Abstract
BackgroundTor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome.ResultsThe analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens.ConclusionsGut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.
Highlights
Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species
Taxonomic composition of fish gut microbiome The Illumina HiSeq 2500 platform generated a total of 284,412,950 paired-end reads, n = 120,716,302 pairedend reads in fish gut metagenome 1 (FGM1) and n = 163,696,648 paired-end reads in fish gut metagenome 2 (FGM2) yielding total 71.3 gigabase high-quality whole metagenome shotgun sequence data
FGM1 and FGM2 were dominated by 95.96% and 91.33% Proteobacteria, respectively
Summary
The largest freshwater fish of the Indian subcontinent, is an endangered species. The shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome. Microbial dysbiosis causes impairment of the normal activity of digestive enzymes, damage to gut tissue, and increased infiltration of opportunistic pathogens and toxicants [14]. This fact has drawn considerable attention to find out potential probiotic, symbiotic, and pathogenic bacteria that may have a profound influence on the host physiology and health. While there are several studies on the fish gut microbiome, hitherto, there are gaps in our understanding on the structure and function of the gut microbiome in endangered fish [1, 2, 15, 16]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
