Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers

Understanding the factors that shape microbiomes can provide insight into the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary and evolutionary influences on gut microbiome structure. We performed faecal metabarcoding to characterize both the gut microbiome and diet of 15 wood-warbler species across a 4-year period and from two geographical localities. We find host taxonomy generally explained similar to 10% of the variation between individuals, which is similar to 6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.

Automated summary

Understanding the factors influencing microbiome diversity is crucial for understanding host-symbiont interactions and co-evolutionary dynamics. This study focused on wood-warblers and found that host evolutionary history has the strongest influence on gut microbiome differentiation, compared to environmental factors and diet diversity. The similarity of gut microbiomes was more congruent with the host phylogeny than with host diet similarity, suggesting that host traits may play a role in colonization and maintenance of microbes.