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Metagenomic analysis of wastewater phageome from a University Hospital in Turkey
Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages....
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| Published in: | Archives of microbiology 2022-06, Vol.204 (6), p.353-353, Article 353 |
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| container_end_page | 353 |
| container_issue | 6 |
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| container_title | Archives of microbiology |
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| creator | Salih, Hanife Karaynir, Abdulkerim Yalcin, Melis Oryasin, Erman Holyavkin, Can Basbulbul, Gamze Bozdogan, Bulent |
| description | Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to
Caudovirales
order and
Myoviridae
(56%),
Siphoviridae
(43%), and
Podoviridae
(0.02%) families. The most common host genera were
Escherichia
(88.20%),
Salmonella
(5.49%) and
Staphylococcus
(5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent
Podoviridae
. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes. |
| doi_str_mv | 10.1007/s00203-022-02962-2 |
| format | article |
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Caudovirales
order and
Myoviridae
(56%),
Siphoviridae
(43%), and
Podoviridae
(0.02%) families. The most common host genera were
Escherichia
(88.20%),
Salmonella
(5.49%) and
Staphylococcus
(5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent
Podoviridae
. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.</description><identifier>ISSN: 0302-8933</identifier><identifier>EISSN: 1432-072X</identifier><identifier>DOI: 10.1007/s00203-022-02962-2</identifier><identifier>PMID: 35637399</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Antibiotic resistance ; Antibiotics ; Bacteriophages - genetics ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Carbohydrate metabolism ; Carbohydrates ; Cell Biology ; Centrifugation ; Chloroform ; Deoxyribonucleic acid ; DNA ; Ecology ; Ecosystem ; Genera ; Genes ; Genetic testing ; Hospitals ; Humans ; Life Sciences ; Metagenomics ; Microbial Ecology ; Microbiology ; Microorganisms ; Nucleotides ; Original Paper ; Orthology ; Phages ; Phenols ; Podoviridae ; Podoviridae - genetics ; Sewage ; Subsystems ; Turkey ; Virome ; Waste Water ; Wastewater ; Wastewater analysis</subject><ispartof>Archives of microbiology, 2022-06, Vol.204 (6), p.353-353, Article 353</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022</rights><rights>2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.</rights><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-11dfbba3bd9c5f52cd4089e4871c19878fff56fdc136a3864c23e8ea0145ca643</citedby><cites>FETCH-LOGICAL-c375t-11dfbba3bd9c5f52cd4089e4871c19878fff56fdc136a3864c23e8ea0145ca643</cites><orcidid>0000-0003-2141-0669 ; 0000-0002-6336-4018 ; 0000-0003-1242-7434 ; 0000-0003-0511-0869 ; 0000-0003-2469-9728 ; 0000-0001-8151-6321 ; 0000-0003-4911-9494</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/35637399$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Salih, Hanife</creatorcontrib><creatorcontrib>Karaynir, Abdulkerim</creatorcontrib><creatorcontrib>Yalcin, Melis</creatorcontrib><creatorcontrib>Oryasin, Erman</creatorcontrib><creatorcontrib>Holyavkin, Can</creatorcontrib><creatorcontrib>Basbulbul, Gamze</creatorcontrib><creatorcontrib>Bozdogan, Bulent</creatorcontrib><title>Metagenomic analysis of wastewater phageome from a University Hospital in Turkey</title><title>Archives of microbiology</title><addtitle>Arch Microbiol</addtitle><addtitle>Arch Microbiol</addtitle><description>Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to
Caudovirales
order and
Myoviridae
(56%),
Siphoviridae
(43%), and
Podoviridae
(0.02%) families. The most common host genera were
Escherichia
(88.20%),
Salmonella
(5.49%) and
Staphylococcus
(5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent
Podoviridae
. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.</description><subject>Antibiotic resistance</subject><subject>Antibiotics</subject><subject>Bacteriophages - genetics</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Carbohydrate metabolism</subject><subject>Carbohydrates</subject><subject>Cell Biology</subject><subject>Centrifugation</subject><subject>Chloroform</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecology</subject><subject>Ecosystem</subject><subject>Genera</subject><subject>Genes</subject><subject>Genetic testing</subject><subject>Hospitals</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Metagenomics</subject><subject>Microbial Ecology</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Nucleotides</subject><subject>Original Paper</subject><subject>Orthology</subject><subject>Phages</subject><subject>Phenols</subject><subject>Podoviridae</subject><subject>Podoviridae - genetics</subject><subject>Sewage</subject><subject>Subsystems</subject><subject>Turkey</subject><subject>Virome</subject><subject>Waste Water</subject><subject>Wastewater</subject><subject>Wastewater analysis</subject><issn>0302-8933</issn><issn>1432-072X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNp9kMFO3DAURa2qVRmgP9AFstQNm4Dtl9jOEiEKSCC6GCR2lsd5noYm8dROOpq_x8wAlViwsCzL596ndwj5ztkJZ0ydJsYEg4IJkU8tRSE-kRkvIT-VePhMZgyYKHQNsEf2U3pkjAut9VeyB5UEBXU9I79ucbRLHELfOmoH221Sm2jwdG3TiGs7YqSr35kIPVIfQ08tvR_afxhTO27oVUirdrQdbQc6n-If3BySL952Cb-93Afk_ufF_PyquLm7vD4_uykcqGosOG_8YmFh0dSu8pVwTcl0jaVW3PFaK-29r6RvHAdpQcvSCUCNlvGyclaWcECOd72rGP5OmEbTt8lh19kBw5SMkEqAUErIjP54hz6GKeZdt1QuBMlVpsSOcjGkFNGbVWx7GzeGM_Ps2-x8m-zbbH0bkUNHL9XTosfmLfIqOAOwA1L-GpYY_8_-oPYJREmLCw</recordid><startdate>20220601</startdate><enddate>20220601</enddate><creator>Salih, Hanife</creator><creator>Karaynir, Abdulkerim</creator><creator>Yalcin, Melis</creator><creator>Oryasin, Erman</creator><creator>Holyavkin, Can</creator><creator>Basbulbul, Gamze</creator><creator>Bozdogan, Bulent</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><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>3V.</scope><scope>7QL</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-2141-0669</orcidid><orcidid>https://orcid.org/0000-0002-6336-4018</orcidid><orcidid>https://orcid.org/0000-0003-1242-7434</orcidid><orcidid>https://orcid.org/0000-0003-0511-0869</orcidid><orcidid>https://orcid.org/0000-0003-2469-9728</orcidid><orcidid>https://orcid.org/0000-0001-8151-6321</orcidid><orcidid>https://orcid.org/0000-0003-4911-9494</orcidid></search><sort><creationdate>20220601</creationdate><title>Metagenomic analysis of wastewater phageome from a University Hospital in Turkey</title><author>Salih, Hanife ; Karaynir, Abdulkerim ; Yalcin, Melis ; Oryasin, Erman ; Holyavkin, Can ; Basbulbul, Gamze ; Bozdogan, Bulent</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-11dfbba3bd9c5f52cd4089e4871c19878fff56fdc136a3864c23e8ea0145ca643</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Antibiotic resistance</topic><topic>Antibiotics</topic><topic>Bacteriophages - 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Academic</collection><jtitle>Archives of microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Salih, Hanife</au><au>Karaynir, Abdulkerim</au><au>Yalcin, Melis</au><au>Oryasin, Erman</au><au>Holyavkin, Can</au><au>Basbulbul, Gamze</au><au>Bozdogan, Bulent</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Metagenomic analysis of wastewater phageome from a University Hospital in Turkey</atitle><jtitle>Archives of microbiology</jtitle><stitle>Arch Microbiol</stitle><addtitle>Arch Microbiol</addtitle><date>2022-06-01</date><risdate>2022</risdate><volume>204</volume><issue>6</issue><spage>353</spage><epage>353</epage><pages>353-353</pages><artnum>353</artnum><issn>0302-8933</issn><eissn>1432-072X</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to
Caudovirales
order and
Myoviridae
(56%),
Siphoviridae
(43%), and
Podoviridae
(0.02%) families. The most common host genera were
Escherichia
(88.20%),
Salmonella
(5.49%) and
Staphylococcus
(5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent
Podoviridae
. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>35637399</pmid><doi>10.1007/s00203-022-02962-2</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-2141-0669</orcidid><orcidid>https://orcid.org/0000-0002-6336-4018</orcidid><orcidid>https://orcid.org/0000-0003-1242-7434</orcidid><orcidid>https://orcid.org/0000-0003-0511-0869</orcidid><orcidid>https://orcid.org/0000-0003-2469-9728</orcidid><orcidid>https://orcid.org/0000-0001-8151-6321</orcidid><orcidid>https://orcid.org/0000-0003-4911-9494</orcidid></addata></record> |
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| issn | 0302-8933 1432-072X |
| language | eng |
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| source | Springer Link |
| subjects | Antibiotic resistance Antibiotics Bacteriophages - genetics Biochemistry Biomedical and Life Sciences Biotechnology Carbohydrate metabolism Carbohydrates Cell Biology Centrifugation Chloroform Deoxyribonucleic acid DNA Ecology Ecosystem Genera Genes Genetic testing Hospitals Humans Life Sciences Metagenomics Microbial Ecology Microbiology Microorganisms Nucleotides Original Paper Orthology Phages Phenols Podoviridae Podoviridae - genetics Sewage Subsystems Turkey Virome Waste Water Wastewater Wastewater analysis |
| title | Metagenomic analysis of wastewater phageome from a University Hospital in Turkey |
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