Land use change can decrease animal biodiversity, but its impact on their gut microbiome is not well understood. Because land use change can result in reduced food variety, it may alter animal diet and consequently the colonization of their gut by microbes via different food items. We sought to quantify the effect of land use change on bird microbiomes in a Costa Rican landscape that contained a diversity of habitat types ranging from pristine forests to agriculture. In this landscape, we collected fresh fecal samples (n = 346) from six common species of insectivorous birds (clay-coloured thrush, Turdus grayi; Swainson’s thrush, Catharus ustulatus; orange-billed nightingale-thrush, Catharus aurantiirostris; yellow warbler, Dendroica petechia; rufous-capped warbler, Basileurerus rufifrons; and buff-throated saltator, Saltator maximus) at 24 sites across a land use gradient. Using these samples, we characterized gut microbial composition by DNA metabarcoding. We extracted DNA from each sample, amplified bacterial 16S rRNA gene via PCR, and assigned taxonomy to OTUs using the Greengenes database on QIIME software.
We identified a total of 3,334 OTUs. The most dominant bacterial phyla across the six species of birds included Cyanobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Diversity indices showed no significant difference among habitat types or bird species identity, suggesting that land use change or host identity may not affect gut microbial diversity. However, PERMANOVA analysis revealed a significant association between bird species identity and microbial species composition (R2 = 0.14). Ordination (NMDS) indicated clustering of gut microbial communities by bird species identity, with two of the six bird species (yellow warbler and Swainson’s thrush) having distinct microbial communities from one another. In addition, when we did NMDS and PERMANOVA separately for individual bird species, we found significant clustering of microbial communities by habitat type in the yellow warbler and marginally significant one in the clay-coloured thrush. These results suggest that the effect of land use change on microbial communities may be host-specific and dependent on habitat type. Overall, our data suggest that both host species identity and habitat type can influence gut microbial composition, but that host identity may affect microbial composition more strongly than habitat type in this landscape.