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

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach
 
Creator Kumar, Narender
Gupta, Amit Kumar
Sudan, Sarabjeet Kour
Pal, Deepika
Randhawa, Vinay
Sahni, Girish
Mayilraj, Shanmugam
Kumar, Manoj
 
Subject QR Microbiology
 
Description 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 (similar to 0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, similar to 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 similar to 90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (similar to 69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (similar to 28%), Burkholderiales (similar to 13.9%), Actinomycetales (similar to 13.7%), and Pseudomonadales (similar to 7.5%) signify the core section. Furthermore, 21,869 (similar to 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, similar to 55%), bacitracin (3,202 reads, similar to 15%), macrolide-lincosamide-streptogramin (1,744 reads, similar to 7.98%), and fosmidomycin (990 reads, similar to 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.
 
Publisher Mary Ann Liebert
 
Date 2021-04-28
 
Type Article
PeerReviewed
 
Relation https://www.liebertpub.com/doi/10.1089/mdr.2020.0431?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed&
http://crdd.osdd.net/open/2675/
 
Identifier Kumar, Narender and Gupta, Amit Kumar and Sudan, Sarabjeet Kour and Pal, Deepika and Randhawa, Vinay and Sahni, Girish and Mayilraj, Shanmugam and Kumar, Manoj (2021) Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. Microbial drug resistance (Larchmont, N.Y.). ISSN 1931-8448