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Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India
•First insight into the viral community composition in a stream sediment ecosystem.•Classified virome fraction indicated the dominance of ssDNA viruses.•Recovered uncultivated viral genomes (UViGs) hint at novel community structure as per existing databases.•Auxiliary metabolic genes (AMGs) involved...
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| Published in: | Virus research 2023-06, Vol.330, p.199110-199110, Article 199110 |
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| container_title | Virus research |
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| creator | Mukhopadhyay, Adhip Choudhury, Shubham Kumar, Manoj |
| description | •First insight into the viral community composition in a stream sediment ecosystem.•Classified virome fraction indicated the dominance of ssDNA viruses.•Recovered uncultivated viral genomes (UViGs) hint at novel community structure as per existing databases.•Auxiliary metabolic genes (AMGs) involved in pyrimidine, carbohydrate, and organosulfur metabolism were detected.•Identified antibiotic resistance genes indicate the potential roles of viruses as ARG reservoirs.
Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs. |
| doi_str_mv | 10.1016/j.virusres.2023.199110 |
| format | article |
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Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.</description><identifier>ISSN: 0168-1702</identifier><identifier>EISSN: 1872-7492</identifier><identifier>DOI: 10.1016/j.virusres.2023.199110</identifier><identifier>PMID: 37031921</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Antibiotic resistance gene ; Auxiliary metabolic gene ; Bacteriophage ; Bacteriophages - genetics ; DNA Viruses - genetics ; Ecosystem ; Freshwater ; Metagenomics ; N-Choe ; Rivers ; ssDNA virus ; Stream ; Virome ; Viruses - genetics</subject><ispartof>Virus research, 2023-06, Vol.330, p.199110-199110, Article 199110</ispartof><rights>2023</rights><rights>Copyright © 2023. Published by Elsevier B.V.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c416t-ee982042feddb5af0a2c3dfc3fa04a92e80b3c3056381298554ee192143522293</citedby><cites>FETCH-LOGICAL-c416t-ee982042feddb5af0a2c3dfc3fa04a92e80b3c3056381298554ee192143522293</cites><orcidid>0000-0003-3769-052X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37031921$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mukhopadhyay, Adhip</creatorcontrib><creatorcontrib>Choudhury, Shubham</creatorcontrib><creatorcontrib>Kumar, Manoj</creatorcontrib><title>Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India</title><title>Virus research</title><addtitle>Virus Res</addtitle><description>•First insight into the viral community composition in a stream sediment ecosystem.•Classified virome fraction indicated the dominance of ssDNA viruses.•Recovered uncultivated viral genomes (UViGs) hint at novel community structure as per existing databases.•Auxiliary metabolic genes (AMGs) involved in pyrimidine, carbohydrate, and organosulfur metabolism were detected.•Identified antibiotic resistance genes indicate the potential roles of viruses as ARG reservoirs.
Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.</description><subject>Antibiotic resistance gene</subject><subject>Auxiliary metabolic gene</subject><subject>Bacteriophage</subject><subject>Bacteriophages - genetics</subject><subject>DNA Viruses - genetics</subject><subject>Ecosystem</subject><subject>Freshwater</subject><subject>Metagenomics</subject><subject>N-Choe</subject><subject>Rivers</subject><subject>ssDNA virus</subject><subject>Stream</subject><subject>Virome</subject><subject>Viruses - genetics</subject><issn>0168-1702</issn><issn>1872-7492</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNqFkMtOAjEUhhujEURfgXTpwhl7metOgjcSxI3uTJrSORNKmCm2HRLe3sKgW1dn853_P-dDaExJTAnN7tfxTtvOWXAxI4zHtCwpJWdoSIucRXlSsnM0DGAR0ZywAbpybk0IyXieXaIBzwmnJaND9PUGXoYo02iFZSs3ewcOmxo_Lib4WIGVaZqu1X6P64BhB5VuoPVHyq8AL6LpygB23oJs7vDCWL_Cs7bS8hpd1HLj4OY0R-jz-elj-hrN319m08k8UgnNfARQFowkrIaqWqayJpIpXtWK15IksmRQkCVXnKQZLygrizRNAA7nJzxljJV8hG773K013x04LxrtFGw2sgXTOcHyYCdnaVEENOtRZY0L-mqxtbqRdi8oEQezYi1-zYqDWdGbDYvjU0e3bKD6W_tVGYCHHoDw6U6DFU5paFXQZUF5URn9X8cPrPGNJw</recordid><startdate>202306</startdate><enddate>202306</enddate><creator>Mukhopadhyay, Adhip</creator><creator>Choudhury, Shubham</creator><creator>Kumar, Manoj</creator><general>Elsevier B.V</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-3769-052X</orcidid></search><sort><creationdate>202306</creationdate><title>Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India</title><author>Mukhopadhyay, Adhip ; Choudhury, Shubham ; Kumar, Manoj</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c416t-ee982042feddb5af0a2c3dfc3fa04a92e80b3c3056381298554ee192143522293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Antibiotic resistance gene</topic><topic>Auxiliary metabolic gene</topic><topic>Bacteriophage</topic><topic>Bacteriophages - genetics</topic><topic>DNA Viruses - genetics</topic><topic>Ecosystem</topic><topic>Freshwater</topic><topic>Metagenomics</topic><topic>N-Choe</topic><topic>Rivers</topic><topic>ssDNA virus</topic><topic>Stream</topic><topic>Virome</topic><topic>Viruses - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mukhopadhyay, Adhip</creatorcontrib><creatorcontrib>Choudhury, Shubham</creatorcontrib><creatorcontrib>Kumar, Manoj</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Virus research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mukhopadhyay, Adhip</au><au>Choudhury, Shubham</au><au>Kumar, Manoj</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India</atitle><jtitle>Virus research</jtitle><addtitle>Virus Res</addtitle><date>2023-06</date><risdate>2023</risdate><volume>330</volume><spage>199110</spage><epage>199110</epage><pages>199110-199110</pages><artnum>199110</artnum><issn>0168-1702</issn><eissn>1872-7492</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>•First insight into the viral community composition in a stream sediment ecosystem.•Classified virome fraction indicated the dominance of ssDNA viruses.•Recovered uncultivated viral genomes (UViGs) hint at novel community structure as per existing databases.•Auxiliary metabolic genes (AMGs) involved in pyrimidine, carbohydrate, and organosulfur metabolism were detected.•Identified antibiotic resistance genes indicate the potential roles of viruses as ARG reservoirs.
Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>37031921</pmid><doi>10.1016/j.virusres.2023.199110</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-3769-052X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Antibiotic resistance gene Auxiliary metabolic gene Bacteriophage Bacteriophages - genetics DNA Viruses - genetics Ecosystem Freshwater Metagenomics N-Choe Rivers ssDNA virus Stream Virome Viruses - genetics |
| title | Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India |
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