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Frontiers in microbiology2022; 13; 886252; doi: 10.3389/fmicb.2022.886252

The Gut Microbiome of 54 Mammalian Species.

Abstract: The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon sequencing. The composition of the gut microbiota clearly reflects diet and the structure of the gastrointestinal system, and it is to a certain degree more similar between closely related animals. Specific clusters of taxa were observed across animals of the same species, diet, and gut morphology. The microbiota retained regardless of captivity status is hypothesized to cover important symbiotic relationships with the host, while the remaining part reflects the artificial living conditions and can therefore be used as a future tool for conservation biologists. For five animal species (giraffes, horses, baboons, elephants, and zebras), it was possible to compare the microbiota of wild and captive individuals. Differences were observed in the proportion of microbiota detected between wild and captive specimens of the same animal species. We propose that the gut microbiota harbours important species, which can potentially serve as indicators for the well-being of the animal and the effect of living in captivity.
Publication Date: 2022-06-16 PubMed ID: 35783446PubMed Central: PMC9246093DOI: 10.3389/fmicb.2022.886252Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article investigates the makeup of gut microbes in 54 different mammalian species, revealing its dependence on aspects such as diet and digestive system structure. This study suggests that the existing microbial community, even under captive conditions, plays a vital role for the host and could be a useful tool for conservation biologists to assess animal well-being.

Overview of the Study

  • The research delves into the gut microbiome of a diverse range of 54 mammalian species. It investigates aspects of animal life such as their diet, gut physiology, and relationship degrees, considering both wild and captive species.
  • The research method used was 16S rRNA gene amplicon sequencing, a common technique to study microbial communities.

Key Findings

  • The composition of the gut microbiota is dependent on different factors such as the animal’s diet and the structure of their gastrointestinal system. In simpler terms, what the animal eats and how their digestive system is structured shapes their gut bacterial population.
  • There is a certain level of similarity in the gut microbiota composition between related animals. Therefore, animals from the same family may harbor similar gut microbes.
  • Specific clusters of bacteria were found prevalent across animals of the same species, diet, and gut morphology, pointing to a connection between these factors.

Implications of the Findings

  • The microbiota that is retained in an animal irrespective of its captivity status could represent important synergistic relationships with the host that help it to survive and thrive.
  • For instance, in the case of five animal species (giraffes, horses, baboons, elephants, and zebras), it was observed that the proportion of gut microbiota differed between wild and captive individuals. This difference may indicate the effects of the living environment, particularly captivity, on the gut microbiome of these animals.
  • The researchers thus propose that gut microbiota can serve as important species indicators, potentially serving as a gauge for the well-being of the animal and the impact of being in captivity. Such indicators could be a useful tool for conservation biologists, helping to optimize animal care in captivity.

Cite This Article

APA
de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL. (2022). The Gut Microbiome of 54 Mammalian Species. Front Microbiol, 13, 886252. https://doi.org/10.3389/fmicb.2022.886252

Publication

ISSN: 1664-302X
NlmUniqueID: 101548977
Country: Switzerland
Language: English
Volume: 13
Pages: 886252
PII: 886252

Researcher Affiliations

de Jonge, Nadieh
  • Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
Carlsen, Benjamin
  • Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
Christensen, Mikkel Hostrup
  • Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
Pertoldi, Cino
  • Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
  • Aalborg Zoo, Aalborg, Denmark.
Nielsen, Jeppe Lund
  • Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

References

This article includes 72 references
  1. Alberdi A, Martin Bideguren G, Aizpurua O. Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis.. Sci Rep 2021 Nov 22;11(1):22660.
    doi: 10.1038/s41598-021-02015-6pmc: PMC8608908pubmed: 34811423google scholar: lookup
  2. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.. Nat Biotechnol 2013 Jun;31(6):533-8.
    doi: 10.1038/nbt.2579pubmed: 23707974google scholar: lookup
  3. Amato KR. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.. Am J Phys Anthropol 2016 Jan;159(Suppl 61):S196-215.
    doi: 10.1002/ajpa.22908pubmed: 26808106google scholar: lookup
  4. Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes.. ISME J 2013 Jul;7(7):1344-53.
    doi: 10.1038/ismej.2013.16pmc: PMC3695285pubmed: 23486247google scholar: lookup
  5. An C, Okamoto Y, Xu S, Eo KY, Kimura J, Yamamoto N. Comparison of fecal microbiota of three captive carnivore species inhabiting Korea.. J Vet Med Sci 2017 Mar 18;79(3):542-546.
    doi: 10.1292/jvms.16-0472pmc: PMC5383174pubmed: 28049922google scholar: lookup
  6. Andersen KS, Kirkegaard RH, Karst SM, Albertsen M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. bioRxiv 1–2.
    doi: 10.1101/299537google scholar: lookup
  7. Azad MAK, Sarker M, Li T, Yin J. Probiotic Species in the Modulation of Gut Microbiota: An Overview.. Biomed Res Int 2018;2018:9478630.
    doi: 10.1155/2018/9478630pmc: PMC5964481pubmed: 29854813google scholar: lookup
  8. Bahrndorff S, Alemu T, Alemneh T, Lund Nielsen J. The Microbiome of Animals: Implications for Conservation Biology.. Int J Genomics 2016;2016:5304028.
    doi: 10.1155/2016/5304028pmc: PMC4852354pubmed: 27195280google scholar: lookup
  9. Bahrndorff S, de Jonge N, Hansen JK, Lauritzen JMS, Spanggaard LH, Sørensen MH, Yde M, Nielsen JL. Diversity and metabolic potential of the microbiota associated with a soil arthropod.. Sci Rep 2018 Feb 6;8(1):2491.
    doi: 10.1038/s41598-018-20967-0pmc: PMC5802828pubmed: 29410494google scholar: lookup
  10. Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning.. Nat Rev Microbiol 2018 Sep;16(9):567-576.
    doi: 10.1038/s41579-018-0024-1pubmed: 29789680google scholar: lookup
  11. Barrett HL, Gomez-Arango LF, Wilkinson SA, McIntyre HD, Callaway LK, Morrison M, Dekker Nitert M. A Vegetarian Diet Is a Major Determinant of Gut Microbiota Composition in Early Pregnancy.. Nutrients 2018 Jul 12;10(7).
    doi: 10.3390/nဇ0890pmc: PMC6073691pubmed: 30002323google scholar: lookup
  12. Bayané A, Guiot SR. Animal digestive strategies versus anaerobic digestion bioprocesses for biogas production from lignocellulosic biomass. Rev. Environ. Sci. Biotechnol. 10, 43–62.
    doi: 10.1007/s11157-010-9209-4google scholar: lookup
  13. Blumstein DT, Rangchi TN, Briggs T, De Andrade FS, Natterson-Horowitz B. A Systematic Review of Carrion Eaters' Adaptations to Avoid Sickness.. J Wildl Dis 2017 Jul;53(3):577-581.
    doi: 10.7589/2016-07-162pubmed: 28192041google scholar: lookup
  14. Borbón-García A, Reyes A, Vives-Flórez M, Caballero S. Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance.. Front Microbiol 2017;8:1316.
    doi: 10.3389/fmicb.2017.01316pmc: PMC5507997pubmed: 28751883google scholar: lookup
  15. Bray J, Curtis J. An ordination of the upland forest communities of Southern Wisconsin. Ecol. Monogr. 27, 325–349.
    doi: 10.2307/1942268google scholar: lookup
  16. Brice KL, Trivedi P, Jeffries TC, Blyton MDJ, Mitchell C, Singh BK, Moore BD. The Koala (Phascolarctos cinereus) faecal microbiome differs with diet in a wild population.. PeerJ 2019;7:e6534.
    doi: 10.7717/peerj.6534pmc: PMC6448554pubmed: 30972242google scholar: lookup
  17. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.. Proc Natl Acad Sci U S A 2011 Mar 15;108 Suppl 1(Suppl 1):4516-22.
    doi: 10.1073/pnas.1000080107pmc: PMC3063599pubmed: 20534432google scholar: lookup
  18. Chao A. Nonparametric estimation of the number of classes in a population author. Scanadinavian J. Stat. 11, 265–270.
    doi: 10.1214/aoms/1177729949google scholar: lookup
  19. Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Tuan BV, Minh VV, Cabana F, Nadler T, Toddes B, Murphy T, Glander KE, Johnson TJ, Knights D. Captivity humanizes the primate microbiome.. Proc Natl Acad Sci U S A 2016 Sep 13;113(37):10376-81.
    doi: 10.1073/pnas.1521835113pmc: PMC5027417pubmed: 27573830google scholar: lookup
  20. Edgar RC. Search and clustering orders of magnitude faster than BLAST.. Bioinformatics 2010 Oct 1;26(19):2460-1.
    doi: 10.1093/bioinformatics/btq461pubmed: 20709691google scholar: lookup
  21. Edgar RC. SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences. bioRxiv 74161.
    doi: 10.1101/074161google scholar: lookup
  22. Edgar RC. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv 81257.
    doi: 10.1101/081257google scholar: lookup
  23. Eisenhofer R, Helgen KM, Taggart D. Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons).. Anim Microbiome 2021 Jan 6;3(1):4.
    doi: 10.1186/s42523-020-00068-ypmc: PMC7934541pubmed: 33499985google scholar: lookup
  24. García-Amado MA, Shin H, Sanz V, Lentino M, Martínez LM, Contreras M, Michelangeli F, Domínguez-Bello MG. Comparison of gizzard and intestinal microbiota of wild neotropical birds.. PLoS One 2018;13(3):e0194857.
  25. Greene LK, Blanco MB, Rambeloson E, Graubics K, Fanelli B, Colwell RR, Drea CM. Gut microbiota of frugo-folivorous sifakas across environments.. Anim Microbiome 2021 May 18;3(1):39.
    doi: 10.1186/s42523-021-00093-5pmc: PMC8132362pubmed: 34006323google scholar: lookup
  26. Hale VL, Tan CL, Niu K, Yang Y, Zhang Q, Knight R, Amato KR. Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi.. Am J Primatol 2019 Oct;81(10-11):e22989.
    doi: 10.1002/ajp.22989pubmed: 31106872google scholar: lookup
  27. Hauffe HC, Barelli C. Conserve the germs: the gut microbiota and adaptive potential. Conserv. Genet. 20, 19–27.
  28. Henderson G, Cox F, Ganesh S, Jonker A, Young W, Janssen PH. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range.. Sci Rep 2015 Oct 9;5:14567.
    doi: 10.1038/srep14567pmc: PMC4598811pubmed: 26449758google scholar: lookup
  29. Houtz JL, Sanders JG, Denice A, Moeller AH. Predictable and host-species specific humanization of the gut microbiota in captive primates.. Mol Ecol 2021 Aug;30(15):3677-3687.
    doi: 10.1111/mec.15994pubmed: 34013536google scholar: lookup
  30. Kamada N, Seo SU, Chen GY, Núñez G. Role of the gut microbiota in immunity and inflammatory disease.. Nat Rev Immunol 2013 May;13(5):321-35.
    doi: 10.1038/nri3430pubmed: 23618829google scholar: lookup
  31. Kartzinel TR, Hsing JC, Musili PM, Brown BRP, Pringle RM. Covariation of diet and gut microbiome in African megafauna.. Proc Natl Acad Sci U S A 2019 Nov 19;116(47):23588-23593.
    doi: 10.1073/pnas.1905666116pmc: PMC6876249pubmed: 31685619google scholar: lookup
  32. Kirkwood JK. Welfare, husbandry and veterinary care of wild animals in captivity: Changes in attitudes, progress in knowledge and techniques. Int. Zoo Yearb. 38, 124–130.
  33. Kogut MH, Lee A, Santin E. Microbiome and pathogen interaction with the immune system.. Poult Sci 2020 Apr;99(4):1906-1913.
    doi: 10.1016/j.psj.2019.12.011pmc: PMC7587753pubmed: 32241470google scholar: lookup
  34. Kohl KD, Skopec MM, Dearing MD. Captivity results in disparate loss of gut microbial diversity in closely related hosts.. Conserv Physiol 2014;2(1):cou009.
    doi: 10.1093/conphys/cou009pmc: PMC4806740pubmed: 27293630google scholar: lookup
  35. Levin D, Raab N, Pinto Y, Rothschild D, Zanir G, Godneva A, Mellul N, Futorian D, Gal D, Leviatan S, Zeevi D, Bachelet I, Segal E. Diversity and functional landscapes in the microbiota of animals in the wild.. Science 2021 Apr 16;372(6539).
    doi: 10.1126/science.abb5352pubmed: 33766942google scholar: lookup
  36. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. Evolution of mammals and their gut microbes.. Science 2008 Jun 20;320(5883):1647-51.
    doi: 10.1126/science.1155725pmc: PMC2649005pubmed: 18497261google scholar: lookup
  37. Li Y, Guo W, Han S, Kong F, Wang C, Li D, Zhang H, Yang M, Xu H, Zeng B, Zhao J. The evolution of the gut microbiota in the giant and the red pandas.. Sci Rep 2015 May 18;5:10185.
    doi: 10.1038/srep10185pmc: PMC4434948pubmed: 25985413google scholar: lookup
  38. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota.. Nature 2012 Sep 13;489(7415):220-30.
    doi: 10.1038/nature11550pmc: PMC3577372pubmed: 22972295google scholar: lookup
  39. McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. Animals in a bacterial world, a new imperative for the life sciences.. Proc Natl Acad Sci U S A 2013 Feb 26;110(9):3229-36.
    doi: 10.1073/pnas.1218525110pmc: PMC3587249pubmed: 23391737google scholar: lookup
  40. McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh C, Orlando L, Mendelson JR, Sanders J, Knight R. The Effects of Captivity on the Mammalian Gut Microbiome.. Integr Comp Biol 2017 Oct 1;57(4):690-704.
    doi: 10.1093/icb/icx090pmc: PMC5978021pubmed: 28985326google scholar: lookup
  41. Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L. Evaluating the impact of domestication and captivity on the horse gut microbiome.. Sci Rep 2017 Nov 14;7(1):15497.
    doi: 10.1038/s41598-017-15375-9pmc: PMC5686199pubmed: 29138485google scholar: lookup
  42. Moeller AH, Peeters M, Ndjango JB, Li Y, Hahn BH, Ochman H. Sympatric chimpanzees and gorillas harbor convergent gut microbial communities.. Genome Res 2013 Oct;23(10):1715-20.
    doi: 10.1101/gr.154773.113pmc: PMC3787267pubmed: 23804402google scholar: lookup
  43. Moeller AH, Sanders JG. Roles of the gut microbiota in the adaptive evolution of mammalian species.. Philos Trans R Soc Lond B Biol Sci 2020 Sep 28;375(1808):20190597.
    doi: 10.1098/rstb.2019.0597pmc: PMC7435157pubmed: 32772670google scholar: lookup
  44. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.. Science 2011 May 20;332(6032):970-4.
    doi: 10.1126/science.1198719pmc: PMC3303602pubmed: 21596990google scholar: lookup
  45. Murtagh F, Legendre P. Ward's Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward's Criterion?. J. Classif. 31, 274–295.
    doi: 10.1007/s00357-014-9161-zgoogle scholar: lookup
  46. Nakamura N, Amato KR, Garber P, Estrada A, Mackie RI, Gaskins HR. Analysis of the hydrogenotrophic microbiota of wild and captive black howler monkeys (Alouatta pigra) in palenque national park, Mexico.. Am J Primatol 2011 Sep;73(9):909-19.
    doi: 10.1002/ajp.20961pubmed: 21557284google scholar: lookup
  47. Nelson TM, Rogers TL, Carlini AR, Brown MV. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals.. Environ Microbiol 2013 Apr;15(4):1132-45.
    doi: 10.1111/1462-2920.12022pubmed: 23145888google scholar: lookup
  48. Neumann AP, McCormick CA, Suen G. Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen.. Environ Microbiol 2017 Sep;19(9):3768-3783.
    doi: 10.1111/1462-2920.13878pmc: PMC5599356pubmed: 28752955google scholar: lookup
  49. O' Donnell MM, Harris HMB, Ross RP, O'Toole PW. Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals.. Microbiologyopen 2017 Oct;6(5).
    doi: 10.1002/mbo3.509pmc: PMC5635170pubmed: 28834331google scholar: lookup
  50. Oksanen AJ, Blanchet FG, Kindt R, Minchin PR, Hara RBO, Simpson GL. Vegan: Community ecology package. R package version 2.3-3 .
  51. Pascoe EL, Hauffe HC, Marchesi JR, Perkins SE. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies.. ISME J 2017 Dec;11(12):2644-2651.
    doi: 10.1038/ismej.2017.133pmc: PMC5702738pubmed: 28800135google scholar: lookup
  52. Pickard JM, Zeng MY, Caruso R, Núñez G. Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease.. Immunol Rev 2017 Sep;279(1):70-89.
    doi: 10.1111/imr.12567pmc: PMC5657496pubmed: 28856738google scholar: lookup
  53. Poulsen AR, de Jonge N, Sugiharto S, Nielsen JL, Lauridsen C, Canibe N. The microbial community of the gut differs between piglets fed sow milk, milk replacer or bovine colostrum.. Br J Nutr 2017 Apr;117(7):964-978.
    doi: 10.1017/S0007114517000216pubmed: 28460652google scholar: lookup
  54. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.. Nucleic Acids Res 2013 Jan;41(Database issue):D590-6.
    doi: 10.1093/nar/gks1219pmc: PMC3531112pubmed: 23193283google scholar: lookup
  55. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria .
  56. Redford KH, Segre JA, Salafsky N, Martinez del Rio C, McAloose D. Conservation and the microbiome.. Conserv Biol 2012 Apr;26(2):195-7.
  57. Roggenbuck M, Bærholm Schnell I, Blom N, Bælum J, Bertelsen MF, Sicheritz-Pontén T, Sørensen SJ, Gilbert MT, Graves GR, Hansen LH. The microbiome of New World vultures.. Nat Commun 2014 Nov 25;5:5498.
    doi: 10.1038/ncomms6498pubmed: 25423494google scholar: lookup
  58. Schmidt JM, Henken S, Dowd SE, McLaughlin RW. Analysis of the Microbial Diversity in the Fecal Material of Giraffes.. Curr Microbiol 2018 Mar;75(3):323-327.
    doi: 10.1007/s00284-017-1383-ypubmed: 29085995google scholar: lookup
  59. Song C, Wang B, Tan J, Zhu L, Lou D, Cen X. Comparative analysis of the gut microbiota of black bears in China using high-throughput sequencing.. Mol Genet Genomics 2017 Apr;292(2):407-414.
    doi: 10.1007/s00438-016-1282-0pubmed: 28028611google scholar: lookup
  60. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R. Cohabiting family members share microbiota with one another and with their dogs.. Elife 2013 Apr 16;2:e00458.
    doi: 10.7554/eLife.00458.018pmc: PMC3628085pubmed: 23599893google scholar: lookup
  61. Stevens CE, Hume ID. Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients.. Physiol Rev 1998 Apr;78(2):393-427.
    doi: 10.1152/physrev.1998.78.2.393pubmed: 9562034google scholar: lookup
  62. Stothart MR, Palme R, Newman AEM. It's what's on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal.. Proc Biol Sci 2019 Oct 23;286(1913):20192111.
    doi: 10.1098/rspb.2019.2111pmc: PMC6834041pubmed: 31640519google scholar: lookup
  63. Stumpf RM, Gomez A, Amato KR, Yeoman CJ, Polk JD, Wilson BA. Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biol. Conserv. 199, 56–66.
  64. Tang GS, Liang XX, Yang MY, Wang TT, Chen JP, Du WG, Li H, Sun BJ. Captivity Influences Gut Microbiota in Crocodile Lizards (Shinisaurus crocodilurus).. Front Microbiol 2020;11:550.
    doi: 10.3389/fmicb.2020.00550pmc: PMC7190797pubmed: 32390955google scholar: lookup
  65. Van Valkenburgh B. Deja vu: the evolution of feeding morphologies in the Carnivora.. Integr Comp Biol 2007 Jul;47(1):147-63.
    doi: 10.1093/icb/icm016pubmed: 21672827google scholar: lookup
  66. Warnes GR, Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T. gplots: various R programming tools for plotting data. Available online .
  67. Wickham H. ggplot2: Elegant graphics for data analysis. New York: Springer-Verlag .
  68. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography.. Nature 2012 May 9;486(7402):222-7.
    doi: 10.1038/nature11053pmc: PMC3376388pubmed: 22699611google scholar: lookup
  69. Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.. Nat Commun 2019 May 16;10(1):2200.
    doi: 10.1038/s41467-019-10191-3pmc: PMC6522487pubmed: 31097702google scholar: lookup
  70. Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise.. Mol Ecol 2015 May;24(10):2521-36.
    doi: 10.1111/mec.13169pubmed: 25809385google scholar: lookup
  71. Zhang C, Xu B, Lu T, Huang Z. Metagenomic Analysis of the Fecal Microbiomes of Wild Asian Elephants Reveals Microflora and Enzymes that Mainly Digest Hemicellulose.. J Microbiol Biotechnol 2019 Aug 28;29(8):1255-1265.
    doi: 10.4014/jmb.1904.04033pubmed: 31337187google scholar: lookup
  72. Zhao Y, Li B, Bai D, Huang J, Shiraigo W, Yang L, Zhao Q, Ren X, Wu J, Bao W, Dugarjaviin M. Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-throughput Sequencing of the V4 Region of the 16S rRNA Gene.. Asian-Australas J Anim Sci 2016 Sep;29(9):1345-52.
    doi: 10.5713/ajas.15.0587pmc: PMC5003997pubmed: 26954132google scholar: lookup

Citations

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  1. Mugetti D, Pastorino P, Beltramo C, Audino T, Arillo A, Esposito G, Prearo M, Bertoli M, Pizzul E, Bozzetta E, Acutis PL, Peletto S. The Gut Microbiota of Farmed and Wild Brook Trout (Salvelinus fontinalis): Evaluation of Feed-Related Differences Using 16S rRNA Gene Metabarcoding. Microorganisms 2023 Jun 22;11(7).
  2. Rojas CA, Holekamp KE, Viladomat Jasso M, Souza V, Eisen JA, Theis KR. Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study. mSystems 2023 Feb 23;8(1):e0096522.
    doi: 10.1128/msystems.00965-22pubmed: 36533929google scholar: lookup
  3. Lebeuf-Taylor E, Cottenie K. Marginal link between sociality and gut microbiome in disparate mammalian hosts. FEMS Microbes 2026;7:xtag004.
    doi: 10.1093/femsmc/xtag004pubmed: 41648806google scholar: lookup
  4. Mastrorilli E, Herd P, Rey FE, Goodman AL, Zimmermann M. Linking interpersonal differences in gut microbiota composition and drug biotransformation activity. bioRxiv 2026 Jan 21;.
    doi: 10.64898/2026.01.21.700809pubmed: 41648142google scholar: lookup
  5. Vasconcelos DS, Harris DJ, Tarroso P, Simões C, Rato C, Santos X, Xavier R. Shaped by Fire: Unravelling the Impact of Fire on Lizard Gut Microbiome. Mol Ecol 2026 Jan;35(2):e70255.
    doi: 10.1111/mec.70255pubmed: 41607112google scholar: lookup
  6. Shaker RAE, Hashem RA, Hassan M, Ibrahim AM, Ragab YM, Khattab RA. Investigation of probiotic, anticancer and antimicrobial activity of Enterococcus bacteria isolated from the gut microbiota of marine snails. Int Microbiol 2026 Feb;29(2):215-230.
    doi: 10.1007/s10123-025-00747-3pubmed: 41501588google scholar: lookup
  7. Liu L, Wang H, Minichino A, Xiao R, Du Y, Wang L, He D, Guo S, Mo X, Xiang Y, Wu J, McGuire P, Yue W, Lu L, Cipriani A, Xie P. Mapping the reciprocal interactions between antidepressants and the gut microbiome: novel targets for the personalisation and optimization of drug response. Mol Psychiatry 2025 Nov 19;.
    doi: 10.1038/s41380-025-03345-xpubmed: 41258378google scholar: lookup
  8. Ren Y, Tao M, Guo G, Chen K, Pu X, Hou Y, Yang X. Gut Microbiota Provide Co-Existing Strategies for Two Species of Symmetrically Distributed Rodents in Competition for Food. Ecol Evol 2025 Oct;15(10):e72290.
    doi: 10.1002/ece3.72290pubmed: 41122693google scholar: lookup
  9. Winarsih S, Hasanah U, Nuraida L, Andarwulan N, Kusuma WA. Microbial community of civet excreta fed by robusta cherry coffee in Indonesian civet coffee production. J Adv Vet Anim Res 2025 Jun;12(2):565-581.
    doi: 10.5455/javar.2025.l921pubmed: 41069730google scholar: lookup
  10. Najafpour B, Canario AVM, Power DM. Bacterial 16S Ribosomal Gene Fingerprints as a Tool to Diagnose and Mitigate Fish Larvae Gut Dysbiosis. Environ Microbiol Rep 2025 Oct;17(5):e70187.
    doi: 10.1111/1758-2229.70187pubmed: 41041974google scholar: lookup
  11. Grant ML, Petri RM, Baecklund TM, Wilson GA, Kyle CJ. Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa. Anim Microbiome 2025 Aug 21;7(1):89.
    doi: 10.1186/s42523-025-00451-7pubmed: 40841983google scholar: lookup
  12. Wei Z, Meng L, Du S, Wang F, Jiang A, Lu R, Liu K, Wang X, Xu Q, Mu X, Meng L, Shao C. Metabolic potentials of the gut microbes in Antarctic krill (Euphausia superba). mSystems 2025 Sep 23;10(9):e0037725.
    doi: 10.1128/msystems.00377-25pubmed: 40772734google scholar: lookup
  13. Zangerolamo L, Carvalho M, Barbosa HCL. The Critical Role of the Bile Acid Receptor TGR5 in Energy Homeostasis: Insights into Physiology and Therapeutic Potential. Int J Mol Sci 2025 Jul 8;26(14).
    doi: 10.3390/ijms26146547pubmed: 40724796google scholar: lookup
  14. Clemente-Suárez VJ, Redondo-Flórez L, Beltrán-Velasco AI, Yáñez-Sepúlveda R, Rubio-Zarapuz A, Martín-Rodríguez A, Navarro-Jimenez E, Tornero-Aguilera JF. Human Digestive Physiology and Evolutionary Diet: A Metabolomic Perspective on Carnivorous and Scavenger Adaptations. Metabolites 2025 Jul 4;15(7).
    doi: 10.3390/metabo15070453pubmed: 40710552google scholar: lookup
  15. Debray R, Tung J, Archie EA. Ecology and evolution of the social microbiome. Annu Rev Ecol Evol Syst 2024;55(1):89-114.
  16. Liu Y, Huang G, Wei F, Hu Y. Non-negligible role of gut morphology in shaping mammalian gut microbiomes. Sci China Life Sci 2025 Aug;68(8):2408-2419.
    doi: 10.1007/s11427-024-2933-1pubmed: 40488951google scholar: lookup
  17. Wang Y, Li X, Li Z, Han Q, Hu T, Zhang Q, Qu H, Zhang H, Qu Y, Shi D, Ma Q, Huang S. Comparative analysis of composition and spatial variations in the foregut microbiota of male and female donkeys. Front Microbiol 2025;16:1532265.
    doi: 10.3389/fmicb.2025.1532265pubmed: 40458714google scholar: lookup
  18. Murtskhvaladze M, Ninua L, Budagashvili N, Tevdoradze E, Gurgenidze Z, Kotorashvili A, Kotaria N, Gavashelishvili A, Javakhishvili Z. Tracheal and cloacal bacterial diversity of red listed Eastern Imperial Eagle (Aquila heliaca). Front Microbiol 2025;16:1477032.
    doi: 10.3389/fmicb.2025.1477032pubmed: 40415931google scholar: lookup
  19. Llarena AK, Haverkamp THA, Gulliksen WS, Herstad K, Holst-Jensen A, Skjerve E, Rannem L, Rodriguez-Campos S, Øines Ø. DNA extraction protocols for animal fecal material on blood spot cards. PLoS One 2025;20(5):e0313808.
    doi: 10.1371/journal.pone.0313808pubmed: 40354439google scholar: lookup
  20. Sugden S, Serrouya R, Neufeld L, Schwantje H, St Clair CC, Stein L, Spribille T. Endangered Deep-Snow Mountain Caribou Have a Distinct Winter Diet and Gut Microbiome That May Be Altered by Maternal Penning. Mol Ecol 2025 Jun;34(11):e17783.
    doi: 10.1111/mec.17783pubmed: 40331250google scholar: lookup
  21. Giacomini A, Lakim MB, Tuh FYY, Hitchings M, Consuegra S, Webster TU, Wells K. Host-Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban-Rural Ecotone. Mol Ecol 2025 Jun;34(11):e17782.
    doi: 10.1111/mec.17782pubmed: 40289691google scholar: lookup
  22. Cao J, Wang S, Ding R, Liu Y, Yuan B. Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing. PeerJ 2025;13:e19260.
    doi: 10.7717/peerj.19260pubmed: 40226542google scholar: lookup
  23. Debray R, Dickson CC, Webb SE, Archie EA, Tung J. Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission. Microbiome 2025 Feb 28;13(1):59.
    doi: 10.1186/s40168-025-02051-8pubmed: 40022204google scholar: lookup
  24. Davison S, Mascellani Bergo A, Ward Z, Sackett A, Strykova A, Jaimes JD, Travis D, Clayton JB, Murphy HW, Danforth MD, Smith BK, Blekhman R, Fuh T, Niatou Singa FS, Havlik J, Petrzelkova K, Gomez A. Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism. NPJ Biofilms Microbiomes 2025 Feb 21;11(1):33.
    doi: 10.1038/s41522-025-00664-3pubmed: 39984469google scholar: lookup
  25. Apostolou K, Radea C, Meziti A, Kormas KA. Bacterial Diversity Associated with Terrestrial and Aquatic Snails. Microorganisms 2024 Dec 24;13(1).
  26. Kanika NH, Liaqat N, Chen H, Ke J, Lu G, Wang J, Wang C. Fish gut microbiome and its application in aquaculture and biological conservation. Front Microbiol 2024;15:1521048.
    doi: 10.3389/fmicb.2024.1521048pubmed: 39839099google scholar: lookup
  27. Klinhom S, Kunasol C, Sriwichaiin S, Kerdphoo S, Chattipakorn N, Chattipakorn SC, Thitaram C. Characteristics of gut microbiota profiles in Asian elephants (Elephas maximus) with gastrointestinal disorders. Sci Rep 2025 Jan 8;15(1):1327.
    doi: 10.1038/s41598-025-85495-0pubmed: 39779898google scholar: lookup
  28. Kou X, Liu Y, Xiang F, Zhang X, Khan MZ, Wu B, Wang H, Gong Y, Wang C, Ma Q, Li Y. Insights into the Donkey Hindgut Microbiome Using Metagenome-Assembled Genomes. Animals (Basel) 2024 Dec 16;14(24).
    doi: 10.3390/ani14243625pubmed: 39765529google scholar: lookup
  29. Singh BK, Thakur K, Kumari H, Mahajan D, Sharma D, Sharma AK, Kumar S, Singh B, Pankaj PP, Kumar R. A review on comparative analysis of marine and freshwater fish gut microbiomes: insights into environmental impact on gut microbiota. FEMS Microbiol Ecol 2025 Jan 7;101(1).
    doi: 10.1093/femsec/fiae169pubmed: 39719366google scholar: lookup
  30. Yu B, Li H, Chen Q, Yang C, Guo Y, Sun B. Dynamic Changes in Intestinal Microorganisms and Hematological Indices in Giraffes of Different Ages, and the Effect of Diarrhea on Intestinal Microbiota. Animals (Basel) 2024 Nov 24;14(23).
    doi: 10.3390/ani14233379pubmed: 39682345google scholar: lookup
  31. Arellano-Hernández HD, Montes-Carreto LM, Guerrero JA, Martinez-Romero E. The fecal microbiota of the mouse-eared bat (Myotis velifer) with new records of microbial taxa for bats. PLoS One 2024;19(12):e0314847.
    doi: 10.1371/journal.pone.0314847pubmed: 39637086google scholar: lookup
  32. Degregori S, Wang X, Kommala A, Schulhof N, Moradi S, MacDonald A, Eblen K, Jukovich S, Smith E, Kelleher E, Suzuki K, Hall Z, Knight R, Amato KR. Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices. Biol Rev Camb Philos Soc 2025 Apr;100(2):748-763.
    doi: 10.1111/brv.13161pubmed: 39530277google scholar: lookup
  33. Fang M, Yu F, Shu L, Wei H, Mu X, Wang X, Xu M, Gu D. Structural and functional differences of gut microbiota in Pomacea canaliculata from different geographical locations and habitats. Ecol Evol 2024 Oct;14(10):e70283.
    doi: 10.1002/ece3.70283pubmed: 39364038google scholar: lookup
  34. Schmartz GP, Rehner J, Schuff MJ, Molano LG, Becker SL, Krawczyk M, Tagirdzhanov A, Gurevich A, Francke R, Müller R, Keller V, Keller A. Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes. Nat Commun 2024 Sep 26;15(1):8263.
    doi: 10.1038/s41467-024-52669-9pubmed: 39327429google scholar: lookup
  35. Guan J, Ramírez GA, Eng C, Oakley B. Microbiome resilience of three-toed box turtles (Terrapene carolina triunguis) in response to rising temperatures. Front Vet Sci 2024;11:1276436.
    doi: 10.3389/fvets.2024.1276436pubmed: 39286599google scholar: lookup
  36. Lindner BG, Choudhury RA, Pinamang P, Bingham L, D'Amico I, Hatt JK, Konstantinidis KT, Graham KE. Advancing Source Tracking: Systematic Review and Source-Specific Genome Database Curation of Fecally Shed Prokaryotes. Environ Sci Technol Lett 2024 Sep 10;11(9):931-939.
    doi: 10.1021/acs.estlett.4c00233pubmed: 39280079google scholar: lookup
  37. Manithody C, Denton C, Mehta S, Carter J, Kurashima K, Bagwe A, Swiderska-Syn M, Guzman M, Besmer S, Jain S, McHale M, Qureshi K, Nazzal M, Caliskan Y, Long J, Lin CJ, Hutchinson C, Ericsson AC, Jain AK. Intraduodenal fecal microbiota transplantation ameliorates gut atrophy and cholestasis in a novel parenteral nutrition piglet model. Am J Physiol Gastrointest Liver Physiol 2024 Nov 1;327(5):G640-G654.
    doi: 10.1152/ajpgi.00012.2024pubmed: 39163019google scholar: lookup
  38. Debray R, Dickson CC, Webb SE, Archie EA, Tung J. Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission. bioRxiv 2024 Nov 15;.
    doi: 10.1101/2024.07.18.604082pubmed: 39071345google scholar: lookup
  39. Toyber I, Kumar R, Jami E. Rumen protozoa are a hub for diverse hydrogenotrophic functions. Environ Microbiol Rep 2024 Aug;16(4):e13298.
    doi: 10.1111/1758-2229.13298pubmed: 38961629google scholar: lookup
  40. Mafra D, Borges NA, Baptista BG, Martins LF, Borland G, Shiels PG, Stenvinkel P. What Can the Gut Microbiota of Animals Teach Us about the Relationship between Nutrition and Burden of Lifestyle Diseases?. Nutrients 2024 Jun 6;16(11).
    doi: 10.3390/nu16111789pubmed: 38892721google scholar: lookup
  41. Amin A, Mekadim C, Modrackova N, Bolechova P, Mrazek J, Neuzil-Bunesova V. Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. Anim Microbiome 2024 May 2;6(1):21.
    doi: 10.1186/s42523-024-00311-wpubmed: 38698458google scholar: lookup
  42. Gani M, Mohd-Ridwan AR, Sitam FT, Kamarudin Z, Selamat SS, Awang NMZ, Karuppannan KV, Md-Zain BM. Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling. World J Microbiol Biotechnol 2024 Feb 28;40(4):111.
    doi: 10.1007/s11274-023-03868-xpubmed: 38416247google scholar: lookup
  43. Kern K, Delaroque N, Boysen A, Puder M, Wendt R, Kölsch A, Ehrentreich-Förster E, Stærk K, Andersen TE, Andersen K, Lund L, Szardenings M. Glycosylation of bacterial antigens changes epitope patterns. Front Immunol 2023;14:1258136.
    doi: 10.3389/fimmu.2023.1258136pubmed: 37954588google scholar: lookup
  44. Scarafile D, Luise D, Motta V, Spiezio C, Modesto M, Porcu MM, Yitzhak Y, Correa F, Sandri C, Trevisi P, Mattarelli P. Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment. Microorganisms 2023 Jun 9;11(6).
  45. Levine BH, Hoffman JM. Gut Microbiome Transplants and Their Health Impacts across Species. Microorganisms 2023 Jun 3;11(6).