Host Species and Captivity Distinguish the Microbiome Compositions of a Diverse Zoo-Resident Non-Human Primate Population

Maya O. Wills, Robin R Shields-Cutler, Emily Brunmeier, Madison Weissenborn, Tami Murphy, Dan Knights, Timothy J. Johnson, Jonathan B Clayton

Research output: Contribution to journalArticlepeer-review


Vast numbers of microorganisms inhabit the mammalian gastrointestinal tract in a complex community referred to as the gut microbiome. An individual’s microbiome may be impacted by genetics, diet, and various environmental factors, and has been associated with many health states and diseases, though specific explanations are lacking. While these communities are well-studied in human populations, non-human primates (NHPs), in particular zoo-resident or captive NHPs, offer distinct advantages to increasing our understanding of factors that influence gut microbiome composition. Here, we characterize the gut microbiome composition of a phylogenetically diverse cohort of NHPs residing in the same urban zoo. We show that despite overlapping and controlled environmental contexts, gut microbiomes are still distinguished between NHP host species. However, when comparing the zoo cohort to wild NHPs, we show that captivity status strongly distinguishes zoo-resident NHPs from their wild counterparts, regardless of host phylogeny. Microbial orders unique to captive NHPs include taxa commonly present in human gut microbiomes. Together, these results demonstrate that differences between NHP species are strongly associated with gut microbiome composition and diversity, suggesting that species-specific approaches should be considered when investigating environmental factors’ influence on gut microbiome composition.

Original languageEnglish (US)
Article number715
Issue number9
StatePublished - Sep 2022

Bibliographical note

Funding Information:
This work was funded by Macalester College through the Anderson-Grosshuech Summer Research Fund (to M.O.W.), the Beltmann Natural Science Summer Research Fund (to M.O.W.), and a Wallace Scholarly Activities award (to R.S.-C.); and by the Morris Animal Foundation Veterinary Student Scholars Grant (to J.B.C.).

Publisher Copyright:
© 2022 by the authors.


  • captivity
  • gut health
  • humanization
  • microbiome
  • microbiota
  • non-human primate


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