Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes
Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E....
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| Veröffentlicht in: | Applied and environmental microbiology 2000, Vol.66 (1), p.375-382 |
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| description | Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces. |
| doi_str_mv | 10.1128/AEM.66.1.375-382.2000 |
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Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.</description><identifier>ISSN: 0099-2240</identifier><identifier>EISSN: 1098-5336</identifier><identifier>DOI: 10.1128/AEM.66.1.375-382.2000</identifier><identifier>PMID: 10618251</identifier><identifier>CODEN: AEMIDF</identifier><language>eng</language><publisher>Washington, DC: American Society for Microbiology</publisher><subject>Bacteria ; Bacteriological methods and techniques used in bacteriology ; Bacteriology ; Biological and medical sciences ; Colony Count, Microbial ; Eubacterium ; Eubacterium - classification ; Eubacterium - genetics ; Eubacterium - growth & development ; Eubacterium - isolation & purification ; Feces ; Feces - microbiology ; Fundamental and applied biological sciences. Psychology ; Humans ; In Situ Hybridization ; Methods ; Microbiology ; Oligonucleotide Probes ; Polymerase Chain Reaction - methods ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Species Specificity</subject><ispartof>Applied and environmental microbiology, 2000, Vol.66 (1), p.375-382</ispartof><rights>2000 INIST-CNRS</rights><rights>Copyright American Society for Microbiology Jan 2000</rights><rights>Copyright © 2000, American Society for Microbiology 2000</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c492t-930521df8b3aa092ba2685749250607fd50d3607428ced967157e4d6ded138383</citedby><cites>FETCH-LOGICAL-c492t-930521df8b3aa092ba2685749250607fd50d3607428ced967157e4d6ded138383</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/PMC91833/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC91833/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,3188,4024,27923,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1269917$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10618251$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>SCHWIERTZ, A</creatorcontrib><creatorcontrib>LE BLAY, G</creatorcontrib><creatorcontrib>BLAUT, M</creatorcontrib><title>Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes</title><title>Applied and environmental microbiology</title><addtitle>Appl Environ Microbiol</addtitle><description>Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.</description><subject>Bacteria</subject><subject>Bacteriological methods and techniques used in bacteriology</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Colony Count, Microbial</subject><subject>Eubacterium</subject><subject>Eubacterium - classification</subject><subject>Eubacterium - genetics</subject><subject>Eubacterium - growth & development</subject><subject>Eubacterium - isolation & purification</subject><subject>Feces</subject><subject>Feces - microbiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Humans</subject><subject>In Situ Hybridization</subject><subject>Methods</subject><subject>Microbiology</subject><subject>Oligonucleotide Probes</subject><subject>Polymerase Chain Reaction - methods</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Species Specificity</subject><issn>0099-2240</issn><issn>1098-5336</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2000</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFksuKFDEUhgtRnJ7RR1CCyOyqzKWSSsBNM7QXGBVv65BOTnVnqKqUSUpx65Obthsd3UgWJ3C-_3Auf1U9IrghhMpn682bRoiGNKzjNZO0oRjjO9WKYCVrzpi4W60wVqqmtMVn1XlKNwVosZD3qzOCBZGUk1X14_1ipux7b032YUKhR873PUSYMtosW2MzRL-MKM1zg_yE9stoJtSDNQNKZpwHSOibz_sCgPWQ6l-x1ENEfETxw9t1nU3cQQaHwuB3YVrsACF7B2iOYQvpQXWvN0OCh6d4UX1-sfl09aq-fvfy9dX6uratorlWDHNKXC-3zBis6NZQIXlXchwL3PWOY8fKp6XSglOiI7yD1gkHjjBZ3kX1_Fh3XrYjOFsmjGbQc_Sjid91MF7_nZn8Xu_CV62IZKzIL0_yGL4skLIefbIwDGaCsCTdYUkYJvS_IOnaDhNBCvjkH_AmLHEqO9AUc9VyLg9d8yNkY0gpQv-7YYL1wQm6OEELoYkuTtDFCfrghKJ7fHvaW6rj6Qvw9ASYVI7ZRzNZn_5wVChFOvYTRY29Sg</recordid><startdate>2000</startdate><enddate>2000</enddate><creator>SCHWIERTZ, A</creator><creator>LE BLAY, G</creator><creator>BLAUT, M</creator><general>American Society for Microbiology</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>7QL</scope><scope>7QO</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>2000</creationdate><title>Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes</title><author>SCHWIERTZ, A ; LE BLAY, G ; BLAUT, M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c492t-930521df8b3aa092ba2685749250607fd50d3607428ced967157e4d6ded138383</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2000</creationdate><topic>Bacteria</topic><topic>Bacteriological methods and techniques used in bacteriology</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Colony Count, Microbial</topic><topic>Eubacterium</topic><topic>Eubacterium - classification</topic><topic>Eubacterium - genetics</topic><topic>Eubacterium - growth & development</topic><topic>Eubacterium - isolation & purification</topic><topic>Feces</topic><topic>Feces - microbiology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Humans</topic><topic>In Situ Hybridization</topic><topic>Methods</topic><topic>Microbiology</topic><topic>Oligonucleotide Probes</topic><topic>Polymerase Chain Reaction - methods</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>SCHWIERTZ, A</creatorcontrib><creatorcontrib>LE BLAY, G</creatorcontrib><creatorcontrib>BLAUT, M</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>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Applied and environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>SCHWIERTZ, A</au><au>LE BLAY, G</au><au>BLAUT, M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes</atitle><jtitle>Applied and environmental microbiology</jtitle><addtitle>Appl Environ Microbiol</addtitle><date>2000</date><risdate>2000</risdate><volume>66</volume><issue>1</issue><spage>375</spage><epage>382</epage><pages>375-382</pages><issn>0099-2240</issn><eissn>1098-5336</eissn><coden>AEMIDF</coden><abstract>Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.</abstract><cop>Washington, DC</cop><pub>American Society for Microbiology</pub><pmid>10618251</pmid><doi>10.1128/AEM.66.1.375-382.2000</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Bacteria Bacteriological methods and techniques used in bacteriology Bacteriology Biological and medical sciences Colony Count, Microbial Eubacterium Eubacterium - classification Eubacterium - genetics Eubacterium - growth & development Eubacterium - isolation & purification Feces Feces - microbiology Fundamental and applied biological sciences. Psychology Humans In Situ Hybridization Methods Microbiology Oligonucleotide Probes Polymerase Chain Reaction - methods RNA, Ribosomal, 16S - genetics rRNA 16S Species Specificity |
| title | Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes |
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