Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India.
Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India.
Microb Drug Resist. 2021 Oct;27(10):1336-1354. doi: 10.1089/mdr.2020.0431. Epub 2021 Apr 28.
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, (782 hits), (403), (386), (279), (232), (196), (166), (163), (146), (143), 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, (∼69.3%) dominates the microbial population structure. Primarily, orders such as (∼28%), (∼13.9%), (∼13.7%), and (∼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%), macrolide-lincosamide-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.
在这项研究中，我们分析了恒河河底沉积物样本的宏基因组 DNA，以探索噬菌体、微生物群落和抗生素耐药基因（ARGs）的丰度和多样性。利用 Illumina 平台的数据，我们将 4,174 条（约 0.0013%）reads 分类为 285 种不同的 DNA 病毒，其中主要是 260 种独特噬菌体（3,602 条 reads，约 86.3%）。在所有病毒中，（782 个命中），（403），（386），（279），（232），（196），（166），（163），（146），（143）和（128）噬菌体的丰度最高，占总鉴定噬菌体的约 90%。此外，我们还鉴定了这些噬菌体的相应宿主。主要的，（约 69.3%）主导着微生物种群结构。主要的目，如（约 28%），（约 13.9%），（约 13.7%）和（约 7.5%）代表核心部分。此外，21,869 条（约 0.00695%）reads 被分为 20 种 ARG 类型（类）和 240 种 ARG（亚型），其中 4 种 ARG 类型，即多药耐药（12,041 条 reads，约 55%）、杆菌肽（3,202 条 reads，约 15%）、大环内酯-林可酰胺-链阳性菌素（1,744 条 reads，约 7.98%）和福米霉素（990 条 reads，约 4.53%）的丰度最高。同时，还识别了六种耐药机制，其中以抗生素外排（72.8%，15,919 条 reads）为主导。研究结果揭示了恒河河底沉积物中噬菌体、微生物群落和各种 ARGs 的分布情况。
