Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Most previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we described the cloacal microbiome (CM) composition in free living barn swallows Hirundo rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. A significant correlation of CM within breeding pair members is consistent with the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. This effect on CM composition had a relatively low effect size, however, possibly due to the species' high level of sexual promiscuity.

Department of Zoology Faculty of Science Charles University Prague Viničná 7 128 44 Prague 2 Czech Republic

Studenec Research Facility Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Květná 8 603 65 Brno Czech Republic

Studenec Research Facility Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Květná 8 603 65 Brno Czech Republic; Department of Zoology Faculty of Science Charles University Prague Viničná 7 128 44 Prague 2 Czech Republic

Studenec Research Facility Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Květná 8 603 65 Brno Czech Republic; Department of Zoology Faculty of Science Charles University Prague Viničná 7 128 44 Prague 2 Czech Republic; Department of Biodiversity and Molecular Ecology Fondazione Edmund Mach Research and Innovation Centre 1 38010 San Michele all'Adige TN Italy

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