Abstract
BackgroundOur understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.ResultsWe analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).ConclusionsCollectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds.2jWna3AEmgLMLS436bvUkuVideo
Highlights
Our understanding of the gut microbiota of animals is largely based on studies of mammals
1,014,240 raw 16S rRNA gene sequence reads were obtained from the intestinal contents of fish, and 653,281 high-quality sequence reads were obtained after the removal of low-quality and chimeric sequences
To determine whether the sampling depth was sufficient to give an overview of the fish gut microbiota, rarefaction curves were generated for the number of Operational taxonomic unit (OTU) per individual or species (Additional file 1: Supplementary Fig. S1)
Summary
Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. Fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. We comprehensively characterized gut bacterial communities in fish. In the last decade, numerous studies have explored gut microbial communities of various animal hosts. These studies have mostly focused on the gut microbiota of mammals [11], which represent less than 10% of all vertebrate diversity. There are more than 33,000 species of fish, representing the
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