Composition and Drivers of Gut Microbial Communities in Arctic-Breeding Shorebirds.

Kirsten Grond,Rebecca L Bentzen,Eunbi Kwon,Brooke L Hill,Andrew C Doll,Megan L Boldenow,Jenny A Cunningham,Steven J Kendall,Richard B Lanctot,Jennie Rausch,Bruce Casler,Lisa Pirie-Dominix,Stephen C Brown,Ari Jumpponen,Scott Freeman,Joseph R Liebezeit,Brett K Sandercock,Jorge W Santo Domingo

doi:10.3389/fmicb.2019.02258

Abstract

Gut microbiota can have important effects on host health, but explanatory factors and pathways that determine gut microbial composition can differ among host lineages. In mammals, host phylogeny is one of the main drivers of gut microbiota, a result of vertical transfer of microbiota during birth. In birds, it is less clear what the drivers might be, but both phylogeny and environmental factors may play a role. We investigated host and environmental factors that underlie variation in gut microbiota composition in eight species of migratory shorebirds. We characterized bacterial communities from 375 fecal samples collected from adults of eight shorebird species captured at a network of nine breeding sites in the Arctic and sub-Arctic ecoregions of North America, by sequencing the V4 region of the bacterial 16S ribosomal RNA gene. Firmicutes (55.4%), Proteobacteria (13.8%), Fusobacteria (10.2%), and Bacteroidetes (8.1%) dominated the gut microbiota of adult shorebirds. Breeding location was the main driver of variation in gut microbiota of breeding shorebirds (R2 = 11.6%), followed by shorebird host species (R2 = 1.8%), and sampling year (R2 = 0.9%), but most variation remained unexplained. Site variation resulted from differences in the core bacterial taxa, whereas rare, low-abundance bacteria drove host species variation. Our study is the first to highlight a greater importance of local environment than phylogeny as a driver of gut microbiota composition in wild, migratory birds under natural conditions.

Highlights

The gut microbiota is important in maintaining gut homeostasis, and contributions to organismal health have received increasing attention over the past decades
Western Sandpipers (WESA) had a slightly lower number of operational taxonomic units (OTUs), while Semipalmated sandpipers (SESA) had a higher number of OTUs compared to all other species
We characterized the fecal microbiota of Arctic- and subArctic-breeding shorebirds and investigated environmental and phylogenetic drivers of fecal microbial composition

Summary

Introduction

The gut microbiota is important in maintaining gut homeostasis, and contributions to organismal health have received increasing attention over the past decades. Timing of bacterial recruitment in the gut differs among vertebrate taxa. Mammals acquire their initial gut microbial communities from passage through the birth canal (Leser and Mølbak, 2009), but recruitment routes for birds are less well known (Grond et al, 2018). Shorebirds have precocial chicks and their gut microbiota establish from environmental inocula after hatching (Grond et al, 2017). Gut microbial communities can be modified by a number of intrinsic and extrinsic factors, including host phylogeny, age, or diet (Ley et al, 2008; Goodrich et al, 2014; Hird et al, 2015)

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