Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

In the present 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. Utilizing data from Illumina platform, 4174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3602 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 (128), Propionibacterium (71), Erwinia (70), Ralstonia (56) phages shows the highest abundance and account for approximately 90% of the total identified phages.

Additionally, 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%), Pseudomonadales (∼7.5%) signify the core section. Further, 21869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes) among which 4 ARG types namely multidrug resistance (MDR) (12041 reads, ∼55%), bacitracin (3202 reads, ∼15%), macrolide-lincosamide-streptogramin (MLS) (1744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%) has the highest abundance.

Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15919 reads). The results unveil the distribution of (pro)-phages; microbial community and various ARGs in the Ganges river sediments. Further research on these identified phage(s) could be used in phage-based therapeutics against pathogenic bacteria.

Authors: Narender Kumar, Amit Kumar Gupta, Sarabjeet Kour Sudan, Deepika Pal, Vinay Randhawa, Girish Sahni, Shanmugam Mayilraj, Manoj Kumar