transplants and dietary interventions all showing promising results in modulating aspects of canine GI function (Berlanda et al., 2021; Le Bon et al., 2023; Schmitz & Suchodolski, 2016), fully elucidating the microbial species inhabiting this niche and their functional importance is of pressing importance. However, the specific taxonomic composition of the microbiota is typically distinct between different mammals with diverse nutritional requirements

[0008] The gut microbiome can now be studied at high resolution, annotating both taxonomic presence and functional potential. Commonly, metagenomic data is annotated via the mapping of sequencing reads to databases of known genes or genomes. These databases are comprised mostly of cultivable microbes that have been isolated and sequenced (Thomas et al., 2012). Consequently, a vast proportion of reads in a metagenomic sequencing run remain unmapped due to the presence of uncultured and unknown microbes (Ye et al., 2022). Lloyd et al. estimated that in nonhuman-associated environments 22% to 87% of genera have not been cultured, compared to 3% to 55% of genera in human-associated environments (Lloyd et al., 2018). These data suggest that current microbiome databases, are not only lacking knowledge, but are also biased towards human-associated taxa, potentially significantly limiting the insights drawn from research in animal species.

[0009] Over a number of decades, research has been performed on the nutritional requirements of dogs leading to substantial findings in key areas such as management of disease, growth, and aging (Bbswald et al., 2019; Larsen & Farcas, 2014; Rudinsky et al., 2018). However, to date, research on the gut microbiome of dogs remains relatively limited, particularly in comparison to humans, mice, and livestock.

[0010] SUMMARY OF THE INVENTION

[0011] In one aspect of the present invention, there is provided a method of detecting one or more bacteria in a sample obtained from a canine, wherein the one or more bacteria:

[0012] (i) is of a genus selected from

[0013] Family Genus

[0014] Erysipelotrichaceae GGB2876

[0015] Erysipelotrichaceae GGB2877

[0016] Erysipelotrichaceae GGB2927

[0017] Anaerovoracaceae GGB2866

[0018] Lachnospiraceae GGB3041 Erysipelatoclostridiaceae GGB2904

[0019] Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915

[0020] Anaeroplasmataceae GGB2900

[0021] Anaeroplasmataceae GGB2899

[0022]

[0023] or

[0024] (ii) is of species selected from

[0025] Family Genus Species

[0026] Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936

[0027]

[0028] Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910 Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828

[0029]

[0030] CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943

[0031] Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918 m

[0032] Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242

[0033]

[0034] Succinivibrionaceae Succini vibrio SGB4535

[0035] T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143

[0036] Phocaeicola_sp9005 Bacteroidaceae Phocaeicola

[0037] 46645 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0038] 00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0039] 00539645 Oscillospiraceae C AG-110 SGB7123 Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122 Eggerthellaceae CAAEEV01 SGB7278 Hel i cob acteraceae Helicobacter B SGB1279 Fusobacteriaceae Cetobacterium SGB3598 Coriobacteriaceae Collinsella SGB7229 Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461 Hel i cob acteraceae Helicobacter D SGB1307

[0040]

[0041] Aci daminococcaceae Phascol arctob acteriu SGB3950

[0042] m_A

[0043]

[0044] In another aspect of the present invention, there is provided a method of detecting one or more bacteria in a sample obtained from a canine, i.e., according to the method of the first aspect, to monitor or determine the health of the canine, optionally the gut health or microbiome of a canine. In some embodiments, the method comprises detection of the bacteria in a sample, and wherein the lack of detection of the bacteria in a sample is indicative of an unhealthy microbiome. In some embodiments, the method comprises determining the relative abundance of bacteria in a sample, wherein the relative abundance is compared to a control data set, and wherein an increase or decrease in the relative abundance of the bacteria is indicative of an unhealthy microbiome.

[0045] In some embodiments, the one or more bacteria has at least 85% sequence identity, or at least 90% sequence identity, or at least 95% sequence identity with SEQ ID NO 1-9, or SEQ ID NO 89. In some embodiments, the detection requires detecting a bacteria that has at least 85% sequence identity, or at least 90% sequence identity with SEQ ID NO 1-9, or SEQ ID NO 89. This may be used to detect bacteria of the novel bacterial genus described herein.

[0046] In some embodiments, the one or more bacteria has at least 95% sequence identity, or at least 96% sequence identity, or at least 97% sequence identity, or at least 98% sequence identity, or at least 99% sequence identity, or at least 99% sequence identity, or 100% sequence identity with SEQ ID NO 1-92. In some embodiments, the detection requires detecting a bacteria that has at least 95% sequence identity, or at least 96% sequence identity, or at least 97% sequence identity, or at least 98% sequence identity, or at least 99% sequence identity, or at least 99% sequence identity, or 100% sequence identity with SEQ ID NO 1-92. This can be used to detect bacteria of the bacterial species described herein.

[0047] In another aspect of the present invention, there is provided one or more bacteria for use as a biomarker, wherein the one or more bacteria:

[0048] (i) is of the genus selected from

[0049] Family Genus

[0050] Erysipelotrichaceae GGB2876

[0051] Erysipelotrichaceae GGB2877

[0052] Erysipelotrichaceae GGB2927

[0053] Anaerovoracaceae GGB2866

[0054] Lachnospiraceae GGB3041

[0055]

[0056] Erysipelatoclostridiaceae GGB2904 Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915 Anaeroplasmataceae GGB2900 Anaeroplasmataceae GGB2899

[0057]

[0058] (ii) is of a species selected from

[0059] Family Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910 Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886

[0060]

[0061] Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942

[0062]

[0063] T uri cibacteraceae Turicibacter SGB3943 Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918

[0064] m

[0065] Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535

[0066] T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143

[0067] Phocaeicola_sp9005 Bacteroidaceae Phocaeicola

[0068] 46645 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0069] 00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0070] 00539645

[0071]

[0072] Oscillospiraceae C AG-110 SGB7123

[0073] Burkhol deri aceae Sutterella SGB4509

[0074] Oscillospiraceae C AG-110 SGB7122

[0075] Eggerthellaceae CAAEEV01 SGB7278

[0076] Hel i cob acteraceae Helicobacter B SGB1279

[0077] Fusobacteriaceae Cetobacterium SGB3598

[0078] Coriobacteriaceae Collinsella SGB7229

[0079] Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461

[0080] Hel i cob acteraceae Helicobacter D SGB1307

[0081] Aci daminococcaceae Phascol arctob acteriu SGB3950

[0082] m_A

[0083]

[0084] Advantages of aspects and embodiments of the present invention will now be described: The present inventors generated the most complete catalogue to date of the canine gut microbiome at taxonomic and functional levels. In doing so, the present inventors identified candidate bacterial species with high abundance and prevalence in the canine gut microbiome. Altogether, the present work provides a better understanding of the main functions of the canine gut microbiome including carbohydrate metabolism, short chain fatty acids metabolism, amino acid homeostasis, and bile acids metabolism, and allows the inventors to further understand the health of the canine microbiome by analysis, detection and study of bacteria, including completely novel bacteria. These bacteria can be used as biomarkers to study the canine microbiome and can be used for monitoring canine health.

[0085] More specifically, the present inventors generated 1,031 metagenome-assembled genomes (MAGs) from canine fecal samples. These correspond to 240 species, of which 89 are candidate novel taxa. Among these, we identified 10 novel candidate genera. Adding these novel genomes to our mapping database resulted in increased mapping rates to as high as 94%. In addition, we annotated the gene content of the MAGs to 4,182 orthologous gene groups and 244 carbohydrateactive enzymes. The genetic material of a collection of microorganisms found in an environmental or clinical sample is known as metagenome. Microorganisms in a metagenomic sample are identified via mapping to databases of known microbial genomes. These databases are comprised mostly of cultivable microbes that have been isolated mostly from environmental, rodent, and human samples. Microbes that are hosted by canines are underrepresented in these databases and their contribution to host health is unknown. The present approach uses an assembly of genomes from metagenomes. In this strategy, overlapping fragments of DNA sequences from shotgun metagenomics are first assembled into longer contiguous sequences (contigs). Contigs are further grouped or ‘binned’ based on nucleotide frequency, marker genes phylogenies, and / or DNA sequence coverage to get near complete metagenome assembled genomes (MAGs). Using this approach, the present inventors discovered the genomes of candidate novel bacterial species, and / or bacteria with relevant functions that contribute to host health including carbohydrate metabolism, short chain fatty acids metabolism, amino acid homeostasis, and bile acids metabolism. Incorporating these bacteria into our database for metagenomic assignment, the present inventors were able to increase the mapping rate of canine faeces samples from around 20% to around 90%, uncovering a wealth of knowledge about the canine microbiome that was previously unknown. In addition, we have shown that novel bacteria are detected within the top abundant taxa within the canine gut microbiome indicating that these species are highly important.

[0086] Detecting one or more of the bacteria samples in the methods disclosed herein can be used as biomarkers of health, in particular, novel bacteria with the ability to perform health associated functions in the gut, namely degradation of complex dietary fibres, production of short chain fatty acids (SCFAs, including propionate and butyrate), lysine biosynthesis, and conversion of primary bile acid to secondary bile acid. Their presence or absence can be used as health trackers or in combination to build a health index.

[0087] In addition, the bacteria disclosed can be used in diagnosis, monitoring and classification tools for a healthy vs. unhealthy microbiome, or healthy vs unhealthy gut. Any significant deviation, e.g., an increase or decrease in relative abundance of the bacteria as compared to a control set based on healthy canines is indicative of an unhealthy microbiome.

[0088] The bacteria disclosed herein, including both novel species and novel genera of bacteria, can be identified in the gut microbiome of dogs of any breed, life stage, sex or neutered status. The bacterial sample can also be readily obtained from a faceal sample. DNA can be extracted from the sample using any appropriate methods, and the sample can be subjected to any molecular method for the identification of nucleic acid sequences, such as DNA sequencing or fluorescence in situ hybridization (FISH), where the DNA sequencing may be shotgun metagenomics sequencing. For DNA sequencing, more particularly shotgun metagenomics sequencing, the resulting data can be mapped or aligned to a database or reference sequence containing the bacteria of interest for identification, and further, the relative abundance of the bacteria can also be calculated. The bacteria can be detected both individually (i.e., one bacteria is detected), or in combination (i.e., two or more bacteria is detected). While MAG recovery has been widely applied with the fields of human health, prior to this work, a large proportion of the canine gut microbiome remained unknown as evidenced by the persistency low mapping rate of their metagenomes. E.g., only 20% of canine metagenomic sequencing reads map to known RefSef prokaryotic genomes and 40-60% to a curated canine-specific database that includes RefSeq genomes and metagenome-assembled genomes from canine samples. Prior to this study, there was also little description of the common core taxa that reside in the canine gut or the functional potential that they possess. The present study overcomes these disadvantages. Thus, also disclosed herein is a method of DNA sequencing where the DNA sequencing readout is aligned to one or more of the sequences described herein.

[0089] In certain embodiments of all aspects, the bacterial species is selected from

[0090] Family Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0091] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154

[0092] Bacteroidaceae Bacteroides SGB180

[0093] Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888

[0094]

[0095] Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123

[0096]

[0097] Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535 T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143 Oscillospiraceae C AG-110 SGB7123 Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122 Eggerthellaceae CAAEEV01 SGB7278

[0098]

[0099] Hel i cob acteraceae Helicobacter B SGB1279 Fusobacteriaceae Cetobacterium SGB3598 Coriobacteriaceae Collinsella SGB7229 Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461 Hel i cob acteraceae Helicobacter D SGB1307 Aci daminococcaceae Phascol arctob acterium A SGB3950

[0100]

[0101] These correspond to the novel bacterial species identified in this work.

[0102] In some embodiments, the bacteria are of a species selected from:

[0103] Family Genus Species Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Erysipelatoclostridiaceae GGB2904 SGB3910 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Cori ob acteri aceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Anaerovoracaceae Eubacterium M SGB3860 Burkholderiaceae Sutterella SGB4510

[0104]

[0105] Selenomonadaceae Megamonas SGB3868

[0106] Bacteroidaceae Paraprevotella SGB128

[0107] Lachnospiraceae Blautia A SGB4123

[0108] Lachnospiraceae Blautia A SGB4119

[0109] Lachnospiraceae UMGS1370 SGB4088

[0110] Turicibacteraceae Turicibacter SGB3942

[0111] Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918

[0112] Lachnospiraceae Blautia A SGB4125

[0113] Lachnospiraceae UBA9414 SGB4151

[0114] Tannerellaceae Parabacteroides SGB145

[0115] Cellulosilyticaceae Cellulosilyticum SGB3626

[0116] Atopobiaceae NM07-P-09 SGB7241

[0117] Lachnospiraceae Ruminococcus A SGB4095

[0118] Burkholderiaceae C AG-521 SGB4507

[0119] Turicibacteraceae Turicibacter SGB3945

[0120] Lachnospiraceae Faecalimonas SGB4134

[0121] Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839

[0122] Ruminococcaceae UMGS966 SGB7192

[0123] Lachnospiraceae Faecalimonas SGB4143

[0124] Oscillospiraceae C AG-110 SGB7123

[0125] Burkholderiaceae Sutterella SGB4509

[0126] Oscillospiraceae C AG-110 SGB7122

[0127] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0128]

[0129] These are the bacterial species found to be most prevalent and present in all canines tested. In some embodiments, the one or more bacteria is of the species selected from GGB2877 SGB3879, Ileibacterium SGB3882, Allobaculum SGB3883, GGB4941 SGB7240, Allobaculum SGB3888, Blautia A SGB4125, GGB2876 SGB3878, and Allobaculum SGB3884, optionally wherein the one or more bacteria is one of the species selected from GGB2877 SGB3879 or Ileibacterium SGB3882. These bacterial species had the highest relative abundance (i.e., > 1%).

[0130] In certain embodiments, the one or more bacteria is

[0131] (i) is of a genus selected from

[0132] Family Genus

[0133] Erysipelotrichaceae GGB2876

[0134] Erysipelotrichaceae GGB2877

[0135] Erysipelotrichaceae GGB2927

[0136] Anaerovoracaceae GGB2866

[0137] Lachnospiraceae GGB3041 Erysipelatoclostridiaceae GGB2904

[0138] Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915

[0139] Anaeroplasmataceae GGB2900

[0140]

[0141] or

[0142] (ii) is of a species selected from

[0143] Family Genus Species

[0144] Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865

[0145] Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0146] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904

[0147] Bacteroidaceae CAG-462 SGB154

[0148] Bacteroidaceae Bacteroides SGB180

[0149] Clostridiaceae Clostridium P SGB3696

[0150]

[0151] Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526

[0152]

[0153] Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943

[0154] Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918 m

[0155] Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535 T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130

[0156]

[0157] Ruminococcaceae Fournierella SGB7172

[0158] Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893

[0159] Lachnospiraceae Faecalimonas SGB4143

[0160] Phocaeicola_sp9005 Bacteroidaceae Phocaeicola

[0161] 46645

[0162] Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0163] 00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0164] 00539645

[0165]

[0166] These bacteria are those with a genus or species most strongly associated with a relevant functions that contributes to host health. More specifically:

[0167] In some embodiments, the bacteria is of a species selected from:

[0168] Family Genus Species

[0169] Erysipelotrichaceae GGB2876 SGB3878

[0170] Erysipelotrichaceae GGB2877 SGB3879

[0171] Erysipelotrichaceae GGB2927 SGB3936

[0172] Anaerovoracaceae GGB2866 SGB3865

[0173] Bacteroidaceae CAG-462 SGB154

[0174] Bacteroidaceae Bacteroides SGB180

[0175] Clostridiaceae Clostridium P SGB3696

[0176] Erysipelotrichaceae Dubosiella SGB3875

[0177] Lachnospiraceae Ruminococcus B SGB4146

[0178] Lachnospiraceae Ruminococcus B SGB4149

[0179] Erysipelotrichaceae Allobaculum SGB3887

[0180] Erysipelotrichaceae Allobaculum SGB3884

[0181] Erysipelotrichaceae Allobaculum SGB3883

[0182] Erysipelotrichaceae Allobaculum SGB3888

[0183] Erysipelotrichaceae Allobaculum SGB3889

[0184] Erysipelotrichaceae Ileibacterium SGB3880

[0185]

[0186] Erysipelotrichaceae Allobaculum SGB3886

[0187] Erysipelotrichaceae Ileibacterium SGB3882

[0188] UBA932 RC9 SGB268

[0189] Bacteroidaceae Bacteroides SGB179

[0190] Bacteroidaceae Prevotellamassilia SGB122

[0191] Clostridiaceae Clostridium P SGB3707

[0192] Clostridiaceae Clostridium SGB3673

[0193] Brachyspiraceae Brachyspira SGB3620

[0194] Oscillospiraceae Dysosmobacter SGB7158

[0195] Buty ri cicoccaceae Butyricicoccus SGB7115

[0196] Lachnospiraceae Anaerobuty ri cum SGB4099

[0197] Brachyspiraceae Brachyspira SGB3622

[0198] Peptostreptococcaceae Peptacetobacter SGB3828

[0199] CAG-826 UBA4855 SGB3902

[0200] Cori ob acteri aceae Collinsella SGB7219

[0201] Fusobacteriaceae Fusobacterium B SGB3587

[0202] Eub acteri aceae Eubacterium SGB4398

[0203] Anaerovoracaceae Eubacterium M SGB3860

[0204] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0205]

[0206] optionally wherein the species is Anaerobutyricum SGB4099 or Clostridium SGB3673. Such bacterial species are understood to be butyrate producing species.

[0207] In some embodiments, the bacteria is of a species selected from:

[0208] Family Genus Species

[0209] Bacteroidaceae CAG-462 SGB154

[0210] Bacteroidaceae Bacteroides SGB180

[0211] Micrococcaceae Rothia SGB8896

[0212] Burkholderiaceae Sutterella SGB4510

[0213] Burkholderiaceae Sutterella SGB4512

[0214] Succinivibrionaceae Anaerobiospirillum SGB4526

[0215]

[0216] Succinivibrionaceae Anaerobiospirillum SGB4530

[0217] Selenomonadaceae Megamonas SGB3868

[0218] Actinomycetaceae Pauljensenia SGB8738

[0219] Helicobacteraceae Helicobacter A SGB1288

[0220] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0221]

[0222] These bacteria are understood to encode for key propionate producing enzymes. In some embodiments, the bacteria is selected from Bacteroides SGB180 or Phocaeicola sp900546645. In some embodiments, the bacteria is of the species Bacteroides SGB180

[0223] In some embodiments, the bacteria is of a species selected from:

[0224] Family Genus Species

[0225] Erysipelotrichaceae GGB2876 SGB3878

[0226] Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0227] Bacteroidaceae CAG-462 SGB154

[0228] Clostridiaceae Clostridium P SGB3696

[0229] Erysipelotrichaceae Dubosiella SGB3875

[0230] Lachnospiraceae Ruminococcus B SGB4146

[0231] Lachnospiraceae Ruminococcus B SGB4149

[0232] Erysipelotrichaceae Allobaculum SGB3887

[0233] Erysipelotrichaceae Allobaculum SGB3884

[0234] Erysipelotrichaceae Allobaculum SGB3883

[0235] Erysipelotrichaceae Allobaculum SGB3888

[0236] Erysipelotrichaceae Allobaculum SGB3889

[0237] Erysipelotrichaceae Ileibacterium SGB3880

[0238] Erysipelotrichaceae Allobaculum SGB3886

[0239] Erysipelotrichaceae Ileibacterium SGB3882

[0240] Micrococcaceae Rothia SGB8896

[0241] Lachnospiraceae Hungatella A SGB4074

[0242] Bacteroidaceae Paraprevotella SGB128

[0243] Lachnospiraceae Blautia A SGB4123

[0244]

[0245] Lachnospiraceae Blautia A SGB4119

[0246] Lachnospiraceae UMGS1370 SGB4088

[0247] Turicibacteraceae Turicibacter SGB3942

[0248] Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918

[0249] Lachnospiraceae Blautia A SGB4125

[0250] Lachnospiraceae UBA9414 SGB4151

[0251] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0252]

[0253] These bacterial species are implicated in lysine biosynthesis.

[0254] In some embodiments, the bacteria is of the species Peptacetobacter. sp900550335 and sp900539645. These species are implicated in bile acid metabolism.

[0255] In some embodiments, the bacteria is of a species selected from:

[0256] Family Genus Species

[0257] Erysipelotrichaceae GGB2877 SGB3879

[0258] Erysipelotrichaceae GGB2927 SGB3936

[0259] Lachnospiraceae GGB3041 SGB4076

[0260] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923

[0261] Anaeroplasmataceae GGB2900 SGB3904

[0262] Bacteroidaceae CAG-462 SGB154

[0263] Bacteroidaceae Bacteroides SGB180

[0264] Clostridiaceae Clostridium P SGB3696

[0265] Erysipelotrichaceae Dubosiella SGB3875

[0266] Lachnospiraceae Ruminococcus B SGB4146

[0267] Lachnospiraceae Ruminococcus B SGB4149

[0268] UBA932 RC9 SGB268

[0269] Bacteroidaceae Bacteroides SGB179

[0270] Bacteroidaceae Prevotellamassilia SGB122

[0271]

[0272] Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobutyricum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enomonadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parabacteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242

[0273]

[0274] Succinivibrionaceae Succini vibrio SGB4535 Turicibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0275]

[0276] These bacterial species are implicated in the breakdown of chitin.

[0277] In some embodiments, the bacteria is of a species selected from:

[0278] Family Genus Species Erysipelotrichaceae GGB2876 SGB3878

[0279] Bacteroidaceae CAG-462 SGB154

[0280] Bacteroidaceae Bacteroides SGB180

[0281] Clostridiaceae Clostridium P SGB3696

[0282] UBA932 RC9 SGB268

[0283] Bacteroidaceae Bacteroides SGB179

[0284] Bacteroidaceae Prevotellamassilia SGB122

[0285] Micrococcaceae Rothia SGB8896

[0286] Lachnospiraceae Hungatella A SGB4074

[0287] Bacteroidaceae Paraprevotella SGB128

[0288] Lachnospiraceae Blautia A SGB4123

[0289]

[0290] Tannerellaceae Parabacteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Lachnospiraceae Faecalimonas SGB4143 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0291]

[0292] These bacterial species are implicated in the breakdown of starch.

[0293] In some embodiments, the bacteria is of a species selected from:

[0294] Family Genus Species

[0295] Erysipelotrichaceae GGB2877 SGB3879

[0296] Erysipelotrichaceae GGB2927 SGB3936

[0297] Atopobiaceae GGB4941 SGB7240

[0298] Erysipelotrichaceae Dubosiella SGB3875

[0299] Erysipelotrichaceae Allobaculum SGB3887

[0300] Erysipelotrichaceae Allobaculum SGB3884

[0301] Erysipelotrichaceae Allobaculum SGB3883

[0302] Erysipelotrichaceae Allobaculum SGB3888

[0303] UBA932 RC9 SGB268

[0304] Bacteroidaceae Bacteroides SGB179

[0305] CAG-826 UBA4855 SGB3902

[0306] C ori ob acteri aceae Collinsella SGB7219

[0307] Burkholderiaceae Sutterella SGB4510

[0308] Burkholderiaceae Sutterella SGB4512

[0309]

[0310] Succinivibrionaceae Anaerobiospirillum SGB4526

[0311] Succinivibrionaceae Anaerobiospirillum SGB4530

[0312] Lachnospiraceae Hungatella A SGB4074

[0313] Tannerellaceae Parabacteroides SGB145

[0314] Atopobiaceae NM07-P-09 SGB7241

[0315] Lachnospiraceae Ruminococcus A SGB4095

[0316] Burkholderiaceae C AG-521 SGB4507

[0317] Atopobiaceae NM07-P-09 SGB7242

[0318] Succinivibrionaceae Succinivibrio SGB4535

[0319] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0320]

[0321] These bacterial species are implicated in the breakdown of cellulose.

[0322] In some embodiments, the bacteria is of a species selected from:

[0323] Family Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Atopobiaceae GGB4941 SGB7240 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888

[0324]

[0325] UBA932 RC9 SGB268

[0326] Bacteroidaceae Bacteroides SGB179

[0327] CAG-826 UBA4855 SGB3902

[0328] Burkholderiaceae Sutterella SGB4510

[0329] Burkholderiaceae Sutterella SGB4512

[0330] Selenomonadaceae Megamonas SGB3868

[0331] Lachnospiraceae Hungatella A SGB4074

[0332] Lachnospiraceae Blautia A SGB4119

[0333] Lachnospiraceae UMGS1370 SGB4088

[0334] Tannerellaceae Parabacteroides SGB145

[0335] Atopobiaceae NM07-P-09 SGB7241

[0336] Lachnospiraceae Ruminococcus A SGB4095

[0337] Burkholderiaceae C AG-521 SGB4507

[0338] T uri cib acteraceae Turicibacter SGB3945

[0339] Lachnospiraceae Faecalimonas SGB4134

[0340] Lachnospiraceae Faecalimonas SGB4143

[0341] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0342]

[0343] These bacterial species are implicated in the breakdown of xylan.

[0344] In some embodiments, the method comprises detecting a single bacteria. In some embodiments, the method comprises detecting a plurality or a combination of bacteria. In some embodiments, the method comprises detecting two or more bacteria, optionally three or more bacteria, or four or more bacteria.

[0345] In some embodiments, the method comprises quantitating the relative abundance of the bacteria. In some embodiments, the method is performed on a plurality of samples, and the method comprises determining the prevalence of the bacteria in the plurality of samples.

[0346] In some embodiments, the sample is from the canine gut. In some embodiments, the sample is from the gastrointestinal tract (i.e., of a canine). In some embodiments, the sample is a faecal sample (i.e., from a canine). In some embodiments, the canine is a dog, optionally wherein the dog is one or more of a beagle, labrador or terrier.

[0347] In some embodiments, the methods disclosed herein are used to determine or monitor the health of a canine, optionally the gut health of a canine. Also disclosed herein is a method of monitoring the health of a canine, comprising a step of determining the health of the canine’s microbiome using the methods disclosed herein at two or more different time points.

[0348] In some embodiments, the method comprises detection of the bacteria in a sample, wherein the lack of detection of the bacteria in a sample is indicative of an unhealthy microbiome.

[0349] In some embodiments, the method comprises determining the relative abundance of the bacteria in a sample, wherein the relative abundance is compared to a control data set, and wherein an increase or decrease in the relative abundance of the bacteria in the sample relative to the control data set is indicative of an unhealthy microbiome. In some embodiments, the control data set is obtained from a canine, or a plurality of canines at the same life stage.

[0350] In certain non-limiting embodiments, the present disclosure provides a method of treating canine chronic enteropathy in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0351] Family Genus Species

[0352] Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865

[0353] Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0354] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904

[0355] Bacteroidaceae CAG-462 SGB154

[0356] Bacteroidaceae Bacteroides SGB180

[0357] Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875

[0358] Lachnospiraceae Ruminococcus B SGB4146

[0359] Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883

[0360]

[0361] Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128

[0362]

[0363] Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088

[0364] T uri cibacteraceae Turicibacter SGB3942

[0365] T uri cibacteraceae Turicibacter SGB3943

[0366] Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918

[0367] m

[0368] Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535

[0369] T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143

[0370] Phocaeicola_sp9005 Bacteroidaceae Phocaeicola

[0371] 46645

[0372]

[0373] Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0374] 00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0375] 00539645

[0376]

[0377] In certain non-limiting embodiments, the present disclosure provides a method of improving butyrate metabolism in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0378] Family Genus Species

[0379] Erysipelotrichaceae GGB2876 SGB3878

[0380] Erysipelotrichaceae GGB2877 SGB3879

[0381] Erysipelotrichaceae GGB2927 SGB3936

[0382] Anaerovoracaceae GGB2866 SGB3865

[0383] Bacteroidaceae CAG-462 SGB154

[0384] Bacteroidaceae Bacteroides SGB180

[0385] Clostridiaceae Clostridium P SGB3696

[0386] Erysipelotrichaceae Dubosiella SGB3875

[0387] Lachnospiraceae Ruminococcus B SGB4146

[0388] Lachnospiraceae Ruminococcus B SGB4149

[0389] Erysipelotrichaceae Allobaculum SGB3887

[0390] Erysipelotrichaceae Allobaculum SGB3884

[0391] Erysipelotrichaceae Allobaculum SGB3883

[0392] Erysipelotrichaceae Allobaculum SGB3888

[0393] Erysipelotrichaceae Allobaculum SGB3889

[0394] Erysipelotrichaceae Ileibacterium SGB3880

[0395] Erysipelotrichaceae Allobaculum SGB3886

[0396] Erysipelotrichaceae Ileibacterium SGB3882

[0397] UBA932 RC9 SGB268

[0398] Bacteroidaceae Bacteroides SGB179

[0399] Bacteroidaceae Prevotellamassilia SGB122

[0400]

[0401] Clostridiaceae Clostridium P SGB3707

[0402] Clostridiaceae Clostridium SGB3673

[0403] Brachyspiraceae Brachyspira SGB3620

[0404] Oscillospiraceae Dysosmobacter SGB7158

[0405] Buty ri cicoccaceae Butyricicoccus SGB7115

[0406] Lachnospiraceae Anaerobuty ri cum SGB4099

[0407] Brachyspiraceae Brachyspira SGB3622

[0408] Peptostreptococcaceae Peptacetobacter SGB3828

[0409] CAG-826 UBA4855 SGB3902

[0410] Cori ob acteri aceae Collinsella SGB7219

[0411] Fusobacteriaceae Fusobacterium B SGB3587

[0412] Eub acteri aceae Eubacterium SGB4398

[0413] Anaerovoracaceae Eubacterium M SGB3860

[0414] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0415]

[0416] In certain embodiments, the microbial consortium comprises Anaerobutyricum SGB4099 and / or Clostridium SGB3673.

[0417] In certain non-limiting embodiments, the present disclosure provides a method of improving propionate metabolism in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0418] Family Genus Species

[0419] Bacteroidaceae CAG-462 SGB154

[0420] Bacteroidaceae Bacteroides SGB180

[0421] Micrococcaceae Rothia SGB8896

[0422] Burkholderiaceae Sutterella SGB4510

[0423] Burkholderiaceae Sutterella SGB4512

[0424] Succinivibrionaceae Anaerobiospirillum SGB4526

[0425] Succinivibrionaceae Anaerobiospirillum SGB4530

[0426] Selenomonadaceae Megamonas SGB3868

[0427]

[0428] Actinomycetaceae Pauljensenia SGB8738

[0429] Helicobacteraceae Helicobacter A SGB1288

[0430] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0431]

[0432] In certain embodiments, the microbial consortium comprises Bacteroides SGB180 and / or Phocaeicola sp900546645. In certain embodiments, the microbial consortium comprises Bacteroides SGB180.

[0433] In certain non-limiting embodiments, the present disclosure provides a method of improving lysine metabolism in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0434] Family Genus Species

[0435] Erysipelotrichaceae GGB2876 SGB3878

[0436] Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0437] Bacteroidaceae CAG-462 SGB154

[0438] Clostridiaceae Clostridium P SGB3696

[0439] Erysipelotrichaceae Dubosiella SGB3875

[0440] Lachnospiraceae Ruminococcus B SGB4146

[0441] Lachnospiraceae Ruminococcus B SGB4149

[0442] Erysipelotrichaceae Allobaculum SGB3887

[0443] Erysipelotrichaceae Allobaculum SGB3884

[0444] Erysipelotrichaceae Allobaculum SGB3883

[0445] Erysipelotrichaceae Allobaculum SGB3888

[0446] Erysipelotrichaceae Allobaculum SGB3889

[0447] Erysipelotrichaceae Ileibacterium SGB3880

[0448] Erysipelotrichaceae Allobaculum SGB3886

[0449] Erysipelotrichaceae Ileibacterium SGB3882

[0450] Micrococcaceae Rothia SGB8896

[0451] Lachnospiraceae Hungatella A SGB4074

[0452] Bacteroidaceae Paraprevotella SGB128

[0453]

[0454] Lachnospiraceae Blautia A SGB4123

[0455] Lachnospiraceae Blautia A SGB4119

[0456] Lachnospiraceae UMGS1370 SGB4088

[0457] Turicibacteraceae Turicibacter SGB3942

[0458] Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918

[0459] Lachnospiraceae Blautia A SGB4125

[0460] Lachnospiraceae UBA9414 SGB4151

[0461] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0462]

[0463] In certain non-limiting embodiments, the present disclosure provides a method of improving bile acid metabolism in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising Peptacetobacter. sp900550335 and / or sp900539645.

[0464] In certain non-limiting embodiments, the present disclosure provides a method of improving breakdown of chitin in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0465] Family Genus Species

[0466] Erysipelotrichaceae GGB2877 SGB3879

[0467] Erysipelotrichaceae GGB2927 SGB3936

[0468] Lachnospiraceae GGB3041 SGB4076

[0469] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923

[0470] Anaeroplasmataceae GGB2900 SGB3904

[0471] Bacteroidaceae CAG-462 SGB154

[0472] Bacteroidaceae Bacteroides SGB180

[0473] Clostridiaceae Clostridium P SGB3696

[0474] Erysipelotrichaceae Dubosiella SGB3875

[0475] Lachnospiraceae Ruminococcus B SGB4146

[0476] Lachnospiraceae Ruminococcus B SGB4149

[0477]

[0478] UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobutyricum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enomonadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turi cib acteraceae Turi cib acter SGB3942 Turi cib acteraceae Turi cib acter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerell aceae Parabacteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241

[0479]

[0480] Lachnospiraceae Ruminococcus A SGB4095

[0481] Burkhol deri aceae C AG-521 SGB4507

[0482] Atopobiaceae NM07-P-09 SGB7242

[0483] Succinivibrionaceae Succini vibrio SGB4535

[0484] Turi cib acteraceae Turi cib acter SGB3945

[0485] Lachnospiraceae Faecalimonas SGB4134

[0486] Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839

[0487] Ruminococcaceae Faecalibacterium SGB7186

[0488] Ruminococcaceae UMGS966 SGB7192

[0489] Ruminococcaceae Anaerofilum SGB3857

[0490] Lachnospiraceae Robinsoniella SGB4130

[0491] Ruminococcaceae Fournierella SGB7172

[0492] Lachnospiraceae Lachnospira SGB4007

[0493] Erysipelotrichaceae Dielma SGB3893

[0494] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0495]

[0496] In certain non-limiting embodiments, the present disclosure provides a method of improving breakdown of starch in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0497] Family Genus Species

[0498] Erysipelotrichaceae GGB2876 SGB3878

[0499] Bacteroidaceae CAG-462 SGB154

[0500] Bacteroidaceae Bacteroides SGB180

[0501] Clostridiaceae Clostridium P SGB3696

[0502] UBA932 RC9 SGB268

[0503] Bacteroidaceae Bacteroides SGB179

[0504] Bacteroidaceae Prevotellamassilia SGB122

[0505]

[0506] Micrococcaceae Rothia SGB8896

[0507] Lachnospiraceae Hungatella A SGB4074

[0508] Bacteroidaceae Paraprevotella SGB128

[0509] Lachnospiraceae Blautia A SGB4123

[0510] Tannerellaceae Parabacteroides SGB145

[0511] Lachnospiraceae Hungatella A SGB4075

[0512] Cellulosilyticaceae Cellulosilyticum SGB3626

[0513] Lachnospiraceae Faecalimonas SGB4143

[0514] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0515]

[0516] In certain non-limiting embodiments, the present disclosure provides a method of improving breakdown of cellulose in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0517] Family Genus Species

[0518] Erysipelotrichaceae GGB2877 SGB3879

[0519] Erysipelotrichaceae GGB2927 SGB3936

[0520] Atopobiaceae GGB4941 SGB7240

[0521] Erysipelotrichaceae Dubosiella SGB3875

[0522] Erysipelotrichaceae Allobaculum SGB3887

[0523] Erysipelotrichaceae Allobaculum SGB3884

[0524] Erysipelotrichaceae Allobaculum SGB3883

[0525] Erysipelotrichaceae Allobaculum SGB3888

[0526] UBA932 RC9 SGB268

[0527] Bacteroidaceae Bacteroides SGB179

[0528] CAG-826 UBA4855 SGB3902

[0529] C ori ob acteri aceae Collinsella SGB7219

[0530] Burkholderiaceae Sutterella SGB4510

[0531] Burkholderiaceae Sutterella SGB4512

[0532] Succinivibrionaceae Anaerobiospirillum SGB4526

[0533] Succinivibrionaceae Anaerobiospirillum SGB4530

[0534] Lachnospiraceae Hungatella A SGB4074

[0535]

[0536] Tannerellaceae Parabacteroides SGB145 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkholderiaceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succinivibrio SGB4535 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Family Genus Species Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Atopobiaceae GGB4941 SGB7240 Erysipelotrichaceae Dubosiella SGB3875 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888

[0537] UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179

[0538] CAG-826 UBA4855 SGB3902

[0539] C ori ob acteri aceae Collinsella SGB7219 Burkholderiaceae Sutterella SGB4510 Burkholderiaceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 Lachnospiraceae Hungatella A SGB4074 Tannerellaceae Parabacteroides SGB145 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkholderiaceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succinivibrio SGB4535 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0540]

[0541] In certain non-limiting embodiments, the present disclosure provides a method of improving breakdown of xylan in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:

[0542] Family Genus Species

[0543] Erysipelotrichaceae GGB2876 SGB3878

[0544] Erysipelotrichaceae GGB2877 SGB3879

[0545] Atopobiaceae GGB4941 SGB7240

[0546] Bacteroidaceae CAG-462 SGB154

[0547] Bacteroidaceae Bacteroides SGB180

[0548] Erysipelotrichaceae Dubosiella SGB3875

[0549] Lachnospiraceae Ruminococcus B SGB4146

[0550] Lachnospiraceae Ruminococcus B SGB4149

[0551] Erysipelotrichaceae Allobaculum SGB3887

[0552] Erysipelotrichaceae Allobaculum SGB3884

[0553] Erysipelotrichaceae Allobaculum SGB3883

[0554] Erysipelotrichaceae Allobaculum SGB3888

[0555] UBA932 RC9 SGB268

[0556] Bacteroidaceae Bacteroides SGB179

[0557] CAG-826 UBA4855 SGB3902

[0558] Burkholderiaceae Sutterella SGB4510

[0559] Burkholderiaceae Sutterella SGB4512

[0560] Selenomonadaceae Megamonas SGB3868

[0561] Lachnospiraceae Hungatella A SGB4074

[0562] Lachnospiraceae Blautia A SGB4119

[0563] Lachnospiraceae UMGS1370 SGB4088

[0564] Tannerellaceae Parabacteroides SGB145

[0565] Atopobiaceae NM07-P-09 SGB7241

[0566] Lachnospiraceae Ruminococcus A SGB4095

[0567] Burkholderiaceae C AG-521 SGB4507

[0568] T uri cib acteraceae Turicibacter SGB3945

[0569]

[0570] Lachnospiraceae Faecalimonas SGB4134

[0571] Lachnospiraceae Faecalimonas SGB4143

[0572] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0573]

[0574] In certain embodiments, the method further comprises detecting one or more bacteria in a sample obtained from the dog.

[0575] BRIEF DESCRIPTION OF FIGURES

[0576] Figure 1 shows a flowchart of the study design from sample collection to metagenome-assembled genomes assembly and validation using an independent set of dogs

[0577] Figure 2. Sankey diagram of the generated MAGs. Genus and species levels were truncated for representation purposes.

[0578] Figure 3 shows a phylogenetic tree at species level. Inner heatmap shows candidate novel taxa at the genus and species levels (blue). Outer heatmap shows relative abundance levels of the 240 species in an independent dataset of 47 dogs.

[0579] Figure 4, formed by 4A-4E in combination, shows a phylogenetic tree displaying 240 recovered bacterial species from the canine gut microbiome. Phylogenetic tree has been visualised using the online iTOLv5.7 tool, with assigned GTDBtk bacterial phylum denoted by coloured range. The presence (filled) or absence (hollow) of genes associated with metabolite biosynthesis (KEGG) or enzymes associated with substrate degradation (CAZyme) are reported in the binary plot. Abundance of specific CAZyme classes is depicted as a heatmap. AA, Auxiliary Activity; CBM, Carbohydrate-Binding Module; CE, Carbohydrate Esterase; GH, Glycoside Hydrolase; GT, GlycosylTransferase; PL, Polysaccharide Lyase.

[0580] DETAILED DESCRIPTION

[0581] As defined herein abundance refers to the % or relative abundance of a particular bacteria (e.g., species) in a sample on average.

[0582] As defined herein prevalence relates to the proportion of samples tested that have a particular bacteria (e.g., species) present.

[0583] The terms used in this specification generally have their ordinary meanings in the art, within the context of this invention and in the specific context where each term is used. Certain terms are discussed below, or elsewhere in the specification, to provide additional guidance to the practitioner in describing the present invention. As used herein, the use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and / or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” Still further, the terms “having,” “including,” “containing” and “comprising” are interchangeable and one of skill in the art is cognizant that these terms are open ended terms

[0584] As defined herein sequence identity refers to the percentage of nucleotides that match exactly between two different sequences over a defined length of sequence (i.e., the same number of nucleotides) in a given alignment. Any suitable sequence alignment algorithm may be used as is known in the art , and / or as described herein.

[0585] Any bacterial genus or species described herein can in instead be described with reference to the corresponding sequence disclosed in Table A.

[0586] Bacteria

[0587] Genus

[0588] In some embodiments, one or more of the bacteria is of a genus selected from

[0589] Family Genus

[0590] Erysipelotrichaceae GGB2876

[0591] Erysipelotrichaceae GGB2877

[0592] Erysipelotrichaceae GGB2927

[0593] Anaerovoracaceae GGB2866

[0594] Lachnospiraceae GGB3041 Erysipelatoclostridiaceae GGB2904

[0595] Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915

[0596] Anaeroplasmataceae GGB2900

[0597] Anaeroplasmataceae GGB2899

[0598]

[0599] These are novel bacterial genus. In some embodiments, the one or more bacteria has or comprises a sequence with at least 85% sequence identity with one of SEQ ID NO: 1-9 or SEQ ID NO 89, or at least 90% sequence identity, or at least 92.5% sequence identity, or at least 95% sequence identity, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or 100% sequence identity with one of SEQ ID NO: 1-9 or SEQ ID NO: 89. These bacteria are those with a novel genus. The specific sequence ID number for identifying one or more of the named bacteria genera is described elsewhere herein. In some embodiments, the bacterial genera belong to the families Erysipelotrichaceae, Erysipelatoclostridiaceae, Atopobiaceae, Anaeroplasmataceae, Lachnospiraceae, or Anaerovoracaceae .

[0600] In some embodiments, the bacterial has a genus selected from

[0601] Family Genus

[0602] Erysipelotrichaceae GGB2876

[0603] Erysipelotrichaceae GGB2877

[0604] Erysipelotrichaceae GGB2927

[0605] Anaerovoracaceae GGB2866

[0606] Lachnospiraceae GGB3041 Erysipelatoclostridiaceae GGB2904

[0607] Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915

[0608] Anaeroplasmataceae GGB2900

[0609]

[0610] In some embodiments, the one or more bacteria has or comprises a sequence with at least 85% sequence identity with one of SEQ ID NO: 1-9.

[0611] Species

[0612] In some embodiments, the one or more bacteria has or comprises at least 95% sequence identity with one of SEQ ID NO: 1-92, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or 100% sequence identity with one of SEQ ID NO: 1-92. The specific sequence ID number which may be used to detect one or more of the named bacteria species is described elsewhere herein.

[0613] In some embodiments, the bacterial species belong to the families Erysipelotrichaceae, Erysipelatoclostridiaceae, Atopobiaceae, Oscillospiraceae, Brachyspiraceae, Anaeroplasmataceae, Lachnospiraceae, Bacteroidaceae, Clostridiaceae or Anaerovoracaceae, Peptostreptococcaceae, Coriobacteriaceae, Fusobacteriaceae, Eubacteriaceae, Micrococcaceae, Burkholderiaceae, Succinivibrionaceae, Turicibacteraceae, Cellulosilyticaceae, Succinivibrionaceae, Peptostreptococcaceae, Ruminococcaceae . Eggerthellaceae, Anaeroplasmataceae, Mycoplasmoidaceae or Helicobacteracea. In some embodiments, the bacterial species belongs to the genera of Blautia, Collinsella, Blautia A Fecalimonas or Phocaeicola.

[0614] In some embodiments, the bacterial species belong to the genera Sutterella, Collinsella, or Fecalimonas.

[0615] In some embodiments, one or more of the bacteria is of a species selected from Family Genus Species

[0616] Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865

[0617] Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0618] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904

[0619] Bacteroidaceae CAG-462 SGB154

[0620] Bacteroidaceae Bacteroides SGB180

[0621] Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875

[0622] Lachnospiraceae Ruminococcus B SGB4146

[0623] Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882

[0624] UBA932 RC9 SGB268

[0625] Bacteroidaceae Bacteroides SGB179

[0626]

[0627] Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943

[0628] Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918 m

[0629]

[0630] Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535

[0631] T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143

[0632] Phocaeicola_sp9005 Bacteroidaceae Phocaeicola

[0633] 46645 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0634] 00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter

[0635] 00539645 Oscillospiraceae C AG-110 SGB7123 Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122

[0636]

[0637] Eggerthellaceae CAAEEV01 SGB7278

[0638] Hel i cob acteraceae Helicobacter B SGB1279

[0639] Fusobacteriaceae Cetobacterium SGB3598

[0640] Coriobacteriaceae Collinsella SGB7229

[0641] Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461

[0642] Hel i cob acteraceae Helicobacter D SGB1307

[0643] Aci daminococcaceae Phascol arctob acteriu SGB3950

[0644] m_A

[0645]

[0646] In certain embodiments, the bacteria have at least 95% sequence identity, or 100% sequence identity with one of SEQ ID NO 1-92. These are novel bacterial species or bacterial species that have not previously been identified or associated with the canine gut. In certain embodiments, the bacteria have at least 95% sequence identity, or 100% sequence identity with one of SEQ ID NO 1-80. These are the bacterial species most strongly associated with a relevant function that contributes to host health.

[0647] In some embodiments, the bacterial species are selected from:

[0648] Family Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0649] Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154

[0650] Bacteroidaceae Bacteroides SGB180

[0651] Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875

[0652]

[0653] Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530

[0654]

[0655] S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535 T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007

[0656]

[0657] Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143 Oscillospiraceae C AG-110 SGB7123

[0658] Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122 Eggerthellaceae CAAEEV01 SGB7278

[0659] Hel i cob acteraceae Helicobacter B SGB1279 Fusobacteriaceae Cetobacterium SGB3598 Coriobacteriaceae Collinsella SGB7229 Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461

[0660] Hel i cob acteraceae Helicobacter D SGB1307

[0661] Aci daminococcaceae Phascol arctob acterium A SGB3950

[0662]

[0663] In certain embodiments, the bacteria have at least 95% sequence identity, or 100% sequence identity with one of SEQ ID NO 1-77 or one of SEQ ID NO 81-92. These are the entirely novel bacterial species. In certain embodiments, the bacteria have at least 95% sequence identity, or 100% sequence identity with one of SEQ ID NO 1-77

[0664] In some embodiments, the bacteria is of a species selected from GGB2877 SGB3879, Ileibacterium SGB3882, Allobaculum SGB3883, GGB4941 SGB7240, Allobaculum SGB3888, Blautia A SGB4125, GGB2876 SGB3878, and Allobaculum SGB3884. These were all novel species with high relative abundances (e.g., >1%). In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 2, 23, 18, 7, 19, 56, 1 or 17. In some embodiments, the bacteria belongs to the phylum Firmicutes.

[0665] In some embodiments, the bacteria is of the species selected from

[0666] Family Genus Species

[0667] Erysipelotrichaceae GGB2927 SGB3936

[0668] Anaerovoracaceae GGB2866 SGB3865 Erysipelatoclostridiaceae GGB2904 SGB3910 Anaeroplasmataceae GGB2900 SGB3904

[0669] Bacteroidaceae CAG-462 SGB154

[0670] Bacteroidaceae Bacteroides SGB180

[0671]

[0672] Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Cori ob acteri aceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Anaerovoracaceae Eubacterium M SGB3860 Burkholderiaceae Sutterella SGB4510 Selenomonadaceae Megamonas SGB3868 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parabacteroides SGB145 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkholderiaceae C AG-521 SGB4507 Turicibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae UMGS966 SGB7192

[0673]

[0674] Lachnospiraceae Faecalimonas SGB4143

[0675] Oscillospiraceae C AG-110 SGB7123

[0676] Burkholderiaceae Sutterella SGB4509

[0677] Oscillospiraceae C AG-110 SGB7122

[0678] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0679]

[0680] These bacterial species were found to be highly prevalent and were notably detected in all canine samples tested. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 3, 4, 6, 9, 10, 11, 14, 15, 25-27, 34-37, 39, 41, 45, 49-58, 60-63, 66-69, 71, 77-83. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 3, 4, 6, 9, 10, 11, 14, 15, 25-27, 34-37, 39, 41, 45, 49-58, 60-63, 66-69, 71, 77-80.

[0681] In some embodiments, the bacterial species is selected from

[0682] Family Genus Species Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Erysipelatoclostridiaceae GGB2904 SGB3910 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Anaerovoracaceae Eubacterium M SGB3860 Burkholderiaceae Sutterella SGB4510 Selenomonadaceae Megamonas SGB3868

[0683]

[0684] Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parabacteroides SGB145 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkholderiaceae C AG-521 SGB4507 Turicibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae UMGS966 SGB7192 Lachnospiraceae Faecalimonas SGB4143

[0685]

[0686] This includes bacterial species which were both novel and prevalent in all canines tested. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 3, 4, 6, 9, 10, 11, 14, 15, 25-27, 34-37, 39, 41, 45, 49-58, 60-63, 66-69, 71, 77 or 81-83. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 3, 4, 6, 9, 10, 11, 14, 15, 25-27, 34-37, 39, 41, 45, 49-58, 60-63, 66-69, 71, or 77.

[0687] In some embodiments, the bacteria is of the species selected from:

[0688] Family Genus Species

[0689] Erysipelotrichaceae GGB2876 SGB3878

[0690] Erysipelotrichaceae GGB2877 SGB3879

[0691] Erysipelotrichaceae GGB2927 SGB3936

[0692] Anaerovoracaceae GGB2866 SGB3865

[0693] Bacteroidaceae CAG-462 SGB154

[0694] Bacteroidaceae Bacteroides SGB180

[0695]

[0696] Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882

[0697] UBA932 RC9 SGB268

[0698] Bacteroidaceae Bacteroides SGB179

[0699] Bacteroidaceae Prevotellamassilia SGB122

[0700] Clostridiaceae Clostridium P SGB3707

[0701] Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158

[0702] Buty ri cicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828

[0703] CAG-826 UBA4855 SGB3902

[0704] Cori ob acteri aceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587

[0705] Eub acteri aceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0706]

[0707] In some embodiments, the bacteria is of the species selected from Anaerobutyricum SGB4099 or Clostridium SGB3673. In some embodiments, the bacteria is of a species selected from GGB2877 SGB3879, Ileibacterium SGB3882 or Allobaculum SGB3883. Such bacterial species were identified to be butyrate producing species. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 1-4, 10-39, 78 or 80.

[0708] In some embodiments, the bacteria is of a species selected from

[0709] Family Genus Species

[0710] Bacteroidaceae CAG-462 SGB154

[0711] Bacteroidaceae Bacteroides SGB180

[0712] Micrococcaceae Rothia SGB8896

[0713] Burkholderiaceae Sutterella SGB4510

[0714] Burkholderiaceae Sutterella SGB4512

[0715] Succinivibrionaceae Anaerobiospirillum SGB4526

[0716] Succinivibrionaceae Anaerobiospirillum SGB4530

[0717] Selenomonadaceae Megamonas SGB3868

[0718] Actinomycetaceae Pauljensenia SGB8738

[0719] Helicobacteraceae Helicobacter A SGB1288

[0720] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0721]

[0722] In certain embodiments, the bacteria is selected from Bacteroides SGB180 or Phocaeicola sp900546645. In some embodiments, the bacteria is of the species Bacteroides SGB180. These bacteria are understood to encode for key propionate producing enzymes. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 10, 11, 40-47, or 78.

[0723] In some embodiments, the bacteria is selected from the species:

[0724] Family Genus Species

[0725] Erysipelotrichaceae GGB2876 SGB3878

[0726] Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910

[0727] Bacteroidaceae CAG-462 SGB154

[0728] Clostridiaceae Clostridium P SGB3696

[0729] Erysipelotrichaceae Dubosiella SGB3875

[0730] Lachnospiraceae Ruminococcus B SGB4146

[0731]

[0732] Lachnospiraceae Ruminococcus B SGB4149

[0733] Erysipelotrichaceae Allobaculum SGB3887

[0734] Erysipelotrichaceae Allobaculum SGB3884

[0735] Erysipelotrichaceae Allobaculum SGB3883

[0736] Erysipelotrichaceae Allobaculum SGB3888

[0737] Erysipelotrichaceae Allobaculum SGB3889

[0738] Erysipelotrichaceae Ileibacterium SGB3880

[0739] Erysipelotrichaceae Allobaculum SGB3886

[0740] Erysipelotrichaceae Ileibacterium SGB3882

[0741] Micrococcaceae Rothia SGB8896

[0742] Lachnospiraceae Hungatella A SGB4074

[0743] Bacteroidaceae Paraprevotella SGB128

[0744] Lachnospiraceae Blautia A SGB4123

[0745] Lachnospiraceae Blautia A SGB4119

[0746] Lachnospiraceae UMGS1370 SGB4088

[0747] Turicibacteraceae Turicibacter SGB3942

[0748] Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918

[0749] Lachnospiraceae Blautia A SGB4125

[0750] Lachnospiraceae UBA9414 SGB4151

[0751] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0752]

[0753] These bacterial species are implicated in lysine biosynthesis. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 1, 5, 6, 10, 12-23, 40, 48-57, 78 or 80.

[0754] In some embodiments, the bacteria is of the species P. sp900550335 and sp900539645. These species are implicated in bile acid metabolism. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 79 or 80.

[0755] In some embodiments, the bacteria is of the species

[0756] Family Genus Species

[0757] Erysipelotrichaceae GGB2877 SGB3879

[0758]

[0759] Erysipelotrichaceae GGB2927 SGB3936 Lachnospiraceae GGB3041 SGB4076 Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobutyricum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enomonadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123

[0760]

[0761] Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parabacteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626

[0762] Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095

[0763] Burkhol deri aceae C AG-521 SGB4507

[0764] Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535 Turicibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645

[0765]

[0766] These bacterial species are implicated in the breakdown of chitin. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 2, 3, 5, 7-15, 24-34, 41-46, 48-76, or 78-80.

[0767] In some embodiments, the bacteria is of the species

[0768] Family Genus Species

[0769] Erysipelotrichaceae GGB2876 SGB3878

[0770] Bacteroidaceae CAG-462 SGB154

[0771] Bacteroidaceae Bacteroides SGB180

[0772] Clostridiaceae Clostridium P SGB3696

[0773] UBA932 RC9 SGB268

[0774] Bacteroidaceae Bacteroides SGB179

[0775] Bacteroidaceae Prevotellamassilia SGB122

[0776] Micrococcaceae Rothia SGB8896

[0777] Lachnospiraceae Hungatella A SGB4074

[0778] Bacteroidaceae Paraprevotella SGB128

[0779] Lachnospiraceae Blautia A SGB4123

[0780] Tannerellaceae Parabacteroides SGB145

[0781] Lachnospiraceae Hungatella A SGB4075

[0782] Cellulosilyticaceae Cellulosilyticum SGB3626

[0783] Lachnospiraceae Faecalimonas SGB4143

[0784] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0785]

[0786] These bacterial species are implicated in the breakdown of starch. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 1, 10-12, 24-26, 40, 48-50, 58-60, 77 or 78.

[0787] In some embodiments, the bacteria is of the species

[0788] Family Genus Species

[0789] Erysipelotrichaceae GGB2877 SGB3879

[0790] Erysipelotrichaceae GGB2927 SGB3936

[0791] Atopobiaceae GGB4941 SGB7240

[0792]

[0793] Erysipelotrichaceae Dubosiella SGB3875

[0794] Erysipelotrichaceae Allobaculum SGB3887

[0795] Erysipelotrichaceae Allobaculum SGB3884

[0796] Erysipelotrichaceae Allobaculum SGB3883

[0797] Erysipelotrichaceae Allobaculum SGB3888

[0798] UBA932 RC9 SGB268

[0799] Bacteroidaceae Bacteroides SGB179

[0800] CAG-826 UBA4855 SGB3902

[0801] C ori ob acteri aceae Collinsella SGB7219

[0802] Burkholderiaceae Sutterella SGB4510

[0803] Burkholderiaceae Sutterella SGB4512

[0804] Succinivibrionaceae Anaerobiospirillum SGB4526

[0805] Succinivibrionaceae Anaerobiospirillum SGB4530

[0806] Lachnospiraceae Hungatella A SGB4074

[0807] Tannerellaceae Parabacteroides SGB145

[0808] Atopobi aceae NM07-P-09 SGB7241

[0809] Lachnospiraceae Ruminococcus A SGB4095

[0810] Burkholderiaceae C AG-521 SGB4507

[0811] Atopobi aceae NM07-P-09 SGB7242

[0812] Succinivibrionaceae Succinivibrio SGB4535

[0813] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0814]

[0815] These bacterial species are implicated in the breakdown of cellulose. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of one of SEQ ID NO: 2, 3, 7, 13, 16-19, 24, 25, 35, 36, 41-44, 48, 58, 61-65 or 78.

[0816] In some embodiments, the bacteria is of the species

[0817] Family Genus Species

[0818] Erysipelotrichaceae GGB2876 SGB3878

[0819] Erysipelotrichaceae GGB2877 SGB3879

[0820] Atopobiaceae GGB4941 SGB7240

[0821] Bacteroidaceae CAG-462 SGB154

[0822] Bacteroidaceae Bacteroides SGB180

[0823] Erysipelotrichaceae Dubosiella SGB3875

[0824] Lachnospiraceae Ruminococcus B SGB4146

[0825] Lachnospiraceae Ruminococcus B SGB4149

[0826] Erysipelotrichaceae Allobaculum SGB3887

[0827] Erysipelotrichaceae Allobaculum SGB3884

[0828] Erysipelotrichaceae Allobaculum SGB3883

[0829] Erysipelotrichaceae Allobaculum SGB3888

[0830] UBA932 RC9 SGB268

[0831] Bacteroidaceae Bacteroides SGB179

[0832] CAG-826 UBA4855 SGB3902

[0833] Burkholderiaceae Sutterella SGB4510

[0834] Burkholderiaceae Sutterella SGB4512

[0835] Selenomonadaceae Megamonas SGB3868

[0836] Lachnospiraceae Hungatella A SGB4074

[0837] Lachnospiraceae Blautia A SGB4119

[0838] Lachnospiraceae UMGS1370 SGB4088

[0839] Tannerellaceae Parabacteroides SGB145

[0840] Atopobiaceae NM07-P-09 SGB7241

[0841] Lachnospiraceae Ruminococcus A SGB4095

[0842] Burkholderiaceae C AG-521 SGB4507

[0843] T uri cib acteraceae Turicibacter SGB3945

[0844]

[0845] Lachnospiraceae Faecalimonas SGB4134

[0846] Lachnospiraceae Faecalimonas SGB4143

[0847] Bacteroidaceae Phocaeicola Phocaeicola_sp900546645

[0848]

[0849] These bacterial species are implicated in the breakdown of xylan. In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 1, 2, 7, 10, 11, 13-19, 24, 25, 35, 41, 42, 45, 48, 51, 52, 58, 61-63, 66, 67, 77 or 78.

[0850] In some embodiments, the one or more bacteria are of the family Erysipelotrichaceae . In some embodiments, the one or more bacteria is of species GGB2877 SGB3879 or Ileibacterium SGB3882. Both are novel bacterial species which are highly abundant in the canine sample and are of the family Erysipelotrichaceae . In some embodiments, the bacteria has at least 95% or 100% sequence identity with one of SEQ ID NO: 2 or 23.

[0851] In some embodiments, the bacteria comprise genes associated with metabolite biosynthesis. In some embodiments, the bacteria comprise enzymes associated with substrate degradation (e.g., CAZyme). In some embodiments, the bacteria comprises Auxiliary Activity (AA). In some embodiments, the bacteria comprises a carbohydrate-binding molecule (CBM). In some embodiments, the bacteria comprises a carbohydrate esterase (CH). In some embodiments, the bacteria comprises glycoside hydrolase (GH). In some embodiments, the bacteria comprises glycosyl transferase (GT). In some embodiments, the bacteria comprises Polysaccharide Lyase (PL). In some embodiments, the bacteria is of the species selected from Bacteroides SGB179, CAG-462 SGB154, Paraprevotella SGB128 or Prevotellamassilia SGB122. These species encoded a large number of CAZymes with expected high carbohydrate breakdown function.

[0852] In some embodiments, the bacteria comprises acetate-CoA / acetoacetate-CoA-transferase (KO 1034 and K01035), butyrate kinase (K00929) and / or butyryl-CoA dehydrogenase (K00248). Such bacteria have butyrate production potential.

[0853] In some embodiments, the bacteria comprises succinyl-CoA synthetase (K01902 and K01903), methylmalonyl-CoA (K01847) and methylmalonyl-CoA decarboxylase (KI 1264). Such bacteria are associated with propionate production.

[0854] In some embodiments, the bacteria comprise the presence of Bile Salt Hydrolase (K01442) and / or genes within the bai operon (baiB (K15868), baiE (K15872) and baiF (K15871)). Such bacteria are associated with secondary bile conversion.

[0855] In some embodiments, the method comprises detecting two or more bacteria, or three or more bacteria, or four or more bacteria (e.g., as disclosed herein).

[0856] Detection In some embodiments, the one or more bacteria is detected by any suitable method which involves nucleic acid identification. In some embodiments, the one of more bacteria is detected by nucleic acid (e.g., DNA) sequencing, qPCR or fluorescence in-situ hybridization (FISH).

[0857] In certain embodiments, the one or more bacteria is detected by DNA sequencing. In some embodiments, the DNA sequencing only detects a portion of the bacteria’s genome or one or more partial sequences of the bacteria’s genome (e.g., according to one of SEQ ID NO 1-92 disclosed herein). In some embodiments, the DNA sequencing detects the entire bacterial genome. In certain embodiments, the DNA sequencing is shotgun sequencing e.g., shotgun metagenomics sequencing. In certain embodiments, the sequences are aligned to reference genome comprising one or more sequences of the bacteria. In certain embodiments, the sequences are aligned to a metagenome assembled genome (MAG) for the bacterial species. The metagenomic assembly may be performed as described herein. In certain embodiments, the sequences are aligned to one or more of the relevant SEQ ID NOs disclosed herein (e.g., SEQ ID 1-92).

[0858] The sequences may be mapped (or “aligned”) using any suitable method, e.g., using the methods disclosed herein. In certain embodiments, the sequences are mapped with an identity threshold of at least 85%, or at least 90%, or at least 95%, and in some examples, 97%. In some embodiments, the sequences are mapped using BURST, e.g., using fully-gapped alignment. In certain embodiments, ambiguously mapped reads are excluded. In some embodiments, each sequencing read was assigned to the lowest common ancestor that was consistent across at least 80% of all reference sequences tied for best hit.

[0859] In some embodiments, the alignment or mapping rate is at least 40% or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 95% to the reference. In some embodiments, the DNA libraries for sequencing are prepared using any suitable method, e.g., using a Nextera library preparation kit. In some embodiments, this may involve one or more of fragmenting of the DNA sample, end repair of the DNA sample, adaptor ligation, size selection, PCR amplification prior to DNA sequencing. In certain embodiments, the DNA sequencing is paired-end sequencing, optionally with a read-length of 150bp. In some embodiments, the DNA sequencing is carried out on any suitable instrument, e.g., NovaSeq 6000.

[0860] In some embodiments, the method comprises quantitating or determining the relative abundance of the bacteria in the sample. In certain embodiments, the relative abundance of the one or more bacteria is calculated by aligning the sequences (e.g., as defined herein).

[0861] In some embodiments, the method is performed on a plurality of samples, and the method comprises determining the prevalence of the bacteria in the plurality of samples. Sample

[0862] The sample may be any suitable sample from a canine. In some embodiments, the canine is a dog. The dog may be of any suitable breed. In some examples, the dog is optionally a beagle, labrador (e.g., labrador retriever) or a terrier (e.g., Norfolk terrier). In some embodiments, the canine is a puppy, an adult, a senior or geriatric canine In certain embodiments of the claimed subject matter, the sample is from the gastrointestinal tract (i.e., of a canine). In certain embodiments of the claimed subject matter, the sample is a faecal sample (i.e., of a canine). In certain embodiments, DNA is isolated and extracted from other components in the sample before detection, e.g., sequencing. This can be done via any suitable DNA extraction method known in the art. In some examples, a PowerSoil pro DNA isolation kit is used (Qiagen). In some embodiments, a buffer (e.g., a stabilization buffer) is added to the sample before extraction which may help to retain the same microbial composition of the freshly collected sample.

[0863] Methods to determine or monitor health of a canine

[0864] In some embodiments, the method of detecting one or more bacteria disclosed herein is used to determine or monitor the health of a canine, optionally the gut health of a canine. In some embodiments, lack of detection or absence of the bacteria in a sample is indicative of an unhealthy genome. In some embodiments, the presence or detection of the bacteria in a sample is indicative of a healthy microbiome. In certain embodiments, the canine is a dog. The canine may be at any suitable life-stage, or be of any suitable breed.

[0865] In some embodiments, the method comprises the detection and quantification of the one or more bacteria to determine or monitor the health of a canine, optionally the gut health of a canine. In some embodiments, the method comprises determining the relative abundance of the bacteria in a sample, wherein the relative abundance is compared to a control data-set. In some embodiments, the control data-set represents a sample from a healthy canine, more preferably a plurality of samples from a plurality of healthy canines. In some embodiments, the control data-set comprises data from a canine at the same life stage. In some embodiments, the control data-set comprises data from a plurality of dogs at the same and / or at different life stages. In some embodiments, the control data-set comprises data from a dog of the same breed. In some embodiments, the control data-set comprises data from a plurality of dogs with the same and / or different breed. In some embodiments, an increase or decrease in the relative abundance of the bacteria is indicative of an unhealthy microbiome.

[0866] The presently disclosed subject matter also provides a method of monitoring a canine, comprising a step of determining the health of the canine’s microbiome by the method disclosed herein at two or more different time points, or three or more different time points, or four or more different time points, or five or more different time points. There may be any suitable time interval between the two or more different time points. In certain embodiments of the claimed method, the two time points are at least 1 day apart or at least 1 week apart, or at least 1 month apart, or at least 6 months apart.

[0867] Biomarkers for canine health

[0868] The present invention also relates to one or more bacteria disclosed herein for use as a biomarker to determine or monitor the health of a canine, optionally the gut health of a canine. The present invention also relates to the use of one or more bacteria as a biomarker for canine health. In certain embodiments, canine health relates to the health of the canine microbiome.

[0869] Microbial Consortium for Canine Health

[0870] The present disclosure also relates to microbial consortia comprising one or more bacteria disclosed herein for the treatment and improvement of the health of a canine.

[0871] As used herein, the term “microbial consortium” refers to a composition comprising two or more distinct microbial species (e.g., bacterial species) that are combined to perform one or more cooperative or complementary biological functions (e.g., breakdown of starch, bile acid metabolism, etc.). The microbial species within the consortium are isolated, meaning they have been removed from their naturally occurring environment and cultured under controlled laboratory conditions. These strains are selected and assembled based on specific functional attributes, such as metabolic compatibility, synergistic activity, or targeted bioactivity. The consortium is not a naturally occurring assemblage, but rather a non-naturally occurring combination of microorganisms designed to improve canine health.

[0872] As outlined in the present disclosure and detailed in the Examples and Experimental Section, certain bacterial species disclosed herein can improve metabolic functions in an animal (e.g., a dog) in need thereof. For example, but without any limitation, the presently disclosed bacterial species and microbial consortia can improve metabolism of short-chain fatty acids and / or complex carbohydrates. In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving butyrate metabolism. In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein. In certain embodiments, the microbial consortium comprises Anaerobutyricum SGB4099 and / or Clostridium SGB3673. In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving propionate metabolism. In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein. In certain embodiments, the microbial consortium

[0873]

[0874] acleroides SGB180 and / or Phocaeicola sp900546645.

[0875] In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving lysine metabolism. In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein.

[0876] In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving bile acid metabolism. In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein. In certain embodiments, the microbial consortium comprises Peptacetobacter. sp900550335 and / or sp900539645.

[0877] In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving chitin metabolism (e.g., breakdown of chitin). In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein.

[0878] In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving starch metabolism (e.g., breakdown of starch). In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein.

[0879] In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving cellulose metabolism (e.g., breakdown of cellulose). In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein. In certain embodiments, the present disclosure provides a microbial consortium comprising one or more bacteria capable of improving xylan metabolism (e.g., breakdown of xylan). In certain embodiments, the microbial consortium comprises one or more bacteria disclosed herein.

[0880] In certain embodiments, the presently disclosed microbial consortia can be administered to an animal (e.g., a dog) identified using one of the methods disclosed herein.

[0881] Further Methods of the disclosure

[0882] Also disclosed herein, there is provided a method of detecting one or more bacteria in a sample obtained from a canine, wherein the one or more bacteria is detected by metagenomic shotgun sequencing with comparison to a reference dataset described herein and / or using one or more sequences (or MAGs) described herein, optionally in combination with one or more additional reference datasets.

[0883] Additionally or alternatively, the present disclosure relates to methods of treating unhealthy animals (e.g., dogs) identified using one of the methods disclosed herein. In certain embodiments, said methods comprise administration of compositions that can improve the microbiome of the animal. Non-limiting examples of compositions that improve the microbiome are described in International Patent Publication No. WO 2021 / 067968 and International Patent Publication No. WO 2021 / 067971, each of which is incorporated by reference.

[0884] Examples and Experimental Section

[0885] Summary of Experimental Data

[0886] Background: Metagenomic data is annotated via mapping to databases of known genes / genomes. These databases are comprised mostly of cultivable microbes that have been isolated mostly from environmental, rodent, and human samples. Microbes that are hosted by canines may be underrepresented in these databases. Consequently, a huge proportion of metagenomic reads from canine samples remain unmapped due to the presence of unknown bacteria. Using currently available databases, we map -50% of the data from a canine fecal sample down to species level, and 60-70% to any taxonomic level. Consequently, culture-independent approaches are needed to increase our knowledge of the canine gut microbiome.

[0887] Results: We generated 1,031 metagenome-assembled genomes (MAGs) from canine fecal samples. These correspond to 240 species, of which 89 are candidate novel taxa. Among these, we identified 10 novel candidate genera. Adding these novel genomes to our mapping database resulted in increased mapping rates to as high as 94%. In addition, we annotated the gene content of the MAGs to 4,182 orthologous gene groups and 244 carbohydrate-active enzymes.

[0888] Conclusions: We have generated the most complete catalogue to date of the canine gut microbiome at taxonomic and functional levels. As part of this, we have discovered candidate novel bacterial species with high abundance and prevalence in the canine gut microbiome. Altogether, we have a better understanding of the main functions of the canine gut microbiome including carbohydrate metabolism, short chain fatty acids metabolism, amino acid homeostasis, and bile acids metabolism.

[0889] Introduction

[0890] Composed primarily of bacteria and archaea, the gastrointestinal microbiome contributes to essential host metabolic function, immune system education and pathogen protection (Pilla & Suchodolski, 2020). Either directly or indirectly, a healthy and resilient gut microbiome is central to countless physiological processes (Barko et al., 2018). Consequently, the role of the microbiome in both human and animal health, as well as in the etiology and progression of various diseases has become increasingly apparent (Ma et al., 2023). Recently, evident correlations have emerged between gut microbial dysbiosis and a number of acute and chronic canine GI disorders such as chronic enteropathy (CE) (Jergens & Heilmann, 2022; Pilla & Suchodolski, 2020). Fully elucidating the microbial species inhabiting this niche and their functional importance is of pressing importance to pet owners and veterinarians alike.

[0891] Leveraging recent advances in shotgun metagenomic sequencing, the gut microbiome can now be studied at high resolution, annotating both taxonomic presence and functional potential. Commonly, metagenomic data is annotated via the mapping of sequencing reads to databases of known genes or genomes. These databases are comprised mostly of cultivable microbes that have been isolated and sequenced (Thomas et al., 2012). Consequently, a vast proportion of reads in a metagenomic sequencing run remain unmapped due to the presence of uncultured and unknown microbes (Ye et al., 2022). Lloyd et al. estimated that in nonhuman-associated environments 22% to 87% of genera have not been cultured, compared to 3% to 55% of genera in human-associated environments (Lloyd et al., 2018). These data suggest that current microbiome databases, are not only lacking knowledge, but are also biased towards human-associated taxa, potentially significantly limiting the insights drawn from research in animal species.

[0892] To increase our knowledge of the microbial world, culture-independent approaches are needed. One approach to test is the assembly of genomes from metagenomes. In this strategy, overlapping fragments of DNA sequences from shotgun metagenomics are first assembled into longer contiguous sequences (contigs). Contigs are further grouped or ‘binned’ based on nucleotide frequency, marker genes phylogenies, and / or DNA sequence coverage to get near complete metagenome assembled genomes (MAGs) (Bowers et al., 2017). After the incorporation of MAGs in reference databases, mapping rates of human gut metagenomic data increased from 67.76% to 87.51% (Pasolli et al., 2019). Beyond their generation within human research, MAG recovery has since been widely applied within the field of animal science. Most notably utilized to study the microbiome of food production species such as pigs (Chen et al., 2021; Holman et al., 2022), cattle (Stewart et al., 2019; Wilkinson et al., 2020; Xie et al., 2021) and poultry (Gilroy et al., 2021; Gl endinning et al., 2020), the expansive catalogue of novel MAGs recovered have rapidly increased our taxonomic and functional understanding of these previously unexplored environments. Only recently, and to a far lesser extent, have MAGs been generated from companion animals including horses (Gilroy et al., 2022; C. Li et al., 2023), dogs (Ateba et al., 2020; Cusco et al., 2021, 2022; Zhao et al., 2022) and cats (X. Ma et al., 2022; Rojas et al., 2023). However, only a small number of individuals (n = 1 to 12) were included within canine studies, resulting in a relatively modest uplift in our understanding of the gut microbiome in this species. A large proportion of the canine gut microbiome remains unknown, with only 20% of reads mapping to known RefSeq prokaryotic genomes and 40-60% to a curated canine-specific database (Diversigen, 2024). Furthermore, there is little description to date of the common core taxa that reside in the canine gut or the functional potential that they possess. Without the increased database granularity provided by novel species discovery and appropriate description of the roles of these organisms, it is expected that the progression of our understanding of the canine gut microbiome and its role in disease is inherently limited.

[0893] Over a number of decades, research has been performed on the nutritional requirements of dogs leading to substantial findings in key areas such as management of disease, growth, and aging (Bbswald et al., 2019; Larsen & Farcas, 2014; Rudinsky et al., 2018). However, to date, research on the gut microbiome of dogs remains relatively limited, particularly in comparison to humans, mice, and livestock. Given the emergence of the microbiome as a key driver of health and disease, we aimed to produce the most comprehensive catalogue of the gut microbiome of dogs to date. Using fecal samples collected from dogs from across the USA and Europe and a combination of long-read and short-read sequencing, we describe the reconstruction of 1,031 genomes, including candidate novel species that account for a cumulative relative abundance >30%, with a comprehensive description of the key functions the canine microbiome delivers ranging from carbohydrate breakdown to virulence.

[0894] Methods

[0895] Sample selection

[0896] This study is based on metagenomic sequencing data from the Mars Petcare archive (Additional table 1). Fecal samples were obtained from four cohorts (Table 1): (1) dogs housed in environmentally enriched kennel facilities at the Waltham Petcare Science Institute (Leicestershire, UK) and the Pet Health and Nutrition Center (Ohio, USA), (2) dogs owned by clients of Mars Veterinary Health (MVH) Hospitals from across the United States of America, and (3) dogs owned by employees of Mars Petcare living in their home environments located in France, United Kingdom and the United States of America (Figure 1). In total, fecal samples from 107 dogs were included in the discovery set. All dogs were deemed healthy without any uncontrolled medical condition at the time of sampling and were not selected for breed, age, sex, or neutered status. An additional cohort (4) of 47 dogs (16 beagles, 23 Labrador retrievers and 8 Norfolk Terriers) housed at the Waltham Petcare Science Institute were used to validate the abundance and prevalence of the MAGs in an independent dataset.

[0897] Table 1. Cohorts used in this study

[0898] Cohort Source Number of dogs (country)

[0899]

[0900] (1) Dogs housed in environmentally enriched kennel 29 (UK)

[0901] facilities at the Waltham Petcare Science Institute and 23 (USA)

[0902] the Pet Health and Nutrition Center

[0903] (2) Dogs owned by clients of MVH in United States of 6 (USA)

[0904] America

[0905] (3) Dogs owned by employees of Mars Petcare living in 41 (UK)

[0906] their home environments located in France, United 6 (France)

[0907] Kingdom or United States of America 2 (USA)

[0908] (4) Dogs housed in environmentally enriched kennel 47 (UK)

[0909] facilities at the Waltham Petcare Science Institute

[0910]

[0911] Figure 1 shows a flowchart of the study design from sample collection to metagenome-assembled genomes assembly and validation using an independent set of dogs.

[0912] Feces collection

[0913] Samples from (1) and (4) were kept at 4 °C until aliquoted (200mg) and frozen at -80 °C within 3 hours of defecation. Samples from (2) and (3) were placed within 1 hour of defecation into Performabiome. GUT collection tubes (DNAgenotek) according to the manufacturer’s instructions (~200mg), shaken for 30 seconds to mix with the stabilizing liquid, sent to the laboratory, aliquoted (250pl), and stored at -80°C (Figure 1).

[0914] Sequences

[0915] Sequencing

[0916] Shotgun metagenomics

[0917] All samples were subjected to short-read metagenomics sequencing following one of two different workflows (Figure 1). For samples from (1) and (2), DNA was extracted with the PowerSoil Pro DNA isolation Kit (Qiagen) automated for high throughput on the QiaCube HT (Qiagen). Mechanical lysis was completed via bead beating using Powerbead Pro plates (Qiagen) which contain 0.5mm and 0.1mm ceramic beads. Genomic DNA was quantified using the Quant-IT PicoGreen dsDNA Assay Kits and Reagents (Thermo Fisher Scientific). Libraries were prepared with a proprietary procedure adapted from the Nextera XT DNA Library Prep Kit (Illumina) and sequenced at Diversigen (USA) on an Illumina NovaSeq 6000 using paired-end sequencing (2x150 bp). Samples from (3) were extracted using the NucleoSpin 96 Soil Kit (MACHEREY-NAGEL) and the standard SL1 buffer according to the manufacturer’s instructions. Genomic DNA was quantified with Qubit dsDNA Quantification Assay Kits (Thermo Fisher Scientific). Libraries were prepared using the NEBNext Ultra DNA Library Kit (New England Biolabs) and sequenced at Eurofins Genomics (Germany) on an Illumina HiSeq 2500 using paired-end sequencing (2x150 bp). DNA sequences were filtered for low quality (Q-Score <30) and length (<50 bp), and adapter sequences were trimmed using Cutadapt (Martin, 2011). Host (CanFam3) sequences were removed using Bowtie2 (Langmead & Salzberg, 2012). Samples in which the read depth was less than 30 million, were pooled with other samples from the same dog until the 30 million were reached. Up to 16 samples per dog were pooled into the same FASTQ file for assembly (Additional table 1).

[0918] Long-read metagenomics

[0919] Samples from (3) were also subjected to long-read sequencing (Figure 1). DNA extraction followed the same methodology as samples from (1) and (2). Purified DNA was submitted to the University of Wisconsin-Madison Biotechnology Center. DNA purity and concentration were measured on a NanoDrop One instrument (ThermoFisher Scientific). DNA concentration was verified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific). DNA size, integrity, and quality were assessed on the Femto Pulse System (Agilent Technologies). Libraries were prepared using the Ligation Sequencing Kit SQK-LSK109 and the Native Barcoding Expansion Kit 96 EXP-NBD 196 (Oxford Nanopore Technologies) according to the manufacturer’ s recommendations. Libraries were quantified using the Qubit dsDNA High Sensitivity Kit (ThermoFisher Scientific). Libraries were sequenced on FLO-PRO002 (R9.4.1) flow cells using the PromethlON 24 device. LongQC 1.2.0c (Fukasawa et al., 2020) was run on the sequencing files and trimmed reads were used in downstream processes.

[0920] Metagenomic assembly

[0921] Metagenomic assembly of short sequencing reads was performed individually per pooled sample using MEGAHIT (vl.2.9) (D. Li et al., 2015) with a minimum length of contigs of 1000 bp. Hybrid assembly of the long-read data and their corresponding short-read data was performed using the hybrid assembler OPERA-MS (v0.8.3) (Bertrand et al., 2019) with disabled referencebased clustering and default values.

[0922] Binning was performed using MetaBAT 2 (v2.15-25) (Kang et al., 2019) and followed by an initial round of de-replication, performed by drep (v3.4.2) (Olm et al., 2017), at 99% average nucleotide identity (ANI) on bins with a minimum completeness of 50% and maximum genome contamination of 25%. Remaining MAGs were decontaminated using Kraken 2 (v2.1.2) (Wood et al., 2019) and the standard Kraken 2 database as follows. For each MAG, contigs that were not assigned to the Bacteria kingdom using Kraken 2 were removed. The phylum with the maximum total length was determined for each MAG from the Kraken 2 classification and only contigs belonging to that phylum were retained. Another round of de-replication was performed using drep (v3.4.2) with a completeness threshold of >50% and contamination <10% before de-replication of the remaining MAGs at 99% ANI.

[0923] Taxonomic assignment

[0924] For each assembly with completeness >50% and contamination <10%, the contigs were concatenated with lONs inserted between them. MAGs were classified using GTDB-Tk (vl.7.0) (Chaumeil et al., 2020) against the GTDB database release 202. Unclassified MAGs were assigned as candidate novel taxa. First, we applied hierarchical clustering with average linkage on the all-versus-all MASH distances of all genomes, including identified and unidentified MAGs, using the fastcluster python package (Milliner, 2013). The resulting dendrogram was divided with cutoffs at 5%, 15% and 30% genetic distance to define clusters of species-level genome bins (SGBs), genuslevel genome bins (GGBs), and family-level genome bins (FGBs), respectively. Each of the resulting clusters at the different cutoffs was given a cluster number for identification (e.g. SGB1, GGB1, FGB1). ANI at 0.95 was used to refine SGBs; these were merged if any pair of their members showed ANI > 0.95. All MAGs in a cluster were given the taxonomy of the most common GTDB assignment. Clusters that did not contain any GTDB assignment at a certain taxonomic level, were named after their cluster number (e.g. SGB1, GGB1, FGB1).

[0925] Functional annotation

[0926] Genes present in the MAGs were annotated using Prokka (vl.14.6) (Seemann, 2014) to Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology groups (KOs) (Kanehisa & Goto, 2000). Antimicrobial resistance genes (AMRs) were annotated using AMRFinderPlus (v3.11.4) (Feldgarden et al., 2021). Nucleotide sequences of MAGs as well as protein sequences characterized by Prokka were used as the inputs of AMRFinderPlus (https: / / github.com / ncbi / amr / wiki). AMRFinderPlus was run in the plus mode. Carbohydrate-Active enZyme (CAZyme) annotation was performed with dbcan (v.3.0.6) (Zhang et al., 2018). From these annotations, inference of specific functions of interest were made according to presence / absence of marker genes within the genomes of species representatives (Sato et al., 2024). Butyrate production potential was determined according to the presence of acetate-CoA / acetoacetate-CoA-transferase (K01034 and K01035), butyrate kinase (K00929) and / or butyryl-CoA dehydrogenase (K00248). Propionate production was assessed by the presence of enzymes within the succinate pathways, these being succinyl-CoA synthetase (K01902 and K01903), methylmalonyl-CoA (K01847) and methylmalonyl-CoA decarboxylase (KI 1264). Secondary bile acid conversion was assessed by the presence of Bile Salt Hydrolase (KO 1442) and genes within the bai operon (baiB (K15868), baiE (K15872) and baiF (K15871)). Presence of CAZymes responsible for the breakdown of different carbohydrate substrate classes (cellulose, starch, chitin and xylan) was determined as described by (Shaffer et al., 2020), requiring the presence of both a backbone CAZyme for the specific substrate and an oligo-cleaving CAZyme within each species.

[0927] Mapping of an independent dataset

[0928] The generated MAGs were combined with a curated database of Ref-Seq prokaryotic genomes and MAGs derived from publicly available data and de-replicated at 99% ANI. Metagenomic data were aligned to this combined database using fully-gapped alignment with BURST at an identity threshold of 97%. Each sequencing read was assigned to the lowest common ancestor that was consistent across at least 80% of all reference sequences tied for best hit. KOs were observed via alignment to a gene database derived from the previously mentioned combined database. Again, all sequencing reads were aligned to all reference gene sequences at an identity threshold of 97% using fully-gapped alignment with BURST. Ambiguously mapped reads were excluded.

[0929] Results and discussion

[0930] Reconstruction of bacterial strains and discovery of novel taxa

[0931] We reconstructed 1,031 bacterial strains (de-replicated at ANI >=99%) with completeness >50% and contamination <10% from a cohort of 107 dogs comprising different breeds and life stages across the USA and Europe. The median completeness and contamination were 78.65% and 0.81%, respectively. Out of this, 291 MAGs had a completeness >90% and contamination <5%, 9 had a completeness of 100%, and 298 had a contamination of 0. The number of contigs that form each MAG ranges from 2 to 584 with a median of 154. Genome sizes ranged from 459 kbp to 4.9 Mbp with a median of 1.8 Mbp.

[0932] These genomes were assigned to 9 phyla, 10 classes, 24 orders, 43 families, 121 genera, and 240 species (Figure 2). In total, 20 MAGs remained unclassified by GTDB-tk at genus level and 229 at species level. To assign taxonomy to such MAGs, we integrated them with all prokaryotic RefSeq genomes and applied hierarchical clustering with average linkage on the all-versus-all MASH distances of all genomes, including classified and unclassified MAGs. The resulting dendrogram was divided with cutoffs at 5%, 15% and 30% genetic distance to define species, genera, and families, respectively. We defined 10 candidate novel genera and 89 candidate novel species (Figure 3). The novel genera belonged to the families Erysipelotrichaceae, Erysipelatoclostridiaceae, Atopobiaceae, Anaeroplasmataceae, Lachnospiraceae, and Anaerovoracaceae. The most represented genera with novel species were Sutterella, Collinsella, and Fecalimonas. While these families and genera are known to inhabit the gut microbiome in mammals, the recovery of these novel species suggest the existence of canine-specific taxa.

[0933] In line with previous 16S and metagenomics reports of the canine gut microbiome (Coelho et al., 2018; Jha et al., 2020; You & Kim, 2021), we assigned the majority of the 1,031 MAGs to Firmicutes_A (n = 422; 41.0%), Actinobacteriota (n = 136; 13.2%), Firmicutes (n = 128; 12.4%), Bacteroidota (n = 114; 11.1%), Proteobacteria (n = 98; 9.5%), Firmicutes_C (n = 49; 4.8%), and Fusobacteriota (n = 43; 4.2%). Members of these phyla are all known important inhabitants of the mammalian gut (Desselberger, 2018). It was of interest the absence of the phylum Verrucomicrobiota, whose member Akkermansia muciniphila, has shown a protective role in the pathogenesis of cardiovascular disease in mice and humans (Garcia-Mazcorro et al., 2020; Pellegrino et al., 2023).

[0934] The remaining MAGs were assigned to the phyla Campylobacterota (n = 39; 3.8%) and Spirochaetota (n = 2; 0.2%), whose most known species are considered pathogens (Prachasilpchai et al., 2007). Campylobacter spp. and Helicobacter spp. have been found in dogs with history of diarrhea or vomiting (Lemos et al., 2021; Prachasilpchai et al., 2007). Spirochaetota spp. have been reported in the canine oral microbiome (Ruparell et al., 2020), which supports the idea of an oral-gut microbiome crosstalk.

[0935] At genus-level, the genera with the highest number of representative MAGs were Blautia (n = 80; 7.8%), Collinsella (n = 68; 6.6%), Blautia A (n = 61; 5.9%), Fecalimonas (n = 56; 5.4%) and Phocaeicola (n = 54; 5.2%), all of which have been studied in the mammalian gut microbiome. Blauta hansenii has been inversely associated with obesity in mice (Shibata et al., 2023). Collinsella intestinalis has not been described previously in the canine gut microbiome but is known to be capable of degrading potentially harmful processed food components (Wolf et al., 2019). Fecalimonas umbilicata is an acetate-producing bacterium proposed as a novel species of a novel genus in 2017 (Sakamoto et al., 2017) and Phocaeicola spp. are considered mutualistic bacteria in the human gut microbiome (Hehemann et al., 2012).

[0936] Independent dataset reveals high abundance and prevalence of candidate novel taxa

[0937] For validation, fecal metagenomic data from a further cohort of 47 dogs from Waltham Petcare Science Institute composed of 16 beagles, 23 Labrador retrievers and 8 Norfolk Terriers were mapped to a reference database combining our generated MAGs with publicly available RefSeq prokaryotic genomes and MAGs generated from publicly available data (refs). Mapping rates at any taxonomic level ranged from 60% to 94% with a median of 87%. At species level, mapping rates ranged from 52% to 79% with a median of 75%, an important uplift compared to mapping rates close to 20% when mapping to RefSeq genomes. The 240 species covered by our generated MAGs accounted on average for 95% of the reads mapped at species-level of the combined database; of great note, the novel species accounted for 32.6%. This is an important proportion that highlights the lack of knowledge we previously had of the canine gut microbiome. While some characteristics are shared with other mammals, genetic and environmental factors shape the dog microbiome to contribute to proper metabolic function and health.

[0938] The most abundant species was Prevotella copri (8.1%) followed by two novel species, GGB2877 SGB3879 (7.3%) and 1 leibacterium SGB3882 (5.7%). Prevotella copri is also the most abundant bacterium in the gut microbiome of humans (Yeoh et al., 2022). It has been described as both beneficial and detrimental to human health as it has been associated with high fiber low fat diets and improved glucose metabolism, but also with hypertension and persistent gut inflammation (Yeoh et al., 2022). Both novel species, GGB2877 SGB3879 and Ileibacterium SGB3882, belong to the family Erysipelotrichaceae, highly abundant in the mammalian gut microbiome (Wu et al., 2021). Its role in mammalian hosts has been associated with metabolic disorders given an observed increase in obese animals and while on high-fat diets (Kaakoush, 2015). In dogs, Erysipelotrichaceae has shown positive correlations with levels of acetate, propionate and butyrate, and negative correlations with crude protein and fat digestibility (Bermingham et al., 2017).

[0939] Relative abundances >1% were observed in 26 species, eight of which were candidate novel species (GGB2877 SGB3879, Ileibacterium SGB3882, Allobaculum SGB3883, GGB4941 SGB7240, Allobaculum SGB3888, Blautia A SGB4125, GGB2876 SGB3878, and Allobaculum SGB3884 the majority of these belonging to the phylum Firmicutes (Figure 3). The abundance of the 89 candidate novel species ranged from IxlO'6to 7.3% with a mean of 0.35%. In terms of prevalence, 131 out of the 240 species covered by our generated MAGs (54.6%) and 41 out of the 89 novel species (46.1%) were present in all 47 independent samples. GGB2877 SGB3879 was present in 46 samples (98%), while Ileibacterium SGB3882 was present in 41 samples (87.2%).

[0940] Functional description of the canine gut microbiome uncovered through metagenomics

[0941] Using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZymes (CAZymes) functional annotation of predicted genes within our canine MAG catalogue, we annotated 4,182 KEGG orthologous groups (KOs) and 244 CAZymes. These could be grouped into a further 187 KEGG pathways and all six CAZyme families encompassing wide functional capacities. KEGG functional pathways were primarily associated with metabolic systems, with carbohydrate (7.7%-29.2%), lipid (1.6%-6.3%) and amino acid metabolism (4.3%-20.7%) predominant, accounting for an average of 32.3% of total KOs per genome. This observation is likely attributed to the canine omnivorous diet, mainly constituted by kibble consisting of cereals, animal proteins and vegetables. A summary of key function presence for each identified species can be found in Figure 4.

[0942] A new view of carbohydrate metabolism capacity of the canine gut microbiome In spite of being a crucial energy source, the canine genome encodes few genes with carbohydrate metabolism functionality. This results in a strong reliance on the commensal bacteria of the gut microbiome to perform this function, accounting for the high percentage of metabolic pathways attributed to carbohydrate metabolism within our recovered species. The carbohydrate degrading enzymes produced by these bacterial species (CAZymes) are crucial to the breakdown of simple and complex carbohydrates that are often present in commercial canine diets into components that can be absorbed by the intestinal epithelium. Our canine gut microbiome species catalogue described an average of 71.3±51.7 CAZymes per species, with glycoside hydrolases (GHs; n=113) consistently accounting for the largest proportion of identified CAZymes per genome (46.1%), as is evident in other omnivorous mammals (Holman et al., 2022; Onyango et al., 2021). This was followed by glycosyltransferases (n=47; 36.8%), carbohydrate esterases (n=17; 9.1%), carbohydrate-binding modules (n = 37; 5.8%), polysaccharide lyases (n=24; 1.3%), and auxiliary activities (n=6; 0.9%). Species encoding the greatest number of CAZymes, and likely showing high carbohydrate breakdown function belong to the fibrolytic Bacteroidaceae family; of which four are candidate novel species with a combined relative abundance of 1.94% within our mapped cohort (Bacteroides SGB179, 0.24%; CAG-462 SGB1540.06%, Paraprevotella SGB128 0.67% and Prevotellamassilia SGB122 0.97%). Primarily attributed to GH families GH2, GH3 GH20, GH29, GH43 and GH92, it is likely that these species are key to dietary, and host derived glycan breakdown in the dog, as has been described previously for Bacteroidaceae spp. in humans (Onyango et al., 2021). More broadly, CAZymes involved in the breakdown of commonly used dietary fibers were identified in a number of species, specifically, cellulose (present in 35.83% [n=86] of species), starch (22.08%, n=52), chitin (75.42%; n=181) or xylan (hemicellulose) (36.67%; n=88). For many identified species, this is the first description of their ability to degrade such complex dietary fibers within the canine gut microbiome (Figure 4).

[0943] Uncovering the SCFA producing potential of the canine gut microbiome Using KEGG annotation of detected species, we can identify the presence of KOs crucial in the production of well described health promoting metabolites generated as a product of the carbohydrate degradation pathways described above. The production of short-chain fatty acids (SCFAs) from dietary fiber degradation is an important function of the gut microbiome in dogs, with dysregulation of these pathways associated with a number of enteropathologies including canine chronic enteropathy (Minamoto et al., 2019). SCFAs comprise three major forms, acetate (60%), propionate (20%), and butyrate (20%), with only specific, phylogenetically diverse bacterial groups possessing the ability to form butyrate and propionate (Morrison & Preston, 2016). The majority of microbial butyrate is synthesized via the acetyl-CoA pathway utilizing butyryl-CoA dehydrogenase (bed), butyryl-CoA: acetate CoA- transferase (but) and butyrate kinase (buk) as enzymes involved in the terminal steps of metabolite synthesis. Here, genes for bed (K00248), but (K01034 & K01035) or buk (K00929) were identified in 37.5% (n=90) of recovered species (collective relative abundance 45.59%). While the majority of these species are previously recognized species, their presence, and as such likely contribution to butyrate production within the canine gut microbiome has been otherwise poorly described. Such species include Bacteroides uniformis and Romboutsia hominis as well as almost all recovered Allobaculum spp., Bacteroides spp. and Phocaeicola spp. Thirty-four of the butyrate-producing species identified are candidate novel species from butyrate-producing genera (e.g. Anaerobutyricum SGB40 Clostridium SGB3673) and together contribute an average relative abundance of 24.6% within the canine gut. Of note, we identified one novel genus and 12 candidate novel species showing butyrate-producing capacity within the Erysipelotrichaceae family, with GGB2877 SGB3879, Ileibacterium SGB3882 and Allobaculum SGB3883 being particularly prominent members of the healthy canine gut microbiome (relative abundance of 7.28%, 5.74% and 3.08% respectively). With increasing links between members of this bacterial family and mammalian metabolic disorders being described (Kaakoush, 2015), the value of uncovering such novelty and abundance within the canine gut is of pressing importance.

[0944] While three propionate production pathways exist within the intestinal microbiome, the succinate (sue) pathway predominates, with three key enzymes used in the production process; methylmalonyl-CoA mutase (muf), methylmalonyl-CoA decarboxylase (mmcD) and succinyl-CoA synthetase (sucC & sue!)). Propionate production potential through detection of these enzymes was determined for 18.8% (n=45) of recovered species in the canine gut (collective relative abundance 11.40%). Known Bifidobacterium spp., Phascolarctobacterium A spp., Megamonas spp., Bacteroides spp. and Anaerobiospirillum spp. account for the vast majority of propionate production potential within our species catalogue (n=19; collective relative abundance 2.02%). However, similar to findings for butyrate production, a number of known species with no previous description within the canine gut (e.g. Phocaeicola sp900546645,' relative abundance 3.93%) alongside novel species (e.g. Bacteroides SGB180,' relative abundance 0.42%) encode key propionate producing enzymes and likely account for a fundamental portion of propionate production within the healthy dog. As such, the described MAG catalogue dramatically expands our understanding of bacterial species capable of supporting SCFA production within the healthy canine gut, particularly pertaining to butyrate production.

[0945] Microbial synthesis of amino acids to support dietary intake.

[0946] The gut microbiome also plays an important role in host amino acid homeostasis. Recent evidence demonstrates that the gut microbiota in the small and large intestine plays a role not only in the breakdown of proteins to amino acids, but also in the synthesis of amino acids themselves, with these subsequently utilized by the host. The amino acids produced by specific bacterial species may compensate for the lack of essential amino acids in a lower-quality protein diet, particularly for lysine, where the bioavailability is reduced during the extrusion process of kibble production. Lysine biosynthesis occurs through metabolism of aspartate through the diaminopimelate pathway (DAP). At least one variant of the complete lysine biosynthesis DAP pathway (succinyl, acetyl, dehydrogenase or aminotransferase) was present in 42.1% (101 / 240) of species, indicating their contribution to this function within the canine gut microbiome. The vast majority of bacterial species containing complete DAP modules show no previous description within the canine gut.

[0947] Expanded potential for secondary bile acid conversion by Peptacetobacter species within the canine gut.

[0948] Bile acids aid in digestion and absorption of lipids in the GI tract. It is proposed that secondary bile acids provide further capability in inhibiting the growth of certain pathogenic bacterial species in dogs, namely E. coli and C. perfrinogens . Primary bile acids are converted to secondary bile acids by bacteria with 7a-dehydroxylation capabilities, a capability possessed by a relatively limited set of bacteria that encode the bile acid inducible (bai operon. Species were examined for the presence of genes involved in the conversion of primary bile acid to secondary bile acid, being bile salt hydrolase (BSH; K01442), alongside the seven bai operon enzyme genes (baiA-F). Of the bai operon genes, only baiB (K15868), baiE (K15872) and baiF (K15871) were detected within our species catalogue, with these likely retained during assembly and binning due to higher gene abundance. Genes for both BSH and the bai operon were present in two Peptacetobacter species (P. sp900550335 (relative abundance 1.13%) and P. sp900539645 (0.56%)), with these uncultured species only previously identified in the human gut. Functional characterization of these species and description of their presence within the canine gut microbiome expands our understanding of the repertoire of bacteria that could influence secondary bile acid concentration during healthy and dysbiotic states beyond the well described P. hiranonis (Clostridium hiranonis) within the same genera (Suchodolski, 2022). We propose that the compiled MAG catalogue comprises species with key functionality in supporting metabolic function of the canine gut. At least 54 candidate novel species show relative abundance of key butyrate, propionate, lysine or secondary bile acid biosynthesis genes and, alongside known species otherwise undescribed in the canine gut microbiome, have the potential to be key contributors to these functions of known health impact within the dog.

[0949] Antimicrobial resistance, stress resistance, and virulence in the canine gut microbiome

[0950] AMRFinderPlus was used to identify the presence of antimicrobial resistance (AMR), stress resistance, and virulence genes in the reconstructed genomes. Among the AMR genes, abc-f known to provide resistance to a broad range of clinically used antibiotic classes (Ero et al., 2019), was found in 49 (20.4%) of the recovered species. This was followed by vanR (n = 41; 17.1%), which plays a role in the resistance to the last resort antibiotic vancomycin (Stogios & Savchenko, 2020) and blaRl (n = 23; 9.6%) involved in resistance to P-lactam antibiotics (Llarrull et al., 2011). AMR genes were found present mainly in members of the genera Fecalimonas (n = 8), Blautia A (n = 6), and Blautia (n = 6), which are members of the fibrolytic Lachnospiraceae family and known to harbor conjugative transposons containing antibiotic resistance genes (Zaplana et al., 2023). Stress resistance genes were found in 10 of the recovered species; eight of them contained genes conferring resistance to arsenicals, one to copper, and one to tellurite. Lastly, virulence factors were found in four species, three of which are known pathogens, Clostridium P perfringens, Escherichia flexneri, Escherichia marmotae, and Peptacetobacter sp900550335, but none in the candidate novel species.

[0951] Conclusion

[0952] Microbiome research has been heavily biased towards human studies, consequently limiting the understanding of the canine gut microbiome mostly to species previously found in humans, which may go some way to explaining prior reports of marked similarities between the human and canine microbiomes (Coelho et al. 2018). The MAGs generated in this study are evidence of a significant taxonomic and functional catalogue of the gut microbiome presently thought to be unique to dogs, with the assembled novel bacterial species accounting for >30% of mapped reads at species-level when tested in an independent cohort. The biological relevance of these novel taxa has also been illustrated, with the second and third most abundant species linked to butyrate production and several other important functions discussed.

[0953] The taxa and functions presented here encompass the expected microbiome of any healthy dog, as the catalogue was not limited to the microbiome of a specific cohort, with samples collected from pets living in a range of environments, across multiple countries. This resource allows us to map metagenomic data from fecal samples at rates not seen before regardless of breed, age, sex or geography, expanding opportunities to understand the role of the microbiome in canine health and disease, as well as more completely map the taxonomic and functional impact of dietary interventions.

[0954] Sequences

[0955] The present application discloses the SEQ ID NO: 1-92. The complement sequences and the reverse complement sequences are also considered to be part of the disclosure. These sequences may be used for detection and / or monitoring the health of a canine, e.g., according to the methods disclosed herein in the corresponding sequence listing, optionally the gut health of a canine. These sequences may be used as a reference sequence for alignment. Bacteria may be detected using one or more of these sequences, wherein said bacteria can be used as a biomarker for health in canines.

[0956] Table A shows how the sequence ID NOs correspond to the bacterial genus and bacterial species disclosed herein. The bacteria disclosed herein may be described with reference to the relevant SEQ ID NO as indicated in Table A. For example, the bacterial species GGB2876 SGB3878 has a sequence with at least 95% identity to, or 100% identity to SEQ ID NO: 1, and so on.

[0957] Table A

[0958] SEQ Phylum Class Order Family Genus Species ID NO:

[0959] 1 Firmicut Bacilli Erysipelotrichales Erysipelotric GGB2876 SGB3878 es haceae

[0960] 2 Firmicut Bacilli Erysipelotrichales Erysipelotric GGB2877 SGB3879 es haceae

[0961] 3 Firmicut Bacilli Erysipelotrichales Erysipelotric GGB2927 SGB3936 es haceae

[0962] 4 Firmicut Clostridi Peptostreptococca Anaerovorac GGB2866 SGB3865 es_A a les aceae

[0963] 5 Firmicut Clostridi Lachnospirales Lachnospirac GGB3041 SGB4076 es_A a eae

[0964]

[0965] SEQ Phylum Class Order Family Genus Species ID NO:

[0966] 6 Firmicut Bacilli Erysipelotrichales Erysipelatocl GGB2904 SGB3910 es ostridiaceae

[0967] 7 Actinoba Coriobac Coriobacteriales Atopobiaceae GGB4941 SGB7240 cteriota teriia

[0968] 8 Firmicut Bacilli Erysipelotrichales Erysipelatocl GGB2915 SGB3923 es ostridiaceae

[0969] 9 Firmicut Bacilli Acholeplasmatale Anaeroplasm GGB2900 SGB3904 es s ataceae

[0970] 10 Bacteroi Bacteroi Bacteroidales Bacteroi dace CAG-462 SGB154 dota di a ae

[0971] 11 Bacteroi Bacteroi Bacteroidales Bacteroi dace Bacteroide SGB180 dota di a ae s

[0972] 12 Firmicut Clostridi Clostridiales Clostridiacea Clostridiu SGB3696 es_A a e m_P

[0973] 13 Firmicut Bacilli Erysipelotrichales Erysipelotric Dubosiella SGB3875 es haceae

[0974] 14 Firmicut Clostridi Lachnospirales Lachnospirac Ruminoco SGB4146 es_A a eae ccus B

[0975] 15 Firmicut Clostridi Lachnospirales Lachnospirac Ruminoco SGB4149 es_A a eae ccus B

[0976] 16 Firmicut Bacilli Erysipelotrichales Erysipelotric Allobacul SGB3887 es haceae um

[0977] 17 Firmicut Bacilli Erysipelotrichales Erysipelotric Allobacul SGB3884 es haceae um

[0978] 18 Firmicut Bacilli Erysipelotrichales Erysipelotric Allobacul SGB3883 es haceae um

[0979] 19 Firmicut Bacilli Erysipelotrichales Erysipelotric Allobacul SGB3888 es haceae um

[0980] 20 Firmicut Bacilli Erysipelotrichales Erysipelotric Allobacul SGB3889 es haceae um

[0981]

[0982] SEQ Phylum Class Order Family Genus Species ID NO:

[0983] 21 Firmicut Bacilli Erysipelotrichales Erysipelotric Ileibacteri SGB3880 es haceae um

[0984] 22 Firmicut Bacilli Erysipelotrichales Erysipelotric Allobacul SGB3886 es haceae um

[0985] 23 Firmicut Bacilli Erysipelotrichales Erysipelotric Ileibacteri SGB3882 es haceae um

[0986] 24 Bacteroi Bacteroi Bacteroidales UBA932 RC9 SGB268 dota di a

[0987] 25 Bacteroi Bacteroi Bacteroidales Bacteroi dace Bacteroide SGB179 dota di a ae s

[0988] 26 Bacteroi Bacteroi Bacteroidales Bacteroi dace Prevotella SGB122 dota di a ae massilia

[0989] 27 Firmicut Clostridi Clostridiales Clostridiacea Clostridiu SGB3707 es_A a e m_P

[0990] 28 Firmicut Clostridi Clostridiales Clostridiacea Clostridiu SGB3673 es_A a e m

[0991] 29 Spirocha Brachysp Brachyspirales Brachyspirac Brachyspir SGB3620 etota irae eae a

[0992] 30 Firmicut Clostridi Oscillospirales Oscillospirac Dysosmob SGB7158 es_A a eae acter

[0993] 31 Firmicut Clostridi Oscillospirales Butyricicocca Butyricico SGB7115 es_A a ceae ecus

[0994] 32 Firmicut Clostridi Lachnospirales Lachnospirac Anaerobut SGB4099 es_A a eae yricum

[0995] 33 Spirocha Brachysp Brachyspirales Brachyspirac Brachyspir SGB3622 etota irae eae a

[0996] 34 Firmicut Clostridi Peptostreptococca Peptostreptoc Peptacetob SGB3828 es_A a les occaceae acter

[0997] 35 Firmicut Bacilli RFN20 CAG-826 UBA4855 SGB3902 es

[0998]

[0999] SEQ Phylum Class Order Family Genus Species ID NO:

[1000] 36 Actinoba Coriobac Coriobacteriales Coriobacteria Collinsella SGB7219 cteriota teriia ceae

[1001] 37 Fusobact Fusobact Fusobacteriales Fusobacteriac Fusobacter SGB3587 eriota eriia eae ium_B

[1002] 38 Firmicut Clostridi Eubacteriales Eubacteriace Eubacteriu SGB4398 es_A a ae m

[1003] 39 Firmicut Clostridi Peptostreptococca Anaerovorac Eubacteriu SGB3860 es_A a les aceae m_M

[1004] 40 Actinoba Actinom Actinomycetales Micrococcac Rothia SGB8896 cteriota ycetia eae

[1005] 41 Proteoba Gammap Burkholderiales Burkholderia Sutterella SGB4510 cteria roteobact ceae

[1006] eria

[1007] 42 Proteoba Gammap Burkholderiales Burkholderia Sutterella SGB4512 cteria roteobact ceae

[1008] eria

[1009] 43 Proteoba Gammap Enterobacterales Succini vibrio Anaerobio SGB4526 cteria roteobact naceae spirillum

[1010] eria

[1011] 44 Proteoba Gammap Enterobacterales Succini vibrio Anaerobio SGB4530 cteria roteobact naceae spirillum

[1012] eria

[1013] 45 Firmicut Negativi Selenomonadales Selenomonad Megamon SGB3868 es_C cutes aceae as

[1014] 46 Actinoba Actinom Actinomycetales Actinomycet Pauljensen SGB8738 cteriota ycetia aceae ia

[1015] 47 Campylo Campylo Campy 1 ob acteral e Heli cob actera Helicobact SGB1288 bacterota bacteria s ceae er_A

[1016] 48 Firmicut Clostridi Lachnospirales Lachnospirac Hungatella SGB4074 es_A a eae _A

[1017]

[1018] SEQ Phylum Class Order Family Genus Species ID NO:

[1019] 49 Bacteroi Bacteroi Bacteroidales Bacteroi dace Paraprevot SGB128 dota di a ae ella

[1020] 50 Firmicut Clostridi Lachnospirales Lachnospirac Blautia A SGB4123 es_A a eae

[1021] 51 Firmicut Clostridi Lachnospirales Lachnospirac Blautia A SGB4119 es_A a eae

[1022] 52 Firmicut Clostridi Lachnospirales Lachnospirac UMGS137 SGB4088 es_A a eae 0

[1023] 53 Firmicut Bacilli Haloplasmatales_ Turicibactera Turicibact SGB3942 es A ceae er

[1024] 54 Firmicut Bacilli Haloplasmatales_ Turicibactera Turicibact SGB3943 es A ceae er

[1025] 55 Firmicut Bacilli Erysipelotrichales Erysipelatocl Erysipelat SGB3918 es ostridiaceae oclostridiu

[1026] m

[1027] 56 Firmicut Clostridi Lachnospirales Lachnospirac Blautia A SGB4125 es_A a eae

[1028] 57 Firmicut Clostridi Lachnospirales Lachnospirac UBA9414 SGB4151 es_A a eae

[1029] 58 Bacteroi Bacteroi Bacteroidales Tannerellace Parabacter SGB145 dota di a ae oides

[1030] 59 Firmicut Clostridi Lachnospirales Lachnospirac Hungatella SGB4075 es_A a eae _A

[1031] 60 Firmicut Clostridi Lachnospirales Cellulosilytic Cellulosily SGB3626 es_A a aceae ticum

[1032] 61 Actinoba Coriobac Coriobacteriales Atopobiaceae NM07-P- SGB7241 cteriota teriia 09

[1033] 62 Firmicut Clostridi Lachnospirales Lachnospirac Ruminoco SGB4095 es_A a eae ccus_A

[1034]

[1035] SEQ Phylum Class Order Family Genus Species ID NO:

[1036] 63 Proteoba Gammap Burkholderiales Burkholderia C AG-521 SGB4507 cteria roteobact ceae

[1037] eria

[1038] 64 Actinoba Coriobac Coriobacteriales Atopobiaceae NM07-P- SGB7242 cteriota teriia 09

[1039] 65 Proteoba Gammap Enterobacterales Succini vibrio Succinivib SGB4535 cteria roteobact naceae rio

[1040] eria

[1041] 66 Firmicut Bacilli Haloplasmatales_ Turicibactera Turicibact SGB3945 es A ceae er

[1042] 67 Firmicut Clostridi Lachnospirales Lachnospirac Faecalimo SGB4134 es_A a eae nas

[1043] 68 Firmicut Clostridi Lachnospirales Lachnospirac Schaedlere SGB4154 es_A a eae Ila

[1044] 69 Firmicut Clostridi Peptostreptococca Peptostreptoc Romboutsi SGB3839 es_A a les occaceae a

[1045] 70 Firmicut Clostridi Oscillospirales Ruminococca Faecalibac SGB7186 es_A a ceae terium

[1046] 71 Firmicut Clostridi Oscillospirales Ruminococca UMGS966 SGB7192 es_A a ceae

[1047] 72 Firmicut Clostridi Oscillospirales Ruminococca Anaerofilu SGB3857 es_A a ceae m

[1048] 73 Firmicut Clostridi Lachnospirales Lachnospirac Robinsoni SGB4130 es_A a eae ella

[1049] 74 Firmicut Clostridi Oscillospirales Ruminococca Foumierel SGB7172 es_A a ceae la

[1050] 75 Firmicut Clostridi Lachnospirales Lachnospirac Lachnospi SGB4007 es_A a eae ra

[1051] 76 Firmicut Bacilli Erysipelotrichales Erysipelotric Dielma SGB3893 es haceae

[1052]

[1053] SEQ Phylum Class Order Family Genus Species ID NO:

[1054] 77 Firmicut Clostridi Lachnospirales Lachnospirac Faecalimo SGB4143 es_A a eae nas

[1055] 78 Bacteroi Bacteroi Bacteroidales Bacteroi dace Phocaeicol Phocaeicol dota di a ae a a_sp90054

[1056] 6645 79 Firmicut Clostridi Peptostreptococca Peptostreptoc Peptacetob Peptacetob es_A a les occaceae acter acter_sp90

[1057] 0550335 80 Firmicut Clostridi Peptostreptococca Peptostreptoc Peptacetob Peptacetob es_A a les occaceae acter acter_sp90

[1058] 0539645 81 Firmicut Clostridi Oscillospirac

[1059] es_A a Oscillospirales eae C AG-110 SGB7123 82 Gammap

[1060] Proteoba roteobact Burkholderia

[1061] cteria eria Burkholderiales ceae Sutterella SGB4509 83 Firmicut Clostridi Oscillospirac

[1062] es_A a Oscillospirales eae C AG-110 SGB7122 84 Actinoba Coriobac Eggerthellace CAAEEV

[1063] cteriota teriia Coriobacteriales ae 01 SGB7278 85 Campylo Campylo Campy 1 ob acteral e Heli cob actera Helicobact bacterota bacteria s ceae er_B SGB1279 86 Fusobact Fusobact Fusobacteriac Cetobacter

[1064] eriota eriia Fusobacteriales eae ium SGB3598 87 Actinoba Coriobac Coriobacteria

[1065] cteriota teriia Coriobacteriales ceae Collinsella SGB7229 88 Fusobact Fusobact Fusobacteriac Cetobacter

[1066] eriota eriia Fusobacteriales eae ium_A SGB3567 89 Firmicut Acholeplasmatale Anaeroplasm

[1067] es Bacilli s ataceae GGB2899 SGB3903

[1068]

[1069] SEQ Phylum Class Order Family Genus Species ID NO:

[1070] 90 Firmicut Mycoplasmoi Malacopla

[1071] es Bacilli Mycoplasmatales daceae sma SGB3461 91 Campylo Campylo Campy 1 ob acteral e Heli cob actera Helicobact

[1072] bacterota bacteria s ceae er_D SGB1307 92 Phascolarc

[1073] Firmicut Negativi Acidaminococcal Acidaminoco tobacteriu

[1074] es_C cutes es ccaceae m_A SGB3950

[1075]

[1076] Table B shows how bacteria indicated above, with reference to their SEQ ID NO, are implicated with biological function.

[1077] SEQ Novel Novel Butyrate Propionate Lysine Bile Chitin Starch Cellulose Xylan ID Genus Species Acid

[1078] NO:

[1079] 1 1 1 1 0 1 0 0 1 0 1

[1080] 2 1 1 1 0 0 0 1 0 1 1

[1081] 3 1 1 1 0 0 0 1 0 1 0

[1082] 4 1 1 1 0 0 0 0 0 0 0

[1083] 5 1 1 0 0 1 0 1 0 0 0

[1084] 6 1 1 0 0 1 0 0 0 0 0

[1085] 7 1 1 0 0 0 0 1 0 1 1

[1086] 8 1 1 0 0 0 0 1 0 0 0

[1087] 9 1 1 0 0 0 0 1 0 0 0

[1088] 10 1 1 1 1 0 1 1 0 1

[1089]

[1090] 1 1 1 0 0 1 1 0 1 1 1 0 1 0 1 1 0 0 1 1 0 1 0 1 0 1 1 1 1 0 1 0 1 0 0 1 1 1 0 1 0 1 0 0 1 1 1 0 1 0 0 0 1 1 1 1 0 1 0 0 0 1 1 1 1 0 1 0 0 0 1 1 1 1 0 1 0 0 0 1 1 1 1 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0

[1091]

[1092] 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 1 1 0 0 1 0 0 1 0 1 0 0 1 0 1 1 1 0 1 0 0 1 0 1 1 1 0 1 0 0 1 0 1 0 1 0 1 0 0 1 0 1 0 1 0 1 0 0 1 0 0 1 1 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 1 0 1 1 1 1 1 0 0 1 0 1 1 0 0 1 0 0 1 0 1 1 0 0 1 0 0 1 0 1 0 0 1 1 0 0 1 0 1 0 0 1

[1093]

[1094] 1 0 0 1 0 1 0 0 0

[1095] 1 0 0 1 0 1 0 0 0

[1096] 1 0 0 1 0 1 0 0 0

[1097] 1 0 0 1 0 1 0 0 0

[1098] 1 0 0 1 0 1 0 0 0

[1099] 1 0 0 0 0 1 1 1 1

[1100] 1 0 0 0 0 1 1 0 0

[1101] 1 0 0 0 0 1 1 0 0

[1102] 1 0 0 0 0 1 0 1 1

[1103] 1 0 0 0 0 1 0 1 1

[1104] 1 0 0 0 0 1 0 1 1

[1105] 1 0 0 0 0 1 0 1 0

[1106] 1 0 0 0 0 1 0 1 0

[1107] 1 0 0 0 0 1 0 0 1

[1108] 1 0 0 0 0 1 0 0 1

[1109] 1 0 0 0 0 1 0 0 0

[1110] 1 0 0 0 0 1 0 0 0

[1111] 1 0 0 0 0 1 0 0 0

[1112] 1 0 0 0 0 1 0 0 0

[1113] 1 0 0 0 0 1 0 0 0

[1114] 1 0 0 0 0 1 0 0 0

[1115]

[1116] 74 1 0 0 0 0 1 0 0 0

[1117] 75 1 0 0 0 0 1 0 0 0

[1118] 76 1 0 0 0 0 1 0 0 0

[1119] 77 1 0 0 0 0 0 1 0 1

[1120] 78 -1 1 1 1 0 1 1 1 1

[1121] 79 -1 0 0 0 1 1 0 0 0

[1122] 80 -1 1 0 1 1 1 0 0 0

[1123]

[1124] Data availability

[1125] Sequencing data and MAGs generated in this study will be deposited in the NCBI SRA.

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[1183] Although the presently disclosed subject matter and its advantages have been described in detail, it should be understood that various changes, substitutions and alterations can be made herein without departing from the spirit and scope of the invention as defined by the appended claims. Moreover, the scope of the present application is not intended to be limited to the particular embodiments of the process, machine, manufacture, composition of matter, means, methods and steps described in the specification. As one of ordinary skill in the art will readily appreciate from the disclosure of the presently disclosed subject matter, processes, machines, manufacture, compositions of matter, means, methods, or steps, presently existing or later to be developed that perform substantially the same function or achieve substantially the same result as the corresponding embodiments described herein can be utilized according to the presently disclosed subject matter. Accordingly, the appended claims are intended to include within their scope such processes, machines, manufacture, compositions of matter, means, methods, or steps.

[1184] Patents, patent applications, publications, product descriptions and protocols are cited throughout this application the disclosures of which are incorporated herein by reference in their entireties for all purposes.

Claims

WHAT IS CLAIMED IS:

1. A method of detecting one or more bacteria in a sample obtained from a canine, wherein the one or more bacteria:(i) is of a genus selected fromFamily GenusErysipelotrichaceae GGB2876Erysipelotrichaceae GGB2877Erysipelotrichaceae GGB2927Anaerovoracaceae GGB2866Lachnospiraceae GGB3041 Erysipelatoclostridiaceae GGB2904Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915Anaeroplasmataceae GGB2900Anaeroplasmataceae GGB2899or(ii) is of a species selected fromFamily Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918 mLachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535 T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143Phocaeicola_sp9005 Bacteroidaceae Phocaeicola46645 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter00539645 Oscillospiraceae C AG-110 SGB7123 Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122 Eggerthellaceae CAAEEV01 SGB7278 Hel i cob acteraceae Helicobacter B SGB1279 Fusobacteriaceae Cetobacterium SGB3598 Coriobacteriaceae Collinsella SGB7229 Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461 Hel i cob acteraceae Helicobacter D SGB1307 Aci daminococcaceae Phascol arctob acteriu SGB3950m_A2. The method of claim 1, wherein the one or more bacteria is of the species Family Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910 Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242Succinivibrionaceae Succini vibrio SGB4535 T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143 Oscillospiraceae C AG-110 SGB7123Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122 Eggerthellaceae CAAEEV01 SGB7278Hel i cob acteraceae Helicobacter B SGB1279 Fusobacteriaceae Cetobacterium SGB3598 Coriobacteriaceae Collinsella SGB7229 Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461Hel i cob acteraceae Helicobacter D SGB1307Aci daminococcaceae Phascol arctob acterium A SGB39503. The method of claim 1, wherein the one or more bacteria comprises a sequence with at least 85% sequence identity, or at least 90% sequence identity with one or more of SEQ ID 1-9 or SEQ ID NO 89.

4. The method of claim 1, wherein the one or more bacteria comprises a sequence with at least 95% sequence identity with one or more of SEQ ID 1-925. The method of any preceding claim, wherein the one or more bacteria is detected by DNA sequencing, qPCR or fluorescence in-situ hybridisation (FISH).

6. The method of any preceding claim, wherein the one or more bacteria is detected by DNA sequencing, preferably wherein sequences are aligned to a metagenome assembled genome (MAG) for the bacterial species.

7. The method of claim 6, wherein the DNA sequencing is paired-end sequencing, optionally with a read-length of 150bp.

8. The method of claim 6, wherein the mapping rate is at least 40%, or at least 50%, optionally wherein the mapping is achieved by BURST and / or as defined herein9. The method of any one of claims 1-8, wherein the one or more bacteria is of the species selected from GGB2877 SGB3879, Ileibacterium SGB3882, Allobaculum SGB3883, GGB4941 SGB7240, Allobaculum SGB3888, Blautia A SGB4125, GGB2876 SGB3878, and Allobaculum SGB3884, optionally wherein the one or more bacteria is one of the species selected from GGB2877 SGB3879 or Ileibacterium SGB3882,10. The method of any one of claims 1-8 wherein the one or more bacteria is of the species selected fromFamily Genus SpeciesErysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Erysipelatoclostridiaceae GGB2904 SGB3910 Anaeroplasmataceae GGB2900 SGB3904Bacteroidaceae CAG-462 SGB154Bacteroidaceae Bacteroides SGB180Lachnospiraceae Ruminococcus B SGB4146Lachnospiraceae Ruminococcus B SGB4149Bacteroidaceae Bacteroides SGB179Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Cori ob acteri aceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Anaerovoracaceae Eubacterium M SGB3860 Burkholderiaceae Sutterella SGB4510 Selenomonadaceae Megamonas SGB3868 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parabacteroides SGB145 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkholderiaceae C AG-521 SGB4507 Turicibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae UMGS966 SGB7192 Lachnospiraceae Faecalimonas SGB4143 Oscillospiraceae C AG-110 SGB7123 Burkholderiaceae Sutterella SGB4509Oscillospiraceae C AG-110 SGB7122 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp90053964511. The method of any one of claims 1-8, wherein the one or more bacteria is of a species selected fromFamily Genus SpeciesErysipelotrichaceae GGB2876 SGB3878Erysipelotrichaceae GGB2877 SGB3879Erysipelotrichaceae GGB2927 SGB3936Anaerovoracaceae GGB2866 SGB3865Bacteroidaceae CAG-462 SGB154Bacteroidaceae Bacteroides SGB180Clostridiaceae Clostridium P SGB3696Erysipelotrichaceae Dubosiella SGB3875Lachnospiraceae Ruminococcus B SGB4146Lachnospiraceae Ruminococcus B SGB4149Erysipelotrichaceae Allobaculum SGB3887Erysipelotrichaceae Allobaculum SGB3884Erysipelotrichaceae Allobaculum SGB3883Erysipelotrichaceae Allobaculum SGB3888Erysipelotrichaceae Allobaculum SGB3889Erysipelotrichaceae Ileibacterium SGB3880Erysipelotrichaceae Allobaculum SGB3886Erysipelotrichaceae Ileibacterium SGB3882UBA932 RC9 SGB268Bacteroidaceae Bacteroides SGB179Bacteroidaceae Prevotellamassilia SGB122Clostridiaceae Clostridium P SGB3707Clostridiaceae Clostridium SGB3673Brachyspiraceae Brachyspira SGB3620Oscillospiraceae Dysosmobacter SGB7158Buty ri cicoccaceae Butyricicoccus SGB7115Lachnospiraceae Anaerobuty ri cum SGB4099Brachyspiraceae Brachyspira SGB3622Peptostreptococcaceae Peptacetobacter SGB3828CAG-826 UBA4855 SGB3902Cori ob acteri aceae Collinsella SGB7219Fusobacteriaceae Fusobacterium B SGB3587Eub acteri aceae Eubacterium SGB4398Anaerovoracaceae Eubacterium M SGB3860Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645optionally wherein the species is Anaerobutyricum SGB4099 or Clostridium SGB3673,orFamily Genus SpeciesBacteroidaceae CAG-462 SGB154Bacteroidaceae Bacteroides SGB180Micrococcaceae Rothia SGB8896Burkholderiaceae Sutterella SGB4510Burkholderiaceae Sutterella SGB4512Succinivibrionaceae Anaerobiospirillum SGB4526Succinivibrionaceae Anaerobiospirillum SGB4530Selenomonadaceae Megamonas SGB3868Actinomycetaceae Pauljensenia SGB8738Heli cob acteraceae Helicobacter A SGB1288Bacteroidaceae Phocaeicola Phocaeicola_sp900546645orFamily Genus Species Erysipelotrichaceae GGB2876 SGB3878 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910 Bacteroidaceae CAG-462 SGB154 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 Micrococcaceae Rothia SGB8896 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125Lachnospiraceae UBA9414 SGB4151Phocaeicola_sp90054664 Bacteroidaceae Phocaeicola5 Peptacetobacter_sp90053 Peptostreptococcaceae Peptacetobacter9645orFamily Genus Species Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645orFamily Genus Species Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Lachnospiraceae GGB3041 SGB4076 Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Buty ri cicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 Burkholderiaceae Sutterella SGB4510 Burkholderiaceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 Selenomonadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 Turicibacteraceae Turicibacter SGB3942 Turicibacteraceae Turicibacter SGB3943 Erysipelatoclostridiaceae Erysipelatoclostridium SGB3918 Lachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parabacteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkholderiaceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succinivibrio SGB4535 Turicibacteraceae Turicibacter SGB3945Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900550335 Peptostreptococcaceae Peptacetobacter Peptacetobacter_sp900539645orFamily Genus Species Erysipelotrichaceae GGB2876 SGB3878 Bacteroidaceae CAG-462 SGB154Bacteroidaceae Bacteroides SGB180Clostridiaceae Clostridium P SGB3696UBA932 RC9 SGB268Bacteroidaceae Bacteroides SGB179Bacteroidaceae Prevotellamassilia SGB122 Micrococcaceae Rothia SGB8896 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123Tannerellaceae Parabacteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626Lachnospiraceae Faecalimonas SGB4143 Bacteroidaceae Phocaeicola Phocaeicola_sp900546645orFamily Genus SpeciesErysipelotrichaceae GGB2877 SGB3879Erysipelotrichaceae GGB2927 SGB3936Atopobiaceae GGB4941 SGB7240Erysipelotrichaceae Dubosiella SGB3875Erysipelotrichaceae Allobaculum SGB3887Erysipelotrichaceae Allobaculum SGB3884Erysipelotrichaceae Allobaculum SGB3883Erysipelotrichaceae Allobaculum SGB3888UBA932 RC9 SGB268Bacteroidaceae Bacteroides SGB179CAG-826 UBA4855 SGB3902Cori ob acteri aceae Collinsella SGB7219Burkholderiaceae Sutterella SGB4510Burkholderiaceae Sutterella SGB4512Succinivibrionaceae Anaerobiospirillum SGB4526Succinivibrionaceae Anaerobiospirillum SGB4530Lachnospiraceae Hungatella A SGB4074Tannerellaceae Parabacteroides SGB145Atopobiaceae NM07-P-09 SGB7241Lachnospiraceae Ruminococcus A SGB4095Burkholderiaceae C AG-521 SGB4507Atopobiaceae NM07-P-09 SGB7242Succinivibrionaceae Succinivibrio SGB4535Bacteroidaceae Phocaeicola Phocaeicola_sp900546645orFamily Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Atopobiaceae GGB4941 SGB7240 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179CAG-826 UBA4855 SGB3902 Burkholderiaceae Sutterella SGB4510 Burkholderiaceae Sutterella SGB4512Selenomonadaceae Megamonas SGB3868Lachnospiraceae Hungatella A SGB4074Lachnospiraceae Blautia A SGB4119Lachnospiraceae UMGS1370 SGB4088Tannerellaceae Parabacteroides SGB145Atopobiaceae NM07-P-09 SGB7241Lachnospiraceae Ruminococcus A SGB4095Burkholderiaceae C AG-521 SGB4507Turicibacteraceae Turicibacter SGB3945Lachnospiraceae Faecalimonas SGB4134Lachnospiraceae Faecalimonas SGB4143Bacteroidaceae Phocaeicola Phocaeicola_sp90054664512. The method of any one of claims 1-8, wherein the bacteria is of species Bacteroides SGB18013. The method of any preceding claim, wherein the method comprises detecting two or more bacteria, optionally three or more bacteria, or four or more bacteria.

14. The method of any preceding claim, wherein the method comprises quantitating the relative abundance of the bacteria.

15. The method of any preceding claim, wherein the method is performed on a plurality of samples, and wherein the method comprises determining the prevalence of the bacteria in the plurality of samples.

16. The method of any preceding claim, wherein the sample is from the gastrointestinal tract.

17. The method of any preceding claim, wherein the sample is a faecal sample.

18. The method of any preceding claim, where the canine is a dog, optionally wherein the dog is one or more of a beagle, labrador or terrier.

19. The method of any preceding claim, wherein the method is used to determine or monitor the health of a canine.

20. The method of claim 19, wherein the method comprises detection of the bacteria in a sample, and wherein lack of detection of the bacteria in a sample is indicative of an unhealthy microbiome.

21. The method of claim 19, wherein the method comprises determining the relative abundance of bacteria in a sample, wherein the relative abundance is compared to a control data set, and wherein an increase or decrease in the relative abundance of the bacteria is indicative of an unhealthy microbiome.

22. The method of claim 21, wherein the control data set is obtained from a canine at the same life stage23. A method of monitoring the health of a canine, comprising a step of determining the health of the canine’s microbiome by the method of any one of claims 21-23, at two or more different time points.

24. The method of any preceding claim, wherein the bacteria is used as a biomarker.

25. One or more bacteria for use as a biomarker to determine or monitor the health of a canine, wherein the one or more bacteria(i) is of the genus selected fromFamily GenusErysipelotrichaceae GGB2876Erysipelotrichaceae GGB2877Erysipelotrichaceae GGB2927Anaerovoracaceae GGB2866Lachnospiraceae GGB3041 Erysipelatoclostridiaceae GGB2904Atopobiaceae GGB4941 Erysipelatoclostridiaceae GGB2915 Anaeroplasmataceae GGB2900 Anaeroplasmataceae GGB2899(ii) is of a species selected fromFamily Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910 Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904 Bacteroidaceae CAG-462 SGB154 Bacteroidaceae Bacteroides SGB180 Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875 Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530 S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918mLachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172 Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143Phocaeicola_sp9005 Bacteroidaceae Phocaeicola46645 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter00539645 Oscillospiraceae C AG-110 SGB7123Burkhol deri aceae Sutterella SGB4509 Oscillospiraceae C AG-110 SGB7122 Eggerthellaceae CAAEEV01 SGB7278Hel i cob acteraceae Helicobacter B SGB1279 Fusobacteriaceae Cetobacterium SGB3598 Coriobacteriaceae Collinsella SGB7229 Fusobacteriaceae C etob acterium A SGB3567 Anaeroplasmataceae GGB2899 SGB3903 Mycoplasmoidaceae Malacoplasma SGB3461Hel i cob acteraceae Helicobacter D SGB1307Aci daminococcaceae Phascol arctob acteriu SGB3950m_A26. A method of treating canine chronic enteropathy and / or improve metabolism in a dog in need thereof, comprising administering a pharmaceutical composition comprising an effective amount of a microbial consortium comprising at least one bacterial species selected from:Family Genus Species Erysipelotrichaceae GGB2876 SGB3878 Erysipelotrichaceae GGB2877 SGB3879 Erysipelotrichaceae GGB2927 SGB3936 Anaerovoracaceae GGB2866 SGB3865 Lachnospiraceae GGB3041 SGB4076 Erysipelatoclostridiaceae GGB2904 SGB3910Atopobiaceae GGB4941 SGB7240 Erysipelatoclostridiaceae GGB2915 SGB3923 Anaeroplasmataceae GGB2900 SGB3904Bacteroidaceae CAG-462 SGB154Bacteroidaceae Bacteroides SGB180Clostridiaceae Clostridium P SGB3696 Erysipelotrichaceae Dubosiella SGB3875Lachnospiraceae Ruminococcus B SGB4146 Lachnospiraceae Ruminococcus B SGB4149 Erysipelotrichaceae Allobaculum SGB3887 Erysipelotrichaceae Allobaculum SGB3884 Erysipelotrichaceae Allobaculum SGB3883 Erysipelotrichaceae Allobaculum SGB3888 Erysipelotrichaceae Allobaculum SGB3889 Erysipelotrichaceae Ileibacterium SGB3880 Erysipelotrichaceae Allobaculum SGB3886 Erysipelotrichaceae Ileibacterium SGB3882 UBA932 RC9 SGB268 Bacteroidaceae Bacteroides SGB179 Bacteroidaceae Prevotellamassilia SGB122 Clostridiaceae Clostridium P SGB3707 Clostridiaceae Clostridium SGB3673 Brachyspiraceae Brachyspira SGB3620 Oscillospiraceae Dysosmobacter SGB7158 Butyricicoccaceae Butyricicoccus SGB7115 Lachnospiraceae Anaerobuty ri cum SGB4099 Brachyspiraceae Brachyspira SGB3622 Peptostreptococcaceae Peptacetobacter SGB3828 CAG-826 UBA4855 SGB3902 Coriobacteriaceae Collinsella SGB7219 Fusobacteriaceae Fusobacterium B SGB3587 Eubacteriaceae Eubacterium SGB4398 Anaerovoracaceae Eubacterium M SGB3860 Micrococcaceae Rothia SGB8896 Burkhol deri aceae Sutterella SGB4510 Burkhol deri aceae Sutterella SGB4512 Succinivibrionaceae Anaerobiospirillum SGB4526 Succinivibrionaceae Anaerobiospirillum SGB4530S el enom onadaceae Megamonas SGB3868 Actinomycetaceae Pauljensenia SGB8738 Hel i cob acteraceae Helicobacter A SGB1288 Lachnospiraceae Hungatella A SGB4074 Bacteroidaceae Paraprevotella SGB128 Lachnospiraceae Blautia A SGB4123 Lachnospiraceae Blautia A SGB4119 Lachnospiraceae UMGS1370 SGB4088 T uri cibacteraceae Turicibacter SGB3942 T uri cibacteraceae Turicibacter SGB3943Erysipelatoclostridiu Erysipelatoclostridiaceae SGB3918 mLachnospiraceae Blautia A SGB4125 Lachnospiraceae UBA9414 SGB4151 Tannerellaceae Parab acteroides SGB145 Lachnospiraceae Hungatella A SGB4075 Cellulosilyticaceae Cellulosilyticum SGB3626 Atopobiaceae NM07-P-09 SGB7241 Lachnospiraceae Ruminococcus A SGB4095 Burkhol deri aceae C AG-521 SGB4507 Atopobiaceae NM07-P-09 SGB7242 Succinivibrionaceae Succini vibrio SGB4535 T uri cibacteraceae Turicibacter SGB3945 Lachnospiraceae Faecalimonas SGB4134 Lachnospiraceae Schaedlerella SGB4154 Peptostreptococcaceae Romboutsia SGB3839 Ruminococcaceae Faecalibacterium SGB7186 Ruminococcaceae UMGS966 SGB7192 Ruminococcaceae Anaerofilum SGB3857 Lachnospiraceae Robinsoniella SGB4130 Ruminococcaceae Fournierella SGB7172Lachnospiraceae Lachnospira SGB4007 Erysipelotrichaceae Dielma SGB3893 Lachnospiraceae Faecalimonas SGB4143Phocaeicola_sp9005 Bacteroidaceae Phocaeicola46645 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter00550335 Peptacetobacter_sp9 Peptostreptococcaceae Peptacetobacter00539645

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