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Background  Current knowledge about seasonal variation in the gut microbiota of vertebrates is limited to a few studies based on mammalian fecal samples. Seasonal changes in the microbiotas of functionally distinct gut regions remain unexplored. We investigated seasonal variation (summer versus winter) and regionalization of the microbiotas of the crop, ventriculus, duodenum, cecum, and colon of the greater sage-grouse ( Centrocercus urophasianus ), an avian folivore specialized on the toxic foliage of sagebrush ( Artemesia spp .) in western North America.    Results  We sequenced the V4 region of the 16S rRNA gene on an Illumina MiSeq and obtained 6,639,051 sequences with a median of 50,232 per sample. These sequences were assigned to 457 bacterial and 4 archaeal OTUs.  Firmicutes  (53.0%),  Bacteroidetes  (15.2%),  Actinobacteria  (10.7%), and  Proteobacteria  (10.1%)were the most abundant and diverse phyla. Microbial composition and richness showed significant differences among gut regions and between summer and winter. Gut region explained almost an order of magnitude more variance in our dataset than did season or the gut region × season interaction. The effect of season was uneven among gut regions. Microbiotas of the crop and cecum showed the greatest seasonal differences.    Conclusions  Our data suggest that seasonal differences in gut microbiota reflect seasonal variation in the microbial communities associated with food and water. Strong differentiation and uneven seasonal changes in the composition and richness of the microbiota among functionally distinct gut regions demonstrate the necessity of wider anatomical sampling for studies of composition and dynamics of the gut microbiota.    Electronic supplementary material  The online version of this article (10.1186/s42523-019-0002-6) contains supplementary material, which is available to authorized users.

Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore