Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction
There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate...
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| creator | Mirsepasi, Hengameh Persson, Søren Struve, Carsten Andersen, Lee O B Petersen, Andreas M Krogfelt, Karen A |
| description | There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE).
In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful.
QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®. |
| doi_str_mv | 10.1186/1756-0500-7-50 |
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In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful.
QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.</description><identifier>ISSN: 1756-0500</identifier><identifier>EISSN: 1756-0500</identifier><identifier>DOI: 10.1186/1756-0500-7-50</identifier><identifier>PMID: 24447346</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adsorption ; Adult ; Automation ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteriolysis ; Bands ; Biodiversity ; Denaturing Gradient Gel Electrophoresis ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial - isolation & purification ; Feces ; Feces - microbiology ; Fluorometry - instrumentation ; Fluorometry - methods ; Humans ; Inflammatory bowel disease ; Inflammatory Bowel Diseases - microbiology ; Intestines - microbiology ; Laboratories ; Methods ; Microbiota - genetics ; Microorganisms ; Microspheres ; Middle Aged ; Reagent Kits, Diagnostic ; Ribotyping ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - genetics ; Silicon Dioxide ; Spectrophotometry, Ultraviolet - instrumentation ; Spectrophotometry, Ultraviolet - methods ; Technical Note ; Young Adult</subject><ispartof>BMC research notes, 2014-01, Vol.7 (1), p.50-50</ispartof><rights>COPYRIGHT 2014 BioMed Central Ltd.</rights><rights>2014 Mirsepasi et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2014 Mirsepasi et al.; licensee BioMed Central Ltd. 2014 Mirsepasi et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b5250-d758c60bcc1e305451875922f49eaccef163b02e940518eb2de227552512b993</citedby><cites>FETCH-LOGICAL-b5250-d758c60bcc1e305451875922f49eaccef163b02e940518eb2de227552512b993</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015497/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015497/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,27907,27908,53774,53776</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24447346$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mirsepasi, Hengameh</creatorcontrib><creatorcontrib>Persson, Søren</creatorcontrib><creatorcontrib>Struve, Carsten</creatorcontrib><creatorcontrib>Andersen, Lee O B</creatorcontrib><creatorcontrib>Petersen, Andreas M</creatorcontrib><creatorcontrib>Krogfelt, Karen A</creatorcontrib><title>Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction</title><title>BMC research notes</title><addtitle>BMC Res Notes</addtitle><description>There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE).
In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful.
QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.</description><subject>Adsorption</subject><subject>Adult</subject><subject>Automation</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteriolysis</subject><subject>Bands</subject><subject>Biodiversity</subject><subject>Denaturing Gradient Gel Electrophoresis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>Feces</subject><subject>Feces - microbiology</subject><subject>Fluorometry - instrumentation</subject><subject>Fluorometry - methods</subject><subject>Humans</subject><subject>Inflammatory bowel disease</subject><subject>Inflammatory Bowel Diseases - microbiology</subject><subject>Intestines - microbiology</subject><subject>Laboratories</subject><subject>Methods</subject><subject>Microbiota - genetics</subject><subject>Microorganisms</subject><subject>Microspheres</subject><subject>Middle Aged</subject><subject>Reagent Kits, Diagnostic</subject><subject>Ribotyping</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Silicon Dioxide</subject><subject>Spectrophotometry, Ultraviolet - instrumentation</subject><subject>Spectrophotometry, Ultraviolet - methods</subject><subject>Technical Note</subject><subject>Young Adult</subject><issn>1756-0500</issn><issn>1756-0500</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</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>eNqFkk1v1DAQhiMEoh9w5YgscYFDytix44QDUlS-VmqpkCquluNMti6JvcRJxf6J_mYcWpbdUoR8sD3zzKvRvJMkzygcUVrkr6kUeQoCIJWpgAfJ_ibwcOu9lxyEcAmQ06Kgj5M9xjmXGc_3k-tTawZfW92Rxl7hEOy4JtaRFk0MBd2vOgykwRW6JhDvyLvPFcEf46DNaOO3x_HCN28I6rA-1cu7aeP7lR6wIaMnXxZVlPtFhNH7jvTWWfLNjlsFT5JHre4CPr29D5PzD-_Pjz-lJ2cfF8fVSVoLJiBtpChMDrUxFDMQXNBCipKxlpeojcGW5lkNDEsOMYU1a5AxKWItZXVZZofJ2xvZ1VT32Bh0sYFOrQbb62GtvLZqN-PshVr6K8WBCl7KKFDdCNTW_0NgNxMHoWY71GyHkkpA1Hh528Tgv08YRtXbYLDrtEM_BUUFiIzJkvH_o7xkEoCJubMXd9BLPw0uDnOmaC7i2mR_qKXuUFnX-tmBWVRVgkORccjySB3dQ8XTYG-Nd9jaGN8peLVTEJkxmrvUUwhqcfb1XvG4fyEM2G6mR0HNu_33vJ5vm7bBfy9z9hM8afIs</recordid><startdate>20140121</startdate><enddate>20140121</enddate><creator>Mirsepasi, Hengameh</creator><creator>Persson, Søren</creator><creator>Struve, Carsten</creator><creator>Andersen, Lee O B</creator><creator>Petersen, Andreas M</creator><creator>Krogfelt, Karen A</creator><general>BioMed Central Ltd</general><general>BioMed Central</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>IOV</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</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>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>7T7</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>5PM</scope></search><sort><creationdate>20140121</creationdate><title>Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction</title><author>Mirsepasi, Hengameh ; Persson, Søren ; Struve, Carsten ; Andersen, Lee O B ; Petersen, Andreas M ; Krogfelt, Karen A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b5250-d758c60bcc1e305451875922f49eaccef163b02e940518eb2de227552512b993</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adsorption</topic><topic>Adult</topic><topic>Automation</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacteriolysis</topic><topic>Bands</topic><topic>Biodiversity</topic><topic>Denaturing Gradient Gel Electrophoresis</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial - isolation & purification</topic><topic>Feces</topic><topic>Feces - microbiology</topic><topic>Fluorometry - instrumentation</topic><topic>Fluorometry - methods</topic><topic>Humans</topic><topic>Inflammatory bowel disease</topic><topic>Inflammatory Bowel Diseases - microbiology</topic><topic>Intestines - microbiology</topic><topic>Laboratories</topic><topic>Methods</topic><topic>Microbiota - genetics</topic><topic>Microorganisms</topic><topic>Microspheres</topic><topic>Middle Aged</topic><topic>Reagent Kits, Diagnostic</topic><topic>Ribotyping</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Silicon Dioxide</topic><topic>Spectrophotometry, Ultraviolet - 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Academic</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC research notes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mirsepasi, Hengameh</au><au>Persson, Søren</au><au>Struve, Carsten</au><au>Andersen, Lee O B</au><au>Petersen, Andreas M</au><au>Krogfelt, Karen A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction</atitle><jtitle>BMC research notes</jtitle><addtitle>BMC Res Notes</addtitle><date>2014-01-21</date><risdate>2014</risdate><volume>7</volume><issue>1</issue><spage>50</spage><epage>50</epage><pages>50-50</pages><issn>1756-0500</issn><eissn>1756-0500</eissn><abstract>There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE).
In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful.
QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>24447346</pmid><doi>10.1186/1756-0500-7-50</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adsorption Adult Automation Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteriolysis Bands Biodiversity Denaturing Gradient Gel Electrophoresis Deoxyribonucleic acid DNA DNA, Bacterial - isolation & purification Feces Feces - microbiology Fluorometry - instrumentation Fluorometry - methods Humans Inflammatory bowel disease Inflammatory Bowel Diseases - microbiology Intestines - microbiology Laboratories Methods Microbiota - genetics Microorganisms Microspheres Middle Aged Reagent Kits, Diagnostic Ribotyping RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics Silicon Dioxide Spectrophotometry, Ultraviolet - instrumentation Spectrophotometry, Ultraviolet - methods Technical Note Young Adult |
| title | Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction |
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