Metagenomic analysis of the African clary catfish intestines grown in the bioflok system

The gut microbiome plays a key role in the nutrition, immunity, and health of the African clary catfish (Clarias gariepinus). The intestinal contents of a catfish grown in the bioflok system were selected for the study. The bioflok system is an interaction of bacteria, algae, fungi and protozoa that contribute to the processing of organic compounds released during the vital activity of fish. The method of metagenomic analysis of the intestinal tract was used to determine the intestinal microbiota. Sequencing was performed on the Oxford Nanopore MinION platform using a 16S rRNA gene amplification and barcoding kit (Rapid Sequencing DNA – 16S Barcoding Kit 24 V14) according to the manufacturer's protocol. According to the results of metagenomic sequencing, representatives of the dominant and minor groups were identified. The taxonomic classification was carried out using the software Kraken2 (v2.0.8-beta) and Bracken (v2.5.0). The method is based on an algorithm for accounting for k-measures that compare readings with taxonomic nodes in the Silva database. The obtained data was visualized in the R environment using the ggplot2 library. According to the data obtained, bacteria were labeled among the most numerous representatives of the microbiota: Pseudomonas (29.91%), Stenotrophomonas (14.6%), Delftia (10.25%), Acinetobacter (6.93%), Massilia (3.9%), Sphingomonas (3.76%), Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium (3.68%), Comamonas (2.72%), Variovorax (2.66%), Rheinheimera (2.52%), Acidovorax (1.9%), Diaphorobacter (1.06%). The composition of the microbiome is influenced by environmental conditions, diet, age, health status, and individual characteristics of aquatic organisms. The ability to manage the state of the intestinal microbiota of fish can help reduce the economic costs of maintenance and improve the marketability of farmed objects.