Difference between revisions of "Canine and Human Microbiome"

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==Introduction==
 
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>
  
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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>
  
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==Starch Metabolism==
 
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>
  
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==Similarities Between Canine and Human Microbiomes==
 
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>   
  
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==Genetics and the Microbiota==
 
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>
  
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==Faecal Microbiomes==
 
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.
  
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==Microbiome Research in Companion Animals==
 
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.
  

Revision as of 11:05, 7 January 2022

Introduction

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.[1]

Since then, man-made selection has led to the development of numerous canine phenotypes and genotypes, and dogs have lived harmoniously with humans, sharing resources such as living environments, food and eating patterns. This close direct contact appears to influence the canine-human skin microbiome relationship.[2][3] In one study, the skin microbiota of humans showed greater similarity to their own dog than to other dogs and significantly increased the common skin microbes in cohabiting adults.[2]

Dogs have historically scavenged human food leftovers and it is thought that the ability thrive on starch containing diets was a key selection pressure in the domestication of the dog, with genome studies supporting this adaptation.[4]

Since diet is known to play an important role in shaping microbiota composition of mammals,[5] 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.[6]

Starch Metabolism

Furthermore, genes linked to starch metabolism are more abundant in microbiome of dogs compared to wolves [7] 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.[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.[8]

Similarities Between Canine and Human Microbiomes

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.[9]

Genetics and the Microbiota

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.[10] To this end, human twin studies concluded the average heritability of gut microbiome taxa is only 1.9%.[11] 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.[12]

Faecal Microbiomes

Healthy dogs have a faecal microbiome dominated by three main phyla: Fusobacterium, Bacteroidetes, and Firmicutes,[13] which bears some resemblance to the predominant phyla found in the human microbiome, Firmicutes, Bacteroidetes and Actinobacteria.[14] Interestingly, Fusobacterium is also found in the human microbiome, however is associated with diseases such as colorectal cancer,[15] demonstrating that bacteria do not have a homogenous role and can act differently between species.

Microbiome Research in Companion Animals

Whilst some similarities exist between the human and canine microbiota, knowledge surrounding the canine microbiota is lagging behind that of humans.[16] 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.

Author: Pippa Coupe BVSc, MRCVS Veterinary Product Manager at Protexin Veterinary. Protexin Veterinary is a brand of ADM Protexin Ltd

In Partnership With Protexin Veterinary

References

  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
  2. ↑ 2.0 2.1 Song S, Lauber C, Costello E, et al. Cohabiting family members share microbiota with one another and with their dogs. Elife 2013; 2:e00458
  3. ↑ Wetzels S, Strachan C, Conrady B. et al. Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota. Sci Rep 2021; 11: 17106
  4. ↑ Axelsson E, Ratnakumar A, Arendt M, et al.The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 2013; 495(7441):360–4
  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
  6. ↑ 6.0 6.1 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
  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)
  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
  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)
  10. ↑ Rothschild D, Weissbrod O, Barkan E, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 2018; 555: 210–215
  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
  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
  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
  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.
  15. ↑ Kostic A, Gevers D, Pedamallu C, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 2012;22:292–298
  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
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