Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

How the microbiome interacts with hosts across evolutionary time is poorly
understood. To address this question, datasets comprised of many host
species are required to conduct comparative analyses. Here, we have
analyzed 142 intestinal microbiome samples from 92 birds
belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene.
Using four definitions for microbial taxonomic units (97%OTU, 99%OTU,
99%OTU with singletons removed, ASV), we conducted alpha and beta
diversity analyses and used phylogenetic comparative methods to assess the
evolution of the microbiome as a trait of bird species. We find that raw
abundances and diversity varied between the datasets but relative patterns
were largely consistent across datasets. Host taxonomy, diet and locality
were significantly associated with microbiomes, at generally similar
levels using three distance metrics. Phylogenetic comparative methods were
used to assess the relationship between the microbiome as a trait of a
host species and the underlying bird phylogeny. We find that a neutral
Brownian motion model does not explain variation in microbiomes. Instead,
a White Noise model that indicates the trait contains little to no
phylogenetic signal, is most likely across many definitions of
"microbiome trait". While there was some support for the
Ornstein-Uhlenbeck model (that invokes selection), the level of support
was similar to our White Noise simulation, further supporting the White
Noise model as the best explanation for the evolution of the microbiome as
a trait of avian hosts. Our study highlights the qualitatively minor
impact that different analytical choices can have on results and that
biological interpretations can be robust to method choice.