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Background  Pupfishes frequently enter paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanol-associated paradoxical anaerobism, gut microbial communities were depleted using a cocktail of antibiotics and profiled using 16S rRNA gene sequencing.    Results  Compared to the control group ( n  = 12), microbiota-depleted fish ( n  = 12) spent more time in paradoxical anaerobism. Our analysis indicated that the bacterial phyla  Proteobacteria ,  Fusobacteria ,  Bacteroidetes ,  Firmicutes ,  Actinobacteria ,  Patescibacteria , and  Dependentiae  dominated the pupfish gut, which is consistent with other fish gut microbiota. Although the gut microbial communities with and without antibiotic treatment were similarly diverse, they were distinct and the greatest contribution to the dissimilarity (27.38%) was the common fish commensal  Cetobacterium .    Conclusions  This study reports the first characterization of gut microbial communities of pupfish and suggests the microbiome may play a critical role in regulating metabolic strategies that are critical for survival in extremes of temperature and oxygen concentration. We speculate that  Cetobacterium , a primary fermenter, also consumes ethanol through secondary fermentation via an alcohol dehydrogenase and therefore regulates the transition from paradoxical anaerobism to aerobic respiration in fish. Given the wide distribution and abundance of  Cetobacterium  in warm-water fishes, this process may be of broad importance, and suggests that the microbiome be carefully considered for both conservation and aquaculture.

The gut microbiome and its potential role in paradoxical anaerobism in pupfishes of the Mojave Desert