The gut microbiota is a large and diverse community of microorganisms that provides many beneficial functions to the animal host; however, any change in the host's external or internal environment can affect microbiota composition. Migratory passerines arriving at stopover sites show highly variable microbiotas, which is likely reflective of the widely different habitats and foods utilized by migrants prior to arrival. If the previous environmental conditions led to the observed initial variability, then the microbiotas of birds should become more similar through stopover when migrants are in the same habitat and able to utilize similar resources. During spring 2014, migratory Swainson's Thrush (Catharus ustulatus), Wood Thrush (Hylocichla mustelina), and Gray Catbird (Dumetella carolinensis) were captured at a site in southwest Louisiana, USA, (1) upon arrival after crossing the Gulf of Mexico and (2) ≥1 day later during stopover. Fecal samples were collected and the microbial communities in them were analyzed using next-generation sequencing. The microbiotas of the majority of birds showed distinct shifts in community composition and became more similar during stopover, with birds stopping at the site for longer periods showing more pronounced changes in their microbiotas. These results are consistent with the hypothesis that local food-resource availability heavily influences the microbiotas of passerines; however, it is likely that gut remodulation during stopover after having crossed an ecological barrier also played a role.
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