Migration, pathogens and the avian microbiome: A comparative study in sympatric migrants and residents

Abstract

Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gut microbiota of free-ranging barn swallows (Hirundo rustica) by studying co-occurring migrant and resident subspecies sampled during the autumn migration at a migratory bottleneck. We found that within-host microbial richness (α-diversity) was similar between migrant and resident microbial communities. In contrast, we found that microbial communities (β-diversity) were significantly different between groups regarding both microbes present and their relative abundances. Compositional differences were found for 36 bacterial genera, with 27 exhibiting greater abundance in migrants and nine exhibiting greater abundance in residents. There was heightened abundance of Mycoplasma spp. and Corynebacterium spp. in migrants, a pattern shared by other studies of migratory species. Screens for key regional pathogens revealed that neither residents nor migrants carried avian influenza viruses and Newcastle disease virus, suggesting that the status of these diseases did not underlie observed differences in microbiome composition. Furthermore, the prevalence and abundance of Salmonella spp., as determined from microbiome data and cultural assays, were both low and similar across the groups. Overall, our results indicate that microbial composition differs between migratory and resident barn swallows, even when they are conspecific and sympatrically occurring. Differences in host origins (breeding sites) may result in microbial community divergence, and varied | 4707 TURJEMAN ET Al.

High-Throughput Sequencing for Examining Salmonella Prevalence and Pathogen—Microbiota Relationships in Barn Swallows

“…Where possible, we collected associated data on age, sex, season of capture, and site for all the birds. Sexing was completed according to standard protocols described in Turjeman et al (2020). We estimated, as described below, Salmonella prevalence for each site using a filtered dataset (n = 108) and visualized the prevalence distribution over our study area by generating a map using QGIS version 2.16.3 with the Apple iPhoto basemap (QGIS Development Team, 2009).…”

“…A detailed protocol for 16S rRNA gene sequencing and processing of resulting reads is available in Corl et al (2020) and Turjeman et al (2020). Briefly, frozen swabs stored in 95% EtOH were extracted using DNeasy PowerLyzer PowerSoil kits (Qiagen Inc., Germantown, MD).…”

“…Data was available for 92 samples to test for the effects of weight and sex at read threshold one, while 88 samples were used for read threshold two. Data for migratory status was available for 37 (one read) and 33 (two reads) samples that were classified as migrant or resident using both feather molt pattern evaluated during field capture and stable isotope analyses (see Turjeman et al, 2020). For each model, we used an ANOVA to identify significant relationships.…”

“…To test for confounding factors that may also influence alpha diversity, we used a linear model and ANOVA, including sex, site, and season as additional factors. Migration status was not included because our previous work showed no differences in alpha diversity between migrants and residents in our study population (Turjeman et al, 2020).…”

“…The barn swallow is a widespread ubiquitous passerine species well studied in terms of its life history (Balbontin et al, 2012;Møller, 2014), behavior (Saino et al, 2002;Lifjeld et al, 2011), physiology (de Ayala et al, 2006Schmidt-Wellenburg et al, 2007;Safran et al, 2008), migration ecology (Altwegg et al, 2011;Liechti et al, 2014;Pancerasa et al, 2018), and host-associated microbiomes (Kreisinger et al, 2015(Kreisinger et al, , 2017Ambrosini et al, 2019;Turjeman et al, 2020), which make the species an ideal exemplar for this study. The breadth of knowledge available on barn swallows allows for the integration of information across fields and more in-depth conclusions from our findings.…”