Abstract
Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
Highlights
Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution
A current challenge is determining whether these inter-study discrepancies are the result of technical artifacts inherent to differing experimental designs or whether the modulating effects of host diet and evolution on the gut microbiome do truly differ among host clades and/or microbial lineages
While various studies have shown that host diet and phylogeny modulate the animal intestinal microbiome[5,6], we have expanded on this previous work by performing a robust assessment of each factor’s effect on a homogeneously generated dataset of highly diverse and predominantly wild animals
Summary
Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. A current challenge is determining whether these inter-study discrepancies are the result of technical artifacts inherent to differing experimental designs or whether the modulating effects of host diet and evolution on the gut microbiome do truly differ among host clades and/or microbial lineages. Resolving this question has been hampered by multiple factors. Host intra-species variation is often removed (i.e., just one randomly selected sample used per species), or alternatively it is retained but the potential biases and treatment group imbalances are ignored in hypothesis testing[8,26]
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