Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico

Abstract

Although the gut microbiota is known to provide many beneficial functions to animal hosts, such as aiding in digestion, fat metabolism, and immune function, relatively little is known about the gut microbiota of passerines. Gut microbes may have both beneficial and detrimental impacts on the fitness of migratory passerines; however physiological and morphological changes associated with prolonged migratory flight may cause disruptions of the stable microbiota and potentially a loss of function. Fecal samples were collected from Swainson's thrushes Catharus ustulatus and gray catbirds Dumetella carolinensis immediately after crossing the Gulf of Mexico during spring migration and before crossing during fall, and microbiota communities were analyzed using next‐generation sequencing. Microbiota communities were generally dominated by Firmicutes and Proteobacteria, with potential pathogens as well as potentially beneficial bacteria identified in all birds. Energetic condition of migrants was not significantly related to overall microbiota community structure though it cannot be conclusively stated that migratory flight does not impact the microbiota. Spring and fall migrants showed clear differences in microbiota communities, indicating that environmental factors influence the gut microbiota of these species more than host genetics.

Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet

“…There are relatively few studies on the gut microbial diversity of birds using next generation sequencing (Waite & Taylor, 2014; Hird et al, 2015; Lewis, Moore & Wang, 2016). The avian microbiome models that have been extensively studied are chickens and turkeys, and avian poultry microbiome studies have focused mainly on improving the health and weight gain of birds without using antibiotics, as in mammals the presence of Lactobacillus has been of particular relevance (Stanley, Hughes & Moore, 2014; Danzeisen et al, 2015).…”

Like mother like nest: similarity in microbial communities of adult female Pied Flycatchers and their nests

“…Dabei handelt es sich wahrscheinlich um eine bidirektionale Introduction Research into host-microbe ecosystems is revolutionising the way we view avian biology (McFall-Ngai et al, 2013;Solar et al 2015). Studies that focus on identifying microbes associated with focal avian species or quantifying the structure of microbiomes with which birds interact are vital for understanding physiological processes, disease and immune responses, bird behaviour and socio-biology, population dynamics, community change, and links between the biotic and abiotic environments (Archie and Theis 2011;Bordenstein and Theis 2015;Moyers et al 2015;Lewis et al 2016). As well as being important from a scientific perspective, such knowledge can be vital in informing effective avian management and conservation initiatives (Dille et al 2016).…”

Full Issue

“…Physical measurements such as unflattened wing chord, mass, and subcutaneous fat (assessed as in Helms and Drury 1960) were recorded from each bird. In order to correct the mass of captured birds for differences in body size, the energetic condition of each bird was calculated on the basis of mass, fat score, and wing chord (Ellegren 1989, Owen and Moore 2006 for further description of the energetic-condition calculations, see Lewis et al 2016). The vast majority of birds captured at the study site depart the night of banding (see below), so it is likely that newly banded birds were recent arrivals to the site.…”

“…The OTUs were classified to genus level based on .95% similarity to reference sequences, to family based on 90-95% similarity, to order based on 85-90%, to class based on 80-85%, and to phylum based on 77-80% (Ishak et al 2011). Nonbacterial OTUs and rare OTUs detected in ,5 samples and composed of ,10 total reads-and, thus, not likely to be of biological significance-were removed as in Stanley et al (2013) and Lewis et al (2016). Read counts were rarefied 100 times to the lowest read count among all samples using the phyloseq package for R (McMurdie and Holmes 2013) and averaged as in Stanley et al (2013).…”

“…Moreover, individual migrants can show variable migratory routes and use of stopover sites (Lemke et al 2013), so birds during stopover along the northern coast of the Gulf of Mexico in spring likely used differing arrays of stopover habitats in the Neotropics. Migratory Swainson's Thrush (Catharus ustulatus) and Gray Catbird (Dumetella carolinensis) arriving at a stopover site along the northern coast of the Gulf of Mexico in spring show high degrees of inter-individual variation in their gut microbiotas, which Lewis et al (2016) attributed to the widely different habitats occupied and foods consumed by migrants prior to arrival.…”