Exploring Intestinal Microbiome of Heteropneustes fossilis (Bloch): A Metagenomic Approach

Heteropneustes fossilis is, an economically important freshwater catfish species with a high population density in the Indian subcontinent. Microbial studies have helped to understand the gut microbiome. Most of the bacterial isolates were gram positive, indole negative, MR positive, oxidase negative, amylase positive, citrate utilization positive, urea hydrolase positive, and nitrate reduction positive. Growth under different physiological conditions indicated that these isolates were as mesophilic, moderately halophilic, and slightly acidophilic in nature. In addition, high-throughput sequencing of gDNA of intestinal bacteria using Illumina platform analyses the structural and functional properties and abundance of antibiotic resistance genes (ARGs) in H. fossilis . Metagenomic data were submitted to the NCBI database (BioProject: PRJNA1231987). Metagenomic profiling of H. fossilis showed different domains: bacteria (99.63%), archaea (0.03%), and eukaryota (<0.01%). A total of 20 phyla, 51 classes, 90 orders, 160 families, 373 genera, and 624 species were identified using sequential analysis. Taxonomic annotation identified phylum Proteobacteria (53.14%), class Gammaproteobacteria (51.60%), order Enterobacterales (50.99%), family Enterobacteriaceae (34.73%), genus Clostridium (20.35%) and species Edwardsiella tarda group (15.99%) was most abundant. Functional analysis of H. fossilis metagenome revealed metabolic pathway dominated by genetic information processing and environmental information processing, metabolism of carbohydrates, amino acids, and vitamins essential for sensory and nutritional qualities. Seven types of ARGs were dominant with their resistance against different drug class such as peptide, aminoglycoside and tetracycline antibiotic. Gut microbiome studies have revealed that several bacterial species like Bifidobacterium, Lactobacillus, Bacillus, Romboutsia, Cetobacterium are used as aquaculture probiotics, a sustainable alternative to antibiotics.