Changes

Dogs and humans have co-existed for thousands of years, with evidence suggesting that domestication of the dog (''Canis lupus familiaris'')  began around 32,000 years ago, when divergence from their wild ancestors, the grey wolf (''Canis lupus laniger''), occurred.<ref name=":1">Wang G, Zhai W, Yang H, et al. The genomics of selection in dogs and the parallel evolution between dogs and humans., ''Nat Commun'' 2013;4:1860</ref>

Dogs and humans have co-existed for thousands of years, with evidence suggesting that domestication of the dog (''Canis lupus familiaris'')  began around 32,000 years ago, when divergence from their wild ancestors, the grey wolf (''Canis lupus laniger''), occurred.<ref name=":1">Wang G, Zhai W, Yang H, et al. The genomics of selection in dogs and the parallel evolution between dogs and humans., ''Nat Commun'' 2013;4:1860</ref>

Since diet is known to play an important role in shaping microbiota composition of mammals,<ref name=":5">Muegge B, Kuczynski J, Knights D, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. ''Science'' 2011;332(6032):970-974</ref> it is logical that domestic dogs possess a microbiome different to that of their largely carnivorous ancestors and in fact, more aligned with humans.  Further to this, five bacterial taxa absent in the wolf microbiota were found to be present in both the humans and dogs, suggesting domestication has partially shaped the composition of the canine microbiota.<ref name=":6">Alessandri G, Milani C, Mancabelli L, et al. Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. ''Environ Microbiol'' 2019;21(4):1331-1343</ref>

Since diet is known to play an important role in shaping microbiota composition of mammals,<ref name=":5">Muegge B, Kuczynski J, Knights D, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. ''Science'' 2011;332(6032):970-974</ref> it is logical that domestic dogs possess a microbiome different to that of their largely carnivorous ancestors and in fact, more aligned with humans.  Further to this, five bacterial taxa absent in the wolf microbiota were found to be present in both the humans and dogs, suggesting domestication has partially shaped the composition of the canine microbiota.<ref name=":6">Alessandri G, Milani C, Mancabelli L, et al. Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. ''Environ Microbiol'' 2019;21(4):1331-1343</ref>

Furthermore, genes linked to starch metabolism are more abundant in microbiome of dogs compared to wolves <ref name=":7">Liu, Y., Liu, B., Liu, C. et al. Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch. ''BMC Vet Res'' 2021;17(112)</ref> and when comparing dogs fed a bones and raw food (BARF) diet (like their ancestors) to those fed a higher carbohydrate commercial food (CF), the latter possessed significantly greater amounts of carbohydrate-metabolising bacteria and higher bacterial diversity.<ref name=":6"/> Specifically, the abundance of Prevotella and Faecalibacterium were significantly higher in CF-fed dogs; the former is also seen in humans consuming a fibre-based diet and the latter is associated with a healthy microbiome in humans, with potential anti-inflammatory effects in the gut.<ref name=":8">Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. ''Proc Natl Acad Sci USA'' 2008; 105(43):16731-6</ref>

Furthermore, genes linked to starch metabolism are more abundant in microbiome of dogs compared to wolves <ref name=":7">Liu, Y., Liu, B., Liu, C. et al. Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch. ''BMC Vet Res'' 2021;17(112)</ref> and when comparing dogs fed a bones and raw food (BARF) diet (like their ancestors) to those fed a higher carbohydrate commercial food (CF), the latter possessed significantly greater amounts of carbohydrate-metabolising bacteria and higher bacterial diversity.<ref name=":6"/> Specifically, the abundance of Prevotella and Faecalibacterium were significantly higher in CF-fed dogs; the former is also seen in humans consuming a fibre-based diet and the latter is associated with a healthy microbiome in humans, with potential anti-inflammatory effects in the gut.<ref name=":8">Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. ''Proc Natl Acad Sci USA'' 2008; 105(43):16731-6</ref>

This may explain why the canine gut microbiome shows significantly more similarity to the human microbiome than the microbiome of other species. In fact, approximately 63% of the canine microbiome gene pool overlaps the human microbiome gene catalog, in contrast to 33% and 20% when mapped against the microbiome of pigs and mice respectively.<ref name=":9">Coelho L, Kultima J, Costea P, et al. Similarity of the dog and human gut microbiomes in gene content and response to diet. ''Microbiome'' 2018; 6 (72)</ref>   

This may explain why the canine gut microbiome shows significantly more similarity to the human microbiome than the microbiome of other species. In fact, approximately 63% of the canine microbiome gene pool overlaps the human microbiome gene catalog, in contrast to 33% and 20% when mapped against the microbiome of pigs and mice respectively.<ref name=":9">Coelho L, Kultima J, Costea P, et al. Similarity of the dog and human gut microbiomes in gene content and response to diet. ''Microbiome'' 2018; 6 (72)</ref>   

The degree to which genetics influence the microbiota remains unknown; some studies report a lack of significance between genetic ancestry and microbiota composition, with a strong heritability identified for only small number of bacterial taxa.<ref name=":10">Rothschild D, Weissbrod O, Barkan E, et al. Environment dominates over host genetics in shaping human gut microbiota. ''Nature'' 2018; 555: 210–215</ref> To this end, human twin studies concluded the average heritability of gut microbiome taxa is only 1.9%.<ref name=":11">Goodrich J, Davenport E, Beaumont M, et al. Genetic Determinants of the Gut Microbiome in UK Twins. ''Cell Host Microbe'' 2016; 19(5):731-43</ref>  However, murine models have suggested that genetics have a greater impact on the microbiota, which could have implications in predicting the development of certain diseases in humans, such as obesity, diabetes, and cardiovascular disease where gut microbiota composition may be a contributing risk factor.<ref name=":12">Benson A, Kelly S, Legge R, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. ''Front Vet Sci'' 2010;107(44):18933-18938</ref>

The degree to which genetics influence the microbiota remains unknown; some studies report a lack of significance between genetic ancestry and microbiota composition, with a strong heritability identified for only small number of bacterial taxa.<ref name=":10">Rothschild D, Weissbrod O, Barkan E, et al. Environment dominates over host genetics in shaping human gut microbiota. ''Nature'' 2018; 555: 210–215</ref> To this end, human twin studies concluded the average heritability of gut microbiome taxa is only 1.9%.<ref name=":11">Goodrich J, Davenport E, Beaumont M, et al. Genetic Determinants of the Gut Microbiome in UK Twins. ''Cell Host Microbe'' 2016; 19(5):731-43</ref>  However, murine models have suggested that genetics have a greater impact on the microbiota, which could have implications in predicting the development of certain diseases in humans, such as obesity, diabetes, and cardiovascular disease where gut microbiota composition may be a contributing risk factor.<ref name=":12">Benson A, Kelly S, Legge R, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. ''Front Vet Sci'' 2010;107(44):18933-18938</ref>

Healthy dogs have a faecal microbiome dominated by three main phyla: Fusobacterium, Bacteroidetes, and Firmicutes,<ref name=":13">Pilla R, Suchodolski J. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. ''Proc Natl Acad Sci USA'' 2020;6:498</ref> which bears some resemblance to the predominant phyla found in the human microbiome, Firmicutes, Bacteroidetes and Actinobacteria.<ref name=":14">Rinninella E, Raoul P, Cintoni M, et al. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. ''Microorganisms'' 2019;7(1):14.</ref> Interestingly, Fusobacterium is also found in the human microbiome, however is associated with diseases such as colorectal cancer,<ref name=":15">Kostic A, Gevers D, Pedamallu C, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. ''Genome Res '' 2012;22:292–298</ref> demonstrating that bacteria do not have a homogenous role and can act differently between species.

Healthy dogs have a faecal microbiome dominated by three main phyla: Fusobacterium, Bacteroidetes, and Firmicutes,<ref name=":13">Pilla R, Suchodolski J. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. ''Proc Natl Acad Sci USA'' 2020;6:498</ref> which bears some resemblance to the predominant phyla found in the human microbiome, Firmicutes, Bacteroidetes and Actinobacteria.<ref name=":14">Rinninella E, Raoul P, Cintoni M, et al. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. ''Microorganisms'' 2019;7(1):14.</ref> Interestingly, Fusobacterium is also found in the human microbiome, however is associated with diseases such as colorectal cancer,<ref name=":15">Kostic A, Gevers D, Pedamallu C, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. ''Genome Res '' 2012;22:292–298</ref> demonstrating that bacteria do not have a homogenous role and can act differently between species.

Whilst some similarities exist between the human and canine microbiota, knowledge surrounding the canine microbiota is lagging behind that of humans.<ref name=":16">Deng P, Swanson K. Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. ''Br J Nutr'' 2015;113:S6-17</ref> However, knowledge and experience from human microbiome studies, such as the Human Microbiome Project and MetaHIT project, has helped pave the way for future companion animal research. Future studies examining the association between the canine microbiome and host physiology and disease could help with the practical application of this knowledge within a clinical setting.

Whilst some similarities exist between the human and canine microbiota, knowledge surrounding the canine microbiota is lagging behind that of humans.<ref name=":16">Deng P, Swanson K. Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. ''Br J Nutr'' 2015;113:S6-17</ref> However, knowledge and experience from human microbiome studies, such as the Human Microbiome Project and MetaHIT project, has helped pave the way for future companion animal research. Future studies examining the association between the canine microbiome and host physiology and disease could help with the practical application of this knowledge within a clinical setting.