Comparative Gut Microbiota of 59 Neotropical Bird Species

Abstract

The gut microbiota of vertebrates are essential to host health. Most non-model vertebrates, however, lack even a basic description of natural gut microbiota biodiversity. Here, we sampled 116 intestines from 59 Neotropical bird species and used the V6 region of the 16S rRNA molecule as a microbial fingerprint (average coverage per bird ~80,000 reads). A core microbiota of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria was identified, as well as several gut-associated genera. We tested 18 categorical variables associated with each bird for significant correlation to the gut microbiota; host taxonomic categories were most frequently significant and explained the most variation. Ecological variables (e.g., diet, foraging stratum) were also frequently significant but explained less variation. Little evidence was found for a significant influence of geographic space. Finally, we suggest that microbial sampling during field collection of organisms would propel biological understanding of evolutionary history and ecological significance of host-associated microbiota.

Keywords: Neotropical birds; V6; evolution; gut microbiota; host-associated microbiota.

Figure 1

Sampling localities in Costa Rica (left) and Peru (right). A, Piedras Blancas; B, Los Charcos; C, Golfo Dulce; D, Londres; E, Santa Juana; F, El Copal; G, Tirimbina; H, La Selva; I, Veragua; J, Tuba Creek; K, Janirvan; L, San Jorge II. Warmer colors indicate higher elevations.

Figure 2

Bacterial composition of bird gut samples. (A) Relative abundance of bacterial phyla in all birds. Bird orders shown in gray boxes and individuals are labeled across the top. (B) Bacterial phyla summarized by bird order, including the individuals in this study and ^*indicates data obtained from Waite and Taylor (2014). Phylogeny on left is a modified version of the phylogenetic relationship of bird orders from Hackett et al. (2008).

Figure 3

PCoA of unweighted Unifrac distances for all 116 bird samples. All three plots are the same, but individuals are colored differently based on metadata, bird order (left), diet (center), and sampling locality (right). Dotted lines connect replicate samples (as described in Materials and Methods).

Figure 4

Bird phylogeny (left) obtained using ND2 locus and a constrained species level phylogeny estimated with ^*BEAST compared to dendrogram of weighted UniFrac distance matrix. Colors indicate bird order and individuals are tracked across the two figures.

Figure 5

Adonis test results for the full dataset (A) and averages for all the datasets (B). Details on variables in Table 2; datasets described in Materials and Methods.