Optimized DNA extraction and metagenomic sequencing of airborne microbial communities
This protocol enables collection of airborne particulate matter; and after sample pretreatment, it allows sufficient quantities of microbial DNA to be extracted and prepared for downstream applications such as metagenomic sequencing. Metagenomic sequencing has been widely used for the study of micro...
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| Veröffentlicht in: | Nature protocols 2015-05, Vol.10 (5), p.768-779 |
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| creator | Jiang, Wenjun Liang, Peng Wang, Buying Fang, Jianhuo Lang, Jidong Tian, Geng Jiang, Jingkun Zhu, Ting F |
| description | This protocol enables collection of airborne particulate matter; and after sample pretreatment, it allows sufficient quantities of microbial DNA to be extracted and prepared for downstream applications such as metagenomic sequencing.
Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2–3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content. |
| doi_str_mv | 10.1038/nprot.2015.046 |
| format | Article |
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Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2–3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.</description><identifier>ISSN: 1754-2189</identifier><identifier>EISSN: 1750-2799</identifier><identifier>DOI: 10.1038/nprot.2015.046</identifier><identifier>PMID: 25906115</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/1647/2234 ; 631/1647/514/1948 ; 631/326/2565/2142 ; 631/61/252/171/1281 ; Air Microbiology ; Airborne particulates ; Analytical Chemistry ; Biochemistry - instrumentation ; Biochemistry - methods ; Biological Techniques ; China ; Computational Biology/Bioinformatics ; Deoxyribonucleic acid ; DNA ; DNA - isolation & purification ; DNA sequencing ; Environmental Monitoring - instrumentation ; Environmental Monitoring - methods ; Equipment Design ; Fresh water ; Gene sequencing ; Genetic aspects ; Genomics ; Life Sciences ; Metagenome ; Metagenomics ; Methods ; Microarrays ; Microbial activity ; Microbial colonies ; Microbial Consortia - genetics ; Microbiomes ; Microorganisms ; Molecular biology ; Nucleotide sequencing ; Organic Chemistry ; Particulate emissions ; Particulate Matter ; protocol ; Quality Control ; Sequence Analysis, DNA ; Soil water ; Workflow</subject><ispartof>Nature protocols, 2015-05, Vol.10 (5), p.768-779</ispartof><rights>Springer Nature Limited 2015</rights><rights>COPYRIGHT 2015 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group May 2015</rights><rights>Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c689t-b0f19ef811257461ec8f32a378c0363f3c89ea6a8d2105631f8821dc186f39bb3</citedby><cites>FETCH-LOGICAL-c689t-b0f19ef811257461ec8f32a378c0363f3c89ea6a8d2105631f8821dc186f39bb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nprot.2015.046$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nprot.2015.046$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25906115$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jiang, Wenjun</creatorcontrib><creatorcontrib>Liang, Peng</creatorcontrib><creatorcontrib>Wang, Buying</creatorcontrib><creatorcontrib>Fang, Jianhuo</creatorcontrib><creatorcontrib>Lang, Jidong</creatorcontrib><creatorcontrib>Tian, Geng</creatorcontrib><creatorcontrib>Jiang, Jingkun</creatorcontrib><creatorcontrib>Zhu, Ting F</creatorcontrib><title>Optimized DNA extraction and metagenomic sequencing of airborne microbial communities</title><title>Nature protocols</title><addtitle>Nat Protoc</addtitle><addtitle>Nat Protoc</addtitle><description>This protocol enables collection of airborne particulate matter; and after sample pretreatment, it allows sufficient quantities of microbial DNA to be extracted and prepared for downstream applications such as metagenomic sequencing.
Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2–3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.</description><subject>631/1647/2234</subject><subject>631/1647/514/1948</subject><subject>631/326/2565/2142</subject><subject>631/61/252/171/1281</subject><subject>Air Microbiology</subject><subject>Airborne particulates</subject><subject>Analytical Chemistry</subject><subject>Biochemistry - instrumentation</subject><subject>Biochemistry - methods</subject><subject>Biological Techniques</subject><subject>China</subject><subject>Computational Biology/Bioinformatics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - isolation & purification</subject><subject>DNA sequencing</subject><subject>Environmental Monitoring - instrumentation</subject><subject>Environmental Monitoring - methods</subject><subject>Equipment Design</subject><subject>Fresh water</subject><subject>Gene sequencing</subject><subject>Genetic aspects</subject><subject>Genomics</subject><subject>Life Sciences</subject><subject>Metagenome</subject><subject>Metagenomics</subject><subject>Methods</subject><subject>Microarrays</subject><subject>Microbial activity</subject><subject>Microbial colonies</subject><subject>Microbial Consortia - genetics</subject><subject>Microbiomes</subject><subject>Microorganisms</subject><subject>Molecular biology</subject><subject>Nucleotide sequencing</subject><subject>Organic Chemistry</subject><subject>Particulate emissions</subject><subject>Particulate Matter</subject><subject>protocol</subject><subject>Quality Control</subject><subject>Sequence Analysis, DNA</subject><subject>Soil water</subject><subject>Workflow</subject><issn>1754-2189</issn><issn>1750-2799</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9ktuL1DAUxou4uOvqq49S8EWRmc1J2iR9EYbxtrDsgu7iY0jT05qlTcakFfWvN92bOzJKCw09v_PlXL4sewZkCYTJI7cJflxSAuWSFPxBdgCiJAsqqurh1blYUJDVfvY4xktCCsG4eJTt07IiHKA8yC7ONqMd7C9s8renqxx_jEGb0XqXa9fkA466Q-cHa_KI3yZ0xrou922ubah9cJinUPC11X1u_DBMzo4W45Nsr9V9xKc338Ps4v278_XHxcnZh-P16mRhuKzGRU1aqLCVALQUBQc0smVUMyENYZy1zMgKNdeyoUBKzqCVkkJjQPKWVXXNDrM317qbqR6wMehS-b3aBDvo8FN5bdV2xNmvqvPflSCSl4IngZc3AsGn9uKoBhsN9r126KeogItSCkqpSOiLv9BLPwWX2lMMivQWUJT_o2YtQiou4A_V6R6Vda2fxz5frVYFpIVRTubiljuo9DSYpu4dtjb930p4tZWQmDFttNNTjOr486dt9vW_2dX5l_XpzlLSsmMM2N7NGIiajaiujKhmI6pkxJTw_P5m7vBb5yXg6BqIKeQ6DPcGtVvyN5lr5mo</recordid><startdate>20150501</startdate><enddate>20150501</enddate><creator>Jiang, Wenjun</creator><creator>Liang, Peng</creator><creator>Wang, Buying</creator><creator>Fang, Jianhuo</creator><creator>Lang, Jidong</creator><creator>Tian, Geng</creator><creator>Jiang, Jingkun</creator><creator>Zhu, Ting F</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</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>ATWCN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7T5</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</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>ATCPS</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>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>RC3</scope><scope>AEUYN</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150501</creationdate><title>Optimized DNA extraction and metagenomic sequencing of airborne microbial communities</title><author>Jiang, Wenjun ; Liang, Peng ; Wang, Buying ; Fang, Jianhuo ; Lang, Jidong ; Tian, Geng ; Jiang, Jingkun ; Zhu, Ting F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c689t-b0f19ef811257461ec8f32a378c0363f3c89ea6a8d2105631f8821dc186f39bb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/1647/2234</topic><topic>631/1647/514/1948</topic><topic>631/326/2565/2142</topic><topic>631/61/252/171/1281</topic><topic>Air Microbiology</topic><topic>Airborne particulates</topic><topic>Analytical Chemistry</topic><topic>Biochemistry - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature protocols</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jiang, Wenjun</au><au>Liang, Peng</au><au>Wang, Buying</au><au>Fang, Jianhuo</au><au>Lang, Jidong</au><au>Tian, Geng</au><au>Jiang, Jingkun</au><au>Zhu, Ting F</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Optimized DNA extraction and metagenomic sequencing of airborne microbial communities</atitle><jtitle>Nature protocols</jtitle><stitle>Nat Protoc</stitle><addtitle>Nat Protoc</addtitle><date>2015-05-01</date><risdate>2015</risdate><volume>10</volume><issue>5</issue><spage>768</spage><epage>779</epage><pages>768-779</pages><issn>1754-2189</issn><eissn>1750-2799</eissn><abstract>This protocol enables collection of airborne particulate matter; and after sample pretreatment, it allows sufficient quantities of microbial DNA to be extracted and prepared for downstream applications such as metagenomic sequencing.
Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2–3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>25906115</pmid><doi>10.1038/nprot.2015.046</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 631/1647/2234 631/1647/514/1948 631/326/2565/2142 631/61/252/171/1281 Air Microbiology Airborne particulates Analytical Chemistry Biochemistry - instrumentation Biochemistry - methods Biological Techniques China Computational Biology/Bioinformatics Deoxyribonucleic acid DNA DNA - isolation & purification DNA sequencing Environmental Monitoring - instrumentation Environmental Monitoring - methods Equipment Design Fresh water Gene sequencing Genetic aspects Genomics Life Sciences Metagenome Metagenomics Methods Microarrays Microbial activity Microbial colonies Microbial Consortia - genetics Microbiomes Microorganisms Molecular biology Nucleotide sequencing Organic Chemistry Particulate emissions Particulate Matter protocol Quality Control Sequence Analysis, DNA Soil water Workflow |
| title | Optimized DNA extraction and metagenomic sequencing of airborne microbial communities |
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