Analysis of the Intestinal Microbiome of Coregonus nasus Using 16S rRNA Sequencing

Abstract In vertebrates, the intestinal microbiota significantly influences metabolic processes, immune development, and resistance to pathogens. Unlike terrestrial animals, fish are in constant contact with an aquatic environment, making their microbiota particularly sensitive to environmental changes. The aim of this study was to determine the structure and taxonomic composition of the intestinal microbiota of Coregonus nasus based on metagenomic sequencing of two 16S rRNA regions. Eighty-eight operational taxonomic units (OTUs) were identified for the V3–V4 region and 25 OTUs for the V4–V5 region. Analysis of the microbial community structure revealed the dominance of Proteobacteria, Firmicutes, and Bacteroidota. Comparison of OTU representation between the two groups (Affected and Control) revealed taxa associated with different host or environmental conditions. The data obtained expand our understanding of the intestinal microbiota of freshwater fish and also open up prospects for the use of microbiome markers to monitor the health of fish in aquaculture and natural populations.