The Effects of Captivity on the Mammalian Gut Microbiome - HAL-SDE - Sciences de l'environnement Access content directly
Journal Articles Integrative and Comparative Biology Year : 2017

The Effects of Captivity on the Mammalian Gut Microbiome

Valerie Mckenzie
  • Function : Author
Se Jin Song
  • Function : Author
Tiffany Prest
  • Function : Author
Angela Oliverio
  • Function : Author
Timothy Korpita
  • Function : Author
Alexandra Alexiev
  • Function : Author
Katherine Amato
Martin Kowalewski
  • Function : Author
Nico Avenant
  • Function : Author
Andres Link
  • Function : Author
Claudia Feh
  • Function : Author
Joseph Mendelson
  • Function : Author
Jon Sanders
  • Function : Author


Synopsis Recent studies increasingly note the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biology (e.g., digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and, consequently, the health of hosts. Animals living in captivity experience a range of changes that may influence the gut bacteria, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity. Thus far, initial results from previous studies point to a pattern of decreased bacterial diversity in captive animals. However, these studies are relatively limited in the scope of species that have been examined. Here we present a dataset that includes paired wild and captive samples from mammalian taxa across six Orders to investigate generalizable patterns of the effects captivity on mammalian gut bacteria. In comparing the wild to the captive condition, our results indicate that alpha diversity of the gut bacteria remains consistent in some mammalian hosts (bovids, giraffes, anteaters, and aardvarks), declines in the captive condition in some hosts (canids, primates, and equids), and increases in the captive condition in one host taxon (rhinoceros). Differences in gut bacterial beta diversity between the captive and wild state were observed for most of the taxa surveyed, except the even-toed ungulates (bovids and giraffes). Additionally, beta diversity variation was also strongly influenced by host taxonomic group, diet type, and gut fermentation physiology. Bacterial taxa that demonstrated larger shifts in relative abundance between the captive and wild states included members of the Firmicutes and Bacteroidetes. Overall, the patterns that we observe will inform a range of disciplines from veterinary practice to captive breeding efforts for biological conservation. Furthermore, bacterial taxa that persist in the captive state provide unique insight into symbiotic relationships with the host.
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hal-01773252 , version 1 (21-04-2018)



Valerie Mckenzie, Se Jin Song, Frédéric Delsuc, Tiffany Prest, Angela Oliverio, et al.. The Effects of Captivity on the Mammalian Gut Microbiome. Integrative and Comparative Biology, 2017, 57 (4), pp.690 - 704. ⟨10.1093/icb/icx090⟩. ⟨hal-01773252⟩
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