Anna's hummingbird microbiome analysis

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 pox virus 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 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 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.