Metagenomic analysis of the intestinal flora and antibiotic resistance genes of yellow catfish (Pelteobagrus fulvidraco)

High-throughput sequencing of intestinal microbial DNA using the Illumina platform was implemented to clarify the structure and function of intestinal flora and antibiotic resistance genes (ARGs) abundances in yellow catfish (Pelteobagrus fulvidraco). Species annotation and gene function analysis were performed on the metagenomic sequencing data. Intestinal bacteria were isolated and identified by 16sRNA. The results showed that intestinal flora was highly similar in the three P. fulvidraco. A total of 37 phyla and 788 genera of intestinal bacteria were identified. Proteobacteria, Streptomyces, and Clostridium are the dominant flora with the average relative abundance of 25.71%, 14.75%, and 5.15%, respectively. Six strains were successfully isolated and identified in our experiment. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the primary metabolic pathway is dominated by metabolism and organic systems, while the secondary metabolic pathway is dominated by sensory system, carbohydrate metabolism, replication, and repair. In addition, 499 ARGs of 37 resistance types were identified based on Antibiotic Resistance Genes Database. Tetracycline, polypeptide, macrolide, glycopeptide, and multiple drug resistance were highly abundant. The intestinal ARGs of P. fulvidraco were macB, bcrA, and evgS. In general, rich bacterial diversity and many types of ARG were detected in the intestine of P. fulvidraco. Moreover, probiotics are potentially a good alternative to antibiotic abuse in aquaculture industry. Therefore, analysis of intestinal flora, intestinal flora ARGs and gene functions is beneficial for the artificial farming of P. fulvidraco.