Abstract
In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina Hiseq 4000 sequencing technology. The raw sequence data from metagenomic paired-end libraries were analysed for taxonomic classification, diversity, and functional annotation using MG-RAST online server. The results showed the presence of total of 57 phyla, 931 genera, and 2068 species, predominantly occupied by Moraxellaceae (Gammaproteobacteria). However, at the species level, we reported the presence of some representative pathogenic taxa, such as Acinetobacter baumannii and Moraxella osloensis. The functional annotation predicted at various levels based on SEED-based subsystem, KEGG ortholog identity (KO), Cluster of Orthologous Groups (COGs) database identified the predominance of genes associated with primary and secondary metabolism along with a crucial role in environmental and genetic signals, cellular communication, and cell signalling. Comparative Genome Analysis (CGA) using The Pathosystem Resource Integration Centre (PATRIC) tool based on genome annotation and assembly of the metagenomic libraries for representative taxon Acinetobacter baumannii (NCBI tax id:470) characterized the reads with a unique genome identifier of 470.20380 (A. baumannii DDLJ4) which is evolutionary closer to A. baumannii ATCC 470.17978 400667.7. In addition, the CARD database results about the presence of potential AMR pathotypes and the prevalence of adeABC, adeIJK, abeM gene-specific clusters that function as multidrug efflux pumps. Overall, the results provided a comprehensive insight into virulence and anti-microbial resistance mechanism and could be useful for developing potential drug targets against the possible AMR pathotypes.
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Data availability
The raw shotgun metagenome sequences of the Sohna hot spring water sample for S1_1 end of paired end libraries publicly available in the National Centre for Biotechnology Information (NCBI)—Sequence Read Archive (SRA) database under the accession number: SRX16388697-Neha Saini project and BioSample ID: SAMN29818005 and Bioproject ID: PRJNA860055.
Abbreviations
- GSI:
-
Geological Survey of India
- NGS:
-
Next generation sequencing
- ADR:
-
Artificial duplicate reads
- CARD:
-
The comprehensive antibiotic resistance database
- AMR:
-
Antimicrobial resistance
- HTS:
-
High throughput sequencing
- DRISEE:
-
Duplicate read inferred sequencing error estimation
- COGs:
-
Clusters of orthologous groups of proteins
- ARGs:
-
Antibiotic resistance genes
- PATRIC:
-
The Pathosystem Resource Integration Centre
- MDR:
-
Multidrug resistance
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Acknowledgements
We are highly thankful for financial assistance in the form of fellowship to Ms. Neha Saini, Ph.D. Scholar provided from National Fellowship for Other Backward Classes (NFOBC) under the scheme funded by the Ministry of Social Justice and Empowerment, Government of India. The authors also acknowledge Centre for Bioinformatics, School of Biotechnology, BHU, India for bioinformatics data analysis.
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Author contributions: NS: designed research, sample collection, preparation for metagenomics analysis, analysis of the outcome data, draft manuscript preparation; MA: bioinformatic analysis, assisted in paper writing, reviewing, and editing; VKS: bioinformatic analysis, reviewing and editing; BD: reviewing and editing; SM: designed research, reviewing and editing, supervision.
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Saini, N., Aamir, M., Singh, V.K. et al. Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach. Arch Microbiol 205, 323 (2023). https://doi.org/10.1007/s00203-023-03664-z
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DOI: https://doi.org/10.1007/s00203-023-03664-z