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Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples
An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific f...
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Published in: | FEMS microbiology letters 2002-08, Vol.213 (2), p.175-182 |
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description | An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides. Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides fragilis, Bacteroides distasonis, Clostridium clostridiiforme, Clostridium leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus albus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium infantis, Eubacterium biforme, Eubacterium aerofaciens, Lactobacillus acidophilus, Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples. |
doi_str_mv | 10.1111/j.1574-6968.2002.tb11302.x |
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The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides. Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides fragilis, Bacteroides distasonis, Clostridium clostridiiforme, Clostridium leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus albus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium infantis, Eubacterium biforme, Eubacterium aerofaciens, Lactobacillus acidophilus, Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2002.tb11302.x</identifier><identifier>PMID: 12167534</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>16S rDNAs amplification ; Adult ; Amplification ; Bacteria ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacterial diseases ; Bacterial diseases of the digestive system and abdomen ; Bacteriological methods and techniques used in bacteriology ; Bacteriology ; Bacteroides ; Bacteroides distasonis ; Bacteroides fragilis ; Bacteroides thetaiotaomicron ; Bacteroides vulgatus ; Bifidobacterium adolescentis ; Bifidobacterium longum subsp. infantis ; Biological and medical sciences ; Clostridium ; Clostridium clostridioforme ; Clostridium leptum ; Collinsella aerofaciens ; Diarrhea - microbiology ; DNA microarrays ; DNA Probes ; DNA, Bacterial - analysis ; E coli ; Enterococcus faecium ; Escherichia coli ; Eubacterium (genus) ; Eubacterium biforme ; Feces ; Feces - microbiology ; Fundamental and applied biological sciences. Psychology ; Fusobacterium ; Human bacterial diseases ; Human intestinal bacterium ; Humans ; Hybridization ; Infectious diseases ; intestinal microorganisms ; Intestine ; Intestines - microbiology ; Lactobacillus acidophilus ; Medical sciences ; Microbiology ; nucleic acid hybridization ; nucleotide sequences ; Oligonucleotide Array Sequence Analysis - methods ; oligonucleotide probes ; Oligonucleotides ; Oligonucleotide‐microarray ; Pathogenicity, virulence, toxins, bacteriocins, pyrogens, host-bacteria relations, miscellaneous strains ; Polymerase Chain Reaction ; Probes ; ribosomal DNA ; RNA, Ribosomal, 16S - analysis ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Ruminococcus albus ; Ruminococcus bromii ; Ruminococcus callidus ; Ruminococcus obeum ; Ruminococcus productus ; Sensitivity and Specificity ; Species ; Yogurt</subject><ispartof>FEMS microbiology letters, 2002-08, Vol.213 (2), p.175-182</ispartof><rights>2002 Federation of European Microbiological Societies 2002</rights><rights>2002 Federation of European Microbiological Societies</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5135-1ccc5cdbe1147e90db24533be0b2e0b0218db52eab27937a69b62af001fcd8fa3</citedby><cites>FETCH-LOGICAL-c5135-1ccc5cdbe1147e90db24533be0b2e0b0218db52eab27937a69b62af001fcd8fa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=14510986$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12167534$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, R.F</creatorcontrib><creatorcontrib>Beggs, M.L</creatorcontrib><creatorcontrib>Robertson, L.H</creatorcontrib><creatorcontrib>Cerniglia, C.E</creatorcontrib><title>Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides. Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides fragilis, Bacteroides distasonis, Clostridium clostridiiforme, Clostridium leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus albus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium infantis, Eubacterium biforme, Eubacterium aerofaciens, Lactobacillus acidophilus, Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples.</description><subject>16S rDNAs amplification</subject><subject>Adult</subject><subject>Amplification</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacterial diseases</subject><subject>Bacterial diseases of the digestive system and abdomen</subject><subject>Bacteriological methods and techniques used in bacteriology</subject><subject>Bacteriology</subject><subject>Bacteroides</subject><subject>Bacteroides distasonis</subject><subject>Bacteroides fragilis</subject><subject>Bacteroides thetaiotaomicron</subject><subject>Bacteroides vulgatus</subject><subject>Bifidobacterium adolescentis</subject><subject>Bifidobacterium longum subsp. infantis</subject><subject>Biological and medical sciences</subject><subject>Clostridium</subject><subject>Clostridium clostridioforme</subject><subject>Clostridium leptum</subject><subject>Collinsella aerofaciens</subject><subject>Diarrhea - microbiology</subject><subject>DNA microarrays</subject><subject>DNA Probes</subject><subject>DNA, Bacterial - analysis</subject><subject>E coli</subject><subject>Enterococcus faecium</subject><subject>Escherichia coli</subject><subject>Eubacterium (genus)</subject><subject>Eubacterium biforme</subject><subject>Feces</subject><subject>Feces - microbiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Fusobacterium</subject><subject>Human bacterial diseases</subject><subject>Human intestinal bacterium</subject><subject>Humans</subject><subject>Hybridization</subject><subject>Infectious diseases</subject><subject>intestinal microorganisms</subject><subject>Intestine</subject><subject>Intestines - microbiology</subject><subject>Lactobacillus acidophilus</subject><subject>Medical sciences</subject><subject>Microbiology</subject><subject>nucleic acid hybridization</subject><subject>nucleotide sequences</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>oligonucleotide probes</subject><subject>Oligonucleotides</subject><subject>Oligonucleotide‐microarray</subject><subject>Pathogenicity, virulence, toxins, bacteriocins, pyrogens, host-bacteria relations, miscellaneous strains</subject><subject>Polymerase Chain Reaction</subject><subject>Probes</subject><subject>ribosomal DNA</subject><subject>RNA, Ribosomal, 16S - analysis</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Ruminococcus albus</subject><subject>Ruminococcus bromii</subject><subject>Ruminococcus callidus</subject><subject>Ruminococcus obeum</subject><subject>Ruminococcus productus</subject><subject>Sensitivity and Specificity</subject><subject>Species</subject><subject>Yogurt</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><recordid>eNqVklGL1DAQx4so3nr6FTQo-tY1k7RJ64Mgp6fCig96z2GaTneztM2atHrrpzfLrh6IIgZCYPL7T2bmnyx7DHwJaT3fLqHURa5qVS0F52I5NQAynde3ssWvq9vZgktd5cBrfZbdi3HLOS8EV3ezMxCgdCmLRfb9NUW3HhmOLaOv2M84OT8y3zHfu7UfZ9uTn1xL-eBs8BgC7tlA08a3rPOBTRtiLU1kf8o284Ajc-NEcXIj9qxBO1FwmGKsI5siEYddT_F-dqfDPtKD03meXV2--XzxLl99fPv-4tUqtyXIMgdrbWnbhgAKTTVvG1GUUjbEG5E2F1C1TSkIG6FrqVHVjRLYcQ6dbasO5Xn27Jh3F_yXOZVlBhct9T2O5OdoNNS6rmr4JwhVURVClAl88hu49XNIzUYjJHCltJJVol4cqTS3GAN1ZhfcgGFvgJuDkWZrDm6Zg1vmYKQ5GWmuk_jh6Ym5Gai9kZ6cS8DTE4AxDbULOFoXb7iiTMZXKnEvj9w319P-P0owlx9WoA_NlscEft79RZ7_uYNHR12H3uA6pOKuPgkOKn3DWitdyR_5_9VG</recordid><startdate>20020806</startdate><enddate>20020806</enddate><creator>Wang, R.F</creator><creator>Beggs, M.L</creator><creator>Robertson, L.H</creator><creator>Cerniglia, C.E</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><scope>FBQ</scope><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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</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>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>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20020806</creationdate><title>Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples</title><author>Wang, R.F ; Beggs, M.L ; Robertson, L.H ; Cerniglia, C.E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5135-1ccc5cdbe1147e90db24533be0b2e0b0218db52eab27937a69b62af001fcd8fa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>16S rDNAs amplification</topic><topic>Adult</topic><topic>Amplification</topic><topic>Bacteria</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacterial diseases</topic><topic>Bacterial diseases of the digestive system and abdomen</topic><topic>Bacteriological methods and techniques used in bacteriology</topic><topic>Bacteriology</topic><topic>Bacteroides</topic><topic>Bacteroides distasonis</topic><topic>Bacteroides fragilis</topic><topic>Bacteroides thetaiotaomicron</topic><topic>Bacteroides vulgatus</topic><topic>Bifidobacterium adolescentis</topic><topic>Bifidobacterium longum subsp. infantis</topic><topic>Biological and medical sciences</topic><topic>Clostridium</topic><topic>Clostridium clostridioforme</topic><topic>Clostridium leptum</topic><topic>Collinsella aerofaciens</topic><topic>Diarrhea - microbiology</topic><topic>DNA microarrays</topic><topic>DNA Probes</topic><topic>DNA, Bacterial - analysis</topic><topic>E coli</topic><topic>Enterococcus faecium</topic><topic>Escherichia coli</topic><topic>Eubacterium (genus)</topic><topic>Eubacterium biforme</topic><topic>Feces</topic><topic>Feces - microbiology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Fusobacterium</topic><topic>Human bacterial diseases</topic><topic>Human intestinal bacterium</topic><topic>Humans</topic><topic>Hybridization</topic><topic>Infectious diseases</topic><topic>intestinal microorganisms</topic><topic>Intestine</topic><topic>Intestines - microbiology</topic><topic>Lactobacillus acidophilus</topic><topic>Medical sciences</topic><topic>Microbiology</topic><topic>nucleic acid hybridization</topic><topic>nucleotide sequences</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>oligonucleotide probes</topic><topic>Oligonucleotides</topic><topic>Oligonucleotide‐microarray</topic><topic>Pathogenicity, virulence, toxins, bacteriocins, pyrogens, host-bacteria relations, miscellaneous strains</topic><topic>Polymerase Chain Reaction</topic><topic>Probes</topic><topic>ribosomal DNA</topic><topic>RNA, Ribosomal, 16S - analysis</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Ruminococcus albus</topic><topic>Ruminococcus bromii</topic><topic>Ruminococcus callidus</topic><topic>Ruminococcus obeum</topic><topic>Ruminococcus productus</topic><topic>Sensitivity and Specificity</topic><topic>Species</topic><topic>Yogurt</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, R.F</creatorcontrib><creatorcontrib>Beggs, M.L</creatorcontrib><creatorcontrib>Robertson, L.H</creatorcontrib><creatorcontrib>Cerniglia, C.E</creatorcontrib><collection>AGRIS</collection><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>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Complete (ProQuest Database)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>ProQuest Biological Science Journals</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, R.F</au><au>Beggs, M.L</au><au>Robertson, L.H</au><au>Cerniglia, C.E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2002-08-06</date><risdate>2002</risdate><volume>213</volume><issue>2</issue><spage>175</spage><epage>182</epage><pages>175-182</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides. Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides fragilis, Bacteroides distasonis, Clostridium clostridiiforme, Clostridium leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus albus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium infantis, Eubacterium biforme, Eubacterium aerofaciens, Lactobacillus acidophilus, Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>12167534</pmid><doi>10.1111/j.1574-6968.2002.tb11302.x</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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subjects | 16S rDNAs amplification Adult Amplification Bacteria Bacteria - genetics Bacteria - isolation & purification Bacterial diseases Bacterial diseases of the digestive system and abdomen Bacteriological methods and techniques used in bacteriology Bacteriology Bacteroides Bacteroides distasonis Bacteroides fragilis Bacteroides thetaiotaomicron Bacteroides vulgatus Bifidobacterium adolescentis Bifidobacterium longum subsp. infantis Biological and medical sciences Clostridium Clostridium clostridioforme Clostridium leptum Collinsella aerofaciens Diarrhea - microbiology DNA microarrays DNA Probes DNA, Bacterial - analysis E coli Enterococcus faecium Escherichia coli Eubacterium (genus) Eubacterium biforme Feces Feces - microbiology Fundamental and applied biological sciences. Psychology Fusobacterium Human bacterial diseases Human intestinal bacterium Humans Hybridization Infectious diseases intestinal microorganisms Intestine Intestines - microbiology Lactobacillus acidophilus Medical sciences Microbiology nucleic acid hybridization nucleotide sequences Oligonucleotide Array Sequence Analysis - methods oligonucleotide probes Oligonucleotides Oligonucleotide‐microarray Pathogenicity, virulence, toxins, bacteriocins, pyrogens, host-bacteria relations, miscellaneous strains Polymerase Chain Reaction Probes ribosomal DNA RNA, Ribosomal, 16S - analysis RNA, Ribosomal, 16S - genetics rRNA 16S Ruminococcus albus Ruminococcus bromii Ruminococcus callidus Ruminococcus obeum Ruminococcus productus Sensitivity and Specificity Species Yogurt |
title | Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples |
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