Cloacal microbiomes and ecology of individual barn swallows

Microbiomes can be considered as 'second genomes' for the host, and can deeply affect its physiology, behaviour and fitness. We investigated the cloacal microbiomes (CMs) of adult and nestling barn swallows (Hirundo rustica), a small insectivorous migratory passerine bird, in order to assess whether CM structure was related to major ecological traits of individuals. Illumina sequencing of the V5-V6 hypervariable regions of the bacterial 16S rRNA gene showed that barn swallow CMs were dominated by Proteobacteria, Firmicutes, Actinobacteria, Tenericutes and Bacteroidetes. Nestling CMs were more similar to one another than adult ones, but showed higher alpha diversity. Sibling nestlings had more similar CMs than non-sibling ones. CMs of adult males also differed from those of adult females, but pair members had more similar CMs than expected by chance. In contrast, CMs did not differ between male and female nestlings. Finally, in adults, CMs strongly different from the 'average' CM were associated to lower survival prospects of the host. The CMs of a bird species in the wild are therefore related to important traits of individuals, such as survival, suggesting that microbiomes should be included among the traits examined in ecological studies.