Construction of a Metagenomic Library for the Marine Sponge Halichondria okadai
Symbionts of the marine sponge Halichondria okadai are promising as a source of natural products. Metagenomic technology is a powerful tool for accessing the genetic and biochemical potential of bacteria. Hence, we established a method of recovering bacterial-enriched metagenomic DNA by stepwise cen...
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| Veröffentlicht in: | Bioscience, biotechnology, and biochemistry biotechnology, and biochemistry, 2012, Vol.76 (4), p.633-639 |
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| creator | ABE, Takahiro SAHIN, Fatma Pinar AKIYAMA, Kiyotaka NAITO, Takayuki KISHIGAMI, Mizoe MIYAMOTO, Kenji SAKAKIBARA, Yasufumi UEMURA, Daisuke |
| description | Symbionts of the marine sponge Halichondria okadai are promising as a source of natural products. Metagenomic technology is a powerful tool for accessing the genetic and biochemical potential of bacteria. Hence, we established a method of recovering bacterial-enriched metagenomic DNA by stepwise centrifugation. The metagenomic DNA was analyzed by ultrafast 454-pyrosequencing technology, and the results suggested that more than three types of bacterial DNA, Alphaproteobacteria, Actinobacteria, and Cyanobacteria, had been recovered, and that eukaryotic genes comprised only 0.02% of the metagenomic DNA. These results indicate that stepwise centrifugation and real-time quantitative PCR were effective for separating sponge cells and symbiotic bacteria, and that we constructed a bacteria-enriched metagenomic library from a marine sponge, H. okadai, selectively for the first time. |
| doi_str_mv | 10.1271/bbb.110533 |
| format | Article |
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Metagenomic technology is a powerful tool for accessing the genetic and biochemical potential of bacteria. Hence, we established a method of recovering bacterial-enriched metagenomic DNA by stepwise centrifugation. The metagenomic DNA was analyzed by ultrafast 454-pyrosequencing technology, and the results suggested that more than three types of bacterial DNA, Alphaproteobacteria, Actinobacteria, and Cyanobacteria, had been recovered, and that eukaryotic genes comprised only 0.02% of the metagenomic DNA. These results indicate that stepwise centrifugation and real-time quantitative PCR were effective for separating sponge cells and symbiotic bacteria, and that we constructed a bacteria-enriched metagenomic library from a marine sponge, H. okadai, selectively for the first time.</description><identifier>ISSN: 0916-8451</identifier><identifier>EISSN: 1347-6947</identifier><identifier>DOI: 10.1271/bbb.110533</identifier><identifier>PMID: 22484923</identifier><language>eng</language><publisher>Tokyo: Japan Society for Bioscience, Biotechnology, and Agrochemistry</publisher><subject>454-pyrosequencing ; Actinobacteria ; Actinobacteria - genetics ; Alphaproteobacteria - genetics ; Animals ; Bacteria ; Biochemistry ; Biological and medical sciences ; Centrifugation ; Cloning, Molecular ; Construction ; Cyanobacteria - genetics ; Deoxyribonucleic acid ; DNA, Bacterial - genetics ; fosmid ; Fundamental and applied biological sciences. Psychology ; Genetics ; Genomic Library ; Halichondria okadai ; High-Throughput Nucleotide Sequencing ; Libraries ; Marine ; metagenomic library ; Metagenomics ; Phylogeny ; Porifera - genetics ; Real-Time Polymerase Chain Reaction ; RNA, Ribosomal, 16S - genetics ; RNA, Ribosomal, 18S - genetics ; sponge ; Sponges ; Symbiosis - physiology</subject><ispartof>Bioscience, biotechnology, and biochemistry, 2012, Vol.76 (4), p.633-639</ispartof><rights>2012 by Japan Society for Bioscience, Biotechnology, and Agrochemistry 2012</rights><rights>2015 INIST-CNRS</rights><rights>Copyright Japan Science and Technology Agency 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c585t-ae1001c230c0e5e7a8eec72f9a44662d6d4d1ad6f8cf0984c7017b71fe4f5e323</citedby><cites>FETCH-LOGICAL-c585t-ae1001c230c0e5e7a8eec72f9a44662d6d4d1ad6f8cf0984c7017b71fe4f5e323</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,4023,27922,27923,27924</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26176393$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22484923$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>ABE, Takahiro</creatorcontrib><creatorcontrib>SAHIN, Fatma Pinar</creatorcontrib><creatorcontrib>AKIYAMA, Kiyotaka</creatorcontrib><creatorcontrib>NAITO, Takayuki</creatorcontrib><creatorcontrib>KISHIGAMI, Mizoe</creatorcontrib><creatorcontrib>MIYAMOTO, Kenji</creatorcontrib><creatorcontrib>SAKAKIBARA, Yasufumi</creatorcontrib><creatorcontrib>UEMURA, Daisuke</creatorcontrib><title>Construction of a Metagenomic Library for the Marine Sponge Halichondria okadai</title><title>Bioscience, biotechnology, and biochemistry</title><addtitle>Biosci Biotechnol Biochem</addtitle><description>Symbionts of the marine sponge Halichondria okadai are promising as a source of natural products. Metagenomic technology is a powerful tool for accessing the genetic and biochemical potential of bacteria. Hence, we established a method of recovering bacterial-enriched metagenomic DNA by stepwise centrifugation. The metagenomic DNA was analyzed by ultrafast 454-pyrosequencing technology, and the results suggested that more than three types of bacterial DNA, Alphaproteobacteria, Actinobacteria, and Cyanobacteria, had been recovered, and that eukaryotic genes comprised only 0.02% of the metagenomic DNA. 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Psychology</subject><subject>Genetics</subject><subject>Genomic Library</subject><subject>Halichondria okadai</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Libraries</subject><subject>Marine</subject><subject>metagenomic library</subject><subject>Metagenomics</subject><subject>Phylogeny</subject><subject>Porifera - genetics</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>RNA, Ribosomal, 18S - genetics</subject><subject>sponge</subject><subject>Sponges</subject><subject>Symbiosis - physiology</subject><issn>0916-8451</issn><issn>1347-6947</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqN0V1rFDEUBuAgil2rN_4ACYggwtScfM5cyqJW2NIL9Xo4k0na1JlkTWaQ_ntTdqsggl4FwnNekvMS8hzYGXADb4dhOANgSogHZANCmkZ30jwkG9aBblqp4IQ8KeWGsXqh4DE54Vy2suNiQy63KZYlr3YJKdLkKdILt-CVi2kOlu7CkDHfUp8yXa4dvcAcoqOf9yleOXqOU7DXKY45IE3fcMTwlDzyOBX37Hiekq8f3n_Znje7y4-ftu92jVWtWhp0wBhYLphlTjmDrXPWcN-hlFrzUY9yBBy1b61nXSutYWAGA95Jr5zg4pS8PuTuc_q-urL0cyjWTRNGl9bSgzagmemU_DdlQrZcSf0_tG5QMG5YpS__oDdpzbH-uQcpu1bxlkFVbw7K5lRKdr7f5zDXjdao_q68vpbXH8qr-MUxch1mN_6i921V8OoIsFicfMZoQ_ntNBgtujunDi7EWtyMP1Kexn7B2ynl-yHxlwf8BPGVsUA</recordid><startdate>2012</startdate><enddate>2012</enddate><creator>ABE, Takahiro</creator><creator>SAHIN, Fatma Pinar</creator><creator>AKIYAMA, Kiyotaka</creator><creator>NAITO, Takayuki</creator><creator>KISHIGAMI, Mizoe</creator><creator>MIYAMOTO, Kenji</creator><creator>SAKAKIBARA, Yasufumi</creator><creator>UEMURA, Daisuke</creator><general>Japan Society for Bioscience, Biotechnology, and Agrochemistry</general><general>Japan Society for Bioscience Biotechnology and Agrochemistry</general><general>Oxford University Press</general><scope>IQODW</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><scope>7QO</scope><scope>7TN</scope><scope>8FD</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>H99</scope><scope>L.F</scope><scope>L.G</scope><scope>P64</scope><scope>RC3</scope><scope>7TB</scope><scope>7U5</scope><scope>L7M</scope></search><sort><creationdate>2012</creationdate><title>Construction of a Metagenomic Library for the Marine Sponge Halichondria okadai</title><author>ABE, Takahiro ; SAHIN, Fatma Pinar ; AKIYAMA, Kiyotaka ; NAITO, Takayuki ; KISHIGAMI, Mizoe ; MIYAMOTO, Kenji ; SAKAKIBARA, Yasufumi ; UEMURA, Daisuke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c585t-ae1001c230c0e5e7a8eec72f9a44662d6d4d1ad6f8cf0984c7017b71fe4f5e323</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>454-pyrosequencing</topic><topic>Actinobacteria</topic><topic>Actinobacteria - genetics</topic><topic>Alphaproteobacteria - genetics</topic><topic>Animals</topic><topic>Bacteria</topic><topic>Biochemistry</topic><topic>Biological and medical sciences</topic><topic>Centrifugation</topic><topic>Cloning, Molecular</topic><topic>Construction</topic><topic>Cyanobacteria - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA, Bacterial - genetics</topic><topic>fosmid</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genetics</topic><topic>Genomic Library</topic><topic>Halichondria okadai</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Libraries</topic><topic>Marine</topic><topic>metagenomic library</topic><topic>Metagenomics</topic><topic>Phylogeny</topic><topic>Porifera - genetics</topic><topic>Real-Time Polymerase Chain Reaction</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>RNA, Ribosomal, 18S - genetics</topic><topic>sponge</topic><topic>Sponges</topic><topic>Symbiosis - physiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>ABE, Takahiro</creatorcontrib><creatorcontrib>SAHIN, Fatma Pinar</creatorcontrib><creatorcontrib>AKIYAMA, Kiyotaka</creatorcontrib><creatorcontrib>NAITO, Takayuki</creatorcontrib><creatorcontrib>KISHIGAMI, Mizoe</creatorcontrib><creatorcontrib>MIYAMOTO, Kenji</creatorcontrib><creatorcontrib>SAKAKIBARA, Yasufumi</creatorcontrib><creatorcontrib>UEMURA, Daisuke</creatorcontrib><collection>Pascal-Francis</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><collection>Biotechnology Research Abstracts</collection><collection>Oceanic Abstracts</collection><collection>Technology Research Database</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>ASFA: Marine Biotechnology Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Marine Biotechnology Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><jtitle>Bioscience, biotechnology, and biochemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>ABE, Takahiro</au><au>SAHIN, Fatma Pinar</au><au>AKIYAMA, Kiyotaka</au><au>NAITO, Takayuki</au><au>KISHIGAMI, Mizoe</au><au>MIYAMOTO, Kenji</au><au>SAKAKIBARA, Yasufumi</au><au>UEMURA, Daisuke</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Construction of a Metagenomic Library for the Marine Sponge Halichondria okadai</atitle><jtitle>Bioscience, biotechnology, and biochemistry</jtitle><addtitle>Biosci Biotechnol Biochem</addtitle><date>2012</date><risdate>2012</risdate><volume>76</volume><issue>4</issue><spage>633</spage><epage>639</epage><pages>633-639</pages><issn>0916-8451</issn><eissn>1347-6947</eissn><abstract>Symbionts of the marine sponge Halichondria okadai are promising as a source of natural products. Metagenomic technology is a powerful tool for accessing the genetic and biochemical potential of bacteria. Hence, we established a method of recovering bacterial-enriched metagenomic DNA by stepwise centrifugation. The metagenomic DNA was analyzed by ultrafast 454-pyrosequencing technology, and the results suggested that more than three types of bacterial DNA, Alphaproteobacteria, Actinobacteria, and Cyanobacteria, had been recovered, and that eukaryotic genes comprised only 0.02% of the metagenomic DNA. These results indicate that stepwise centrifugation and real-time quantitative PCR were effective for separating sponge cells and symbiotic bacteria, and that we constructed a bacteria-enriched metagenomic library from a marine sponge, H. okadai, selectively for the first time.</abstract><cop>Tokyo</cop><pub>Japan Society for Bioscience, Biotechnology, and Agrochemistry</pub><pmid>22484923</pmid><doi>10.1271/bbb.110533</doi><tpages>7</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0916-8451 |
| ispartof | Bioscience, biotechnology, and biochemistry, 2012, Vol.76 (4), p.633-639 |
| issn | 0916-8451 1347-6947 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1034825464 |
| source | J-STAGE Free; MEDLINE; Oxford University Press Journals All Titles (1996-Current); Freely Accessible Japanese Titles; EZB-FREE-00999 freely available EZB journals; Free Full-Text Journals in Chemistry |
| subjects | 454-pyrosequencing Actinobacteria Actinobacteria - genetics Alphaproteobacteria - genetics Animals Bacteria Biochemistry Biological and medical sciences Centrifugation Cloning, Molecular Construction Cyanobacteria - genetics Deoxyribonucleic acid DNA, Bacterial - genetics fosmid Fundamental and applied biological sciences. Psychology Genetics Genomic Library Halichondria okadai High-Throughput Nucleotide Sequencing Libraries Marine metagenomic library Metagenomics Phylogeny Porifera - genetics Real-Time Polymerase Chain Reaction RNA, Ribosomal, 16S - genetics RNA, Ribosomal, 18S - genetics sponge Sponges Symbiosis - physiology |
| title | Construction of a Metagenomic Library for the Marine Sponge Halichondria okadai |
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