Natural variability of cloacal microbiomes linked to ecological features of individuals in the Barn swallow

Microbiomes, the ensemble of the genes of the microorganisms that live in association with a host organism, are considered “second genomes” for the host, and can affect its physiology, behaviour and survival. In May-July 2016, we investigated the cloacal microbiomes (CMs) of adult and nestling Barn swallows (Hirundo rustica), a small insectivorous passerine and a long-distance migrant breeding on a farm in northern Italy. Illumina sequencing of the V5–V6 hypervariable regions of the bacterial 16S rRNA gene showed that Barn Swallow CMs were dominated by bacteria of the phyla Proteobacteria, Firmicutes, Actinobacteria, Tenericutes and Bacteroidetes. CMs of nestlings were more similar to one another than those of adults, but showed higher alpha diversity. Sibling nestlings, in particular, had more similar CMs than non-sibling ones. CMs also differed between adult males and adult females, but not between male and female nestlings. Finally, CMs of surviving adults were less differentiated to one another than those of non-surviving ones. The CMs of a bird species in the wild are therefore related to important traits of individuals, such as survival, suggesting that microbiomes should t be included among the traits examined by animal and behavioural ecologists.