The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
Metagenomics approaches and recent improvements in the next‐generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction pro...
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| Veröffentlicht in: | MicrobiologyOpen (Weinheim) 2017-08, Vol.6 (4), p.n/a |
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| creator | Zielińska, Sylwia Radkowski, Piotr Blendowska, Aleksandra Ludwig‐Gałęzowska, Agnieszka Łoś, Joanna M. Łoś, Marcin |
| description | Metagenomics approaches and recent improvements in the next‐generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits. The comparative analysis of microbial community composition, displayed differences in microbial community structure depending on which kit was used. Statistical analysis indicated significant differences in recovery of the genetic material for 24 out of 32 analyzed phyla, and the most pronounced differences were seen for Actinobacteria. Also, diversity indexes and reproducibility of DNA extraction with the use of a given kit, varied among the tested methods. As the extraction protocol may influence the apparent structure of a microbial population, at the beginning of each project many extraction kits should be tested in order to choose one that would yield the most representative results and present the closest view to the actual structure of microbial population.
The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used commercial kits. Differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. |
| doi_str_mv | 10.1002/mbo3.453 |
| format | Article |
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The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used commercial kits. Differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately.</description><subject>16S rDNA</subject><subject>Biota</subject><subject>commercial kits</subject><subject>Communities</subject><subject>Community composition</subject><subject>Community structure</subject><subject>Comparative analysis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>DNA - genetics</subject><subject>DNA - isolation & purification</subject><subject>DNA extraction</subject><subject>DNA structure</subject><subject>Extraction</subject><subject>Genetic diversity</subject><subject>Materials recovery</subject><subject>Metagenomics - methods</subject><subject>Metagenomics - standards</subject><subject>microbial community</subject><subject>Microbiomes</subject><subject>NGS library</subject><subject>Optimization</subject><subject>Original Research</subject><subject>Physicochemical properties</subject><subject>Population (statistical)</subject><subject>Population structure</subject><subject>Reproducibility</subject><subject>Soil analysis</subject><subject>Soil Microbiology</subject><subject>Soil microorganisms</subject><subject>Soil properties</subject><subject>soil sample</subject><subject>Soil structure</subject><subject>Soils</subject><subject>Statistical analysis</subject><subject>Statistical methods</subject><subject>Structural analysis</subject><issn>2045-8827</issn><issn>2045-8827</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><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>eNp1kU9PFjEQxhujEYIkfgLTxIuXxWl3u9teTBBRSUAueG66fbu-Je0W-0fdb0834CuY0MtMM78-nZkHodcEjggAfe_H0B51rH2G9il0rOGcDs8f5HvoMKVrqGcA2nfkJdqjnJJBANlH-WprsN4Gqw0OE8719unbMTZ_clQ62zBjb_I2bLBXC7bz5IqZK7pyoWQd_O5ZCtZhb3UMo1UO15Ivs80LTjkWnUs0WM3KLcmmV-jFpFwyh_fxAH3_fHp18rU5v_xydnJ83mgGXdsIqlquWiHEpuPjpExNuAGt-64dYeSKMNZB36m-Z5yQkethpABaATVio0h7gD7c6d6U0ZuNNnOdysmbaL2KiwzKyseV2W7lj_BLMsaogKEKvLsXiOFnMSlLb5M2zqnZhJIk4UP9v-_7FX37H3odSqwDV0rQYQABnP8TrGtKKZpp1wwBubopVzdldbOibx42vwP_eleB5g74bZ1ZnhSSFx8v21XwFlorqek</recordid><startdate>201708</startdate><enddate>201708</enddate><creator>Zielińska, Sylwia</creator><creator>Radkowski, Piotr</creator><creator>Blendowska, Aleksandra</creator><creator>Ludwig‐Gałęzowska, Agnieszka</creator><creator>Łoś, Joanna M.</creator><creator>Łoś, Marcin</creator><general>John Wiley & Sons, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>WIN</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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7X7</scope><scope>7XB</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0293-9858</orcidid></search><sort><creationdate>201708</creationdate><title>The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis</title><author>Zielińska, Sylwia ; Radkowski, Piotr ; Blendowska, Aleksandra ; Ludwig‐Gałęzowska, Agnieszka ; Łoś, Joanna M. ; Łoś, Marcin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5043-92a38a3999d48bfae99d8e0cc643b0b8a1554064a665811b8c7b200ca02e9da13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>16S rDNA</topic><topic>Biota</topic><topic>commercial kits</topic><topic>Communities</topic><topic>Community composition</topic><topic>Community structure</topic><topic>Comparative analysis</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>MicrobiologyOpen (Weinheim)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zielińska, Sylwia</au><au>Radkowski, Piotr</au><au>Blendowska, Aleksandra</au><au>Ludwig‐Gałęzowska, Agnieszka</au><au>Łoś, Joanna M.</au><au>Łoś, Marcin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis</atitle><jtitle>MicrobiologyOpen (Weinheim)</jtitle><addtitle>Microbiologyopen</addtitle><date>2017-08</date><risdate>2017</risdate><volume>6</volume><issue>4</issue><epage>n/a</epage><issn>2045-8827</issn><eissn>2045-8827</eissn><abstract>Metagenomics approaches and recent improvements in the next‐generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits. The comparative analysis of microbial community composition, displayed differences in microbial community structure depending on which kit was used. Statistical analysis indicated significant differences in recovery of the genetic material for 24 out of 32 analyzed phyla, and the most pronounced differences were seen for Actinobacteria. Also, diversity indexes and reproducibility of DNA extraction with the use of a given kit, varied among the tested methods. As the extraction protocol may influence the apparent structure of a microbial population, at the beginning of each project many extraction kits should be tested in order to choose one that would yield the most representative results and present the closest view to the actual structure of microbial population.
The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used commercial kits. Differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately.</abstract><cop>England</cop><pub>John Wiley & Sons, Inc</pub><pmid>28217901</pmid><doi>10.1002/mbo3.453</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0003-0293-9858</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 16S rDNA Biota commercial kits Communities Community composition Community structure Comparative analysis Deoxyribonucleic acid DNA DNA - chemistry DNA - genetics DNA - isolation & purification DNA extraction DNA structure Extraction Genetic diversity Materials recovery Metagenomics - methods Metagenomics - standards microbial community Microbiomes NGS library Optimization Original Research Physicochemical properties Population (statistical) Population structure Reproducibility Soil analysis Soil Microbiology Soil microorganisms Soil properties soil sample Soil structure Soils Statistical analysis Statistical methods Structural analysis |
| title | The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis |
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