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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
Main Authors: Wang, R.F, Beggs, M.L, Robertson, L.H, Cerniglia, C.E
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Language:English
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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 &amp; 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&amp;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. 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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>
fulltext fulltext
identifier ISSN: 0378-1097
ispartof FEMS microbiology letters, 2002-08, Vol.213 (2), p.175-182
issn 0378-1097
1574-6968
language eng
recordid cdi_proquest_miscellaneous_71979891
source Oxford Journals Online
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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