Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data

Gut feeling: Extent of virulence and antibiotic resistance genes inHelicobacter pyloriand campylobacteria

“…The integrated and automatic pipeline VFanalyzer (http://www.mgc.ac.cn/cgi-bin/VFs/v5/main.cgi) in the VFDB systematically identifies known/potential VFs in complete genomes based on iterative and exhaustive sequence similarity searches of orthologous groups within the query genome and preanalyzed reference genomes from VFDB to eliminate potential false positives from paralogs (Liu et al, 2019). We used Abricate 0.9.8 (https://github.com/tseemann/abricate) interface to screen the VFDB using the parameters – percentage identity of ≥60□%□and coverage of ≥40□% (Mootapally et al, 2021).…”

Bacterial diversity in the aquatic system in India based on metagenome analysis—a critical review

“…Streptomyces was predominant in this ecosystem (Table 5 ). Mootapally et al ( 2021 ) studied metagenomics from open AS in Gulf of Kathiawar analyzed the plasmid content from this study region which reveals that the plasmids encoded genes for metal, antibiotic, phage resistance, and virulence systems and that these traits would benefit the hosts (Mootapally et al 2021 ) (Table 5 ).…”

“…In the coastal and offshore waters, the phylum Proteobacteria and Firmicutes, predominates and other phylum reported were Bacteroidetes, Actinobacteria, Cyanobacteria, Chloroflexi, and Planctomycetes, with dominating classes of Alphaproteobacteria and Gammaproteobacteria (Kumar et al 2019 ; Mootapally et al 2021 ; Sachithanandam et al 2020 ; Lincy and Manohar 2020 ; Raiyani and Singh 2020 ). This observation was concurrence with reports from the international studies such as Korean coastal waters (Won et al 2017 ) Indian Ocean (Wang et al 2021 ), Ofunato Bay in Iwate Prefecture, Japan (Reza et al 2018 ), Coastal West Antarctic Peninsula (Bowman and Ducklow 2015 ), and Baltic Sea (Ininbergs et al 2015 ).…”

Insights into the Circular: The Cryptic Plasmidome and its Derived Antibiotic Resistome in the Urban Water Systems

“…Various plasmidome approaches have been made in diverse environments, such as cow rumen (Brown Kav et al, 2020), rat cecum (Jorgensen et al, 2014b), human gut (Suzuki et al, 2019;Willmann et al, 2019), soil (Luo et al, 2016), sediments (Mootapally et al, 2021), surface water (Perez et al, 2020), groundwater (Kothari et al, 2019), and extensively in wastewater (Ferreira et al, 2019;Li et al, 2015;Li et al, 2012;Zhang et al, 2011). However, the methodologies in previous studies were compromised in terms of biased targets and lack of needed bioinformatic tools.…”