Microbiome composition of Anna's hummingbirds differs among regions of the gastrointestinal tract

Abstract

The gastrointestinal (GI) microbiome is an important mediator and indicator of host physiology, health and fitness in many vertebrate systems, but sources of variation in microbiome composition within species are poorly understood, particularly in free‐ranging birds. Hummingbirds have GI anatomy and physiology similar to other avian species, but they have a relatively rapid gastrointestinal transit rate, which could affect microbiome structure. To date, it has not been elucidated if microbiomes isolated from feces and samples from sections of the GI tract differ in an avian organism that has a rapid gastrointestinal time. Here, we test the hypothesis that the microbiome in free‐ranging and wildlife rehabilitation‐sourced Anna's hummingbirds Calypte anna differ between fecal and samples from three sections of the GI tract and between birds that differ in sex, age and poxvirus infection status. We characterized bacterial composition in fecal and GI tract samples from Anna's hummingbirds by amplicon sequencing of the 16S rRNA gene. We found strong evidence of differentiation in bacterial composition among GI tract regions and compared it to fecal samples. Actinobacteria, primarily genus Corynebacterium, Firmicutes and Fusobacteria were abundant in bird samples from regions of the GI tract. In contrast, fecal bacterial communities were more diverse and variable compared to GI tract samples. Bacterial community composition differed between male and female hummingbirds and with bird age (hatch year vs after‐hatch year). Finally, birds with symptoms of avian poxvirus infection had a higher relative abundance of Staphylococcus spp. than birds with no symptoms of pox. Our results suggest that Anna's hummingbirds host differentiated microbiome among GI tract regions that is consistent among individual birds. The GI bacterial community also contained taxa not represented in fecal samples. This provides evidence for the possibility of a residential gut microbiome in Anna's hummingbirds, although functional significance of the bacterial microbiome remains unknown.