The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels

TLDR

The vertebrate gut microbiome supports host metabolism, yet its dependence on fish trophic level was previously unclear. The authors sequenced 24 16S rRNA libraries (985,000 reads) to compare gut microbiota across four trophic categories. The study found that carnivorous and herbivorous fish gut bacterial communities cluster separately, share a core microbiota but differ at the genus level, with herbivores enriched in cellulose‑degrading bacteria and higher cellulase/amylase activity, while carnivores harbor protease‑producing bacteria and higher trypsin activity, indicating trophic level shapes microbiota composition, metabolic potential, and enzyme activity.

Abstract

Abstract Vertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium , Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity.