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Background  Rabbits are cecotrophic, hindgut-fermenters that rely heavily on their gastrointestinal microbiota for optimal digestion of plant-based diets. Dysbiosis, caused by disruption of the gastrointestinal microbiota, is known to predispose rabbits to rabbit enteritis complex (REC), a major cause of morbidity and mortality. The objectives of this study were to describe the fecal microbiota of domestic rabbits from a variety of settings (commercial meat, companion, laboratory, and shelter) and to identify how factors such as age, season, and routine antimicrobial use affect the fecal microbiota composition.    Results  A total of 86 pooled commercial meat, 54 companion, 14 pooled laboratory, and 14 shelter rabbit fecal samples were evaluated using 16S rRNA gene sequencing of the V4 region. In all sample types, the predominant bacterial phylum was Firmicutes. Other commonly identified phyla (composing ≥ 1% of the total microbiota composition) were Verrucomicrobia, Proteobacteria, and Bacteroidetes. Significant differences in composition were noted between commercial, companion, laboratory, and shelter rabbit samples for proportions of Verrucomicrobia ( P  < 0.01), Proteobacteria ( P  < 0.01), and Lentisphaerae ( P  = 0.01) within the total microbiota. Within the commercial meat rabbit samples, significant differences between the microbiota composition of growers ( n  = 42) and does ( n  = 44) were limited to one unclassified Firmicutes ( P  = 0.03) and no differences were identified at the phylum level. Significant differences were present between fecal samples taken from rabbits during the summer ( n  = 44) compared to the winter ( n  = 42), with Firmicutes ( P  = 0.04), Verrucomicrobia ( P  = 0.03), Proteobacteria ( P  = 0.02), Deinococcus-Thermus (P = 0.04), Armatimonadates ( P  = 0.003), and Actinobacteria (P = 0.03) forming significantly different proportions of the microbiota. The only significant difference in composition between those farms that routinely reported antimicrobial use and those that did not was in one unclassified Bacteroidetes ( P  < 0.05) and no differences were identified at the phylum level.    Conclusions  Rabbit husbandry and diet, in addition to season, significantly influence the fecal microbiota composition of domestic rabbits, while age of the rabbit post-weaning has minimal impact.    Electronic supplementary material  The online version of this article (10.1186/s12917-018-1464-6) contains supplementary material, which is available to authorized users.

Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi)