Localized gut tissue and digesta bacterial communities of five pelagic fish species from the Atlantic Ocean: Insights from 16S rRNA gene diversity

Abstract

Gut microbes are now considered inseparable from their hosts. Compared to farmed fish, gut microorganisms of wild-living fish are largely understudied despite they constitute the natural microbiome fully adapted to the host’s natural life mode. In this study, we investigated for the first time whether the gut bacterial microbiota, based on 16S rRNA gene diversity, of the Atlantic Ocean fast-swimming fish Auxis sp., Coryphaena hippurus, Euthynnus alletteratus, Kajikia albida and Sarda sarda, differentiate among their proximal, intermediate and distal gut sections. Between 61 and 247 operational taxonomic units (OTUs) were found in each gut section, with the highest numbers mostly in the distal section. The most important OTUs belonged to the Acinetobacter, Bacillus, Corynebacteriales, Cutibacterium, Escherichia-Shigella, Lactobacillus, Massilia, Photobacterium, Pirellulaceae, Shewanella, Staphylococcus, Streptococcus, Synechococcus, Weissella, Xanthomonas taxa, most of which occur frequently in the gut of many fish, while a few additional OTUs remained unaffiliated. The bacterial communities differed significantly between the gut sections while a distinct turnover of unique and newly appearing/disappearing OTUs were found along the gut sections transition. Bacterial presumptive metabolic pathways with considerable abundance changes along the gut sections included polysaccharide and protein degradation, fermentation and vitamins biosynthesis. In E. alletteratus, the comparison between the microbiota of each gut section with its respective digesta microbiota, showed that the highest overlap (34.2 %) occurred in the distal part of the gut. Overall, this study showed that in some wild fish, gut microbiota is considerably localized for both their taxonomic and potential metabolic profiles.