Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach

Abstract

In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (*0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, *86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for *90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (*69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (*28%), Burkholderiales (*13.9%), Actinomycetales (*13.7%), and Pseudomonadales (*7.5%) signify the core section. Furthermore, 21,869 (*0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, *55%), bacitracin (3,202 reads, *15%), macrolidelincosamide-streptogramin (1,744 reads, *7.98%), and fosmidomycin (990 reads, *4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.

Microbial diversity of river Ganga at Haridwar (Uttarakhand) through metagenomic approaches

“…A recent metagenomic study explored the viral habitats of Ganges, focusing primarily on phage identification and assessment of their diversity. It provided insights into the abundance and diversity of phages, microbial communities, and antibiotic resistance genes in river sediment [11]. Very little is known about the types of microbes that are prevalent in freshwater habitats, except species from the division cyanobacteria, which are rather suitable for cultivation and morphological differentiation.…”

Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India

“…However, recent research utilizing advanced metagenomic approaches has begun to unveil a bacterial population capable of bioremediating significant contaminants in the river's sediments [5,[14][15][16]. A handful of studies have also employed metagenomic techniques to explore the presence of antibiotic resistance genes in the water and sediments of the Ganga [4,17,18].…”

Immunomodulating, Prophylactic, and Therapeutic Potential of Natural Phages in Ganga Water

“…In the comparative study with control Rivers Yamuna and Narmada, pathogenic bacteriophages were found lesser in numbers than pathogenic bacterial species in both Rivers compared to River Ganga" [11]. The Institute of Microbial Technology has reported a variety of different phages having specific bactericidal activity against clinical isolates and pathogens Microcystis, Haemophilus, Synechococcus, Pseudomonas, Enterococcus, Bacillus, Rhodococcus, Caulobacter, Salmonella, Enterobacteria, and Mycobacterium [12]. These studies give us a reason to explore the use of phages in Ganga water for immunomodulating, prophylactic, and therapeutic purposes.…”