Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.
Identifieur interne : 003321 ( Main/Exploration ); précédent : 003320; suivant : 003322Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.
Auteurs : Alexander Loy [Allemagne] ; Angelika Lehner ; Natuschka Lee ; Justyna Adamczyk ; Harald Meier ; Jens Ernst ; Karl-Heinz Schleifer ; Michael WagnerSource :
- Applied and environmental microbiology [ 0099-2240 ] ; 2002.
Descripteurs français
- KwdFr :
- ARN bactérien (), ARN ribosomique 16S (analyse), ARN ribosomique 16S (génétique), Analyse de séquence d'ADN, Bactéries sulfato-réductrices (), Bactéries sulfato-réductrices (génétique), Bactéries sulfato-réductrices (métabolisme), Dent (microbiologie), Hybridation d'acides nucléiques, Phylogénie, Reproductibilité des résultats, Sensibilité et spécificité, Sondes oligonucléotidiques (génétique), Sulfates (métabolisme), Séquençage par oligonucléotides en batterie ().
- MESH :
- analyse : ARN ribosomique 16S.
- génétique : ARN ribosomique 16S, Bactéries sulfato-réductrices, Sondes oligonucléotidiques.
- microbiologie : Dent.
- métabolisme : Bactéries sulfato-réductrices, Sulfates.
- ARN bactérien, Analyse de séquence d'ADN, Bactéries sulfato-réductrices, Hybridation d'acides nucléiques, Phylogénie, Reproductibilité des résultats, Sensibilité et spécificité, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis (methods), Oligonucleotide Probes (genetics), Phylogeny, RNA, Bacterial (chemistry), RNA, Ribosomal, 16S (analysis), RNA, Ribosomal, 16S (genetics), Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, DNA, Sulfates (metabolism), Sulfur-Reducing Bacteria (classification), Sulfur-Reducing Bacteria (genetics), Sulfur-Reducing Bacteria (metabolism), Tooth (microbiology).
- MESH :
- chemical , analysis : RNA, Ribosomal, 16S.
- chemical , chemistry : RNA, Bacterial.
- chemical , genetics : Oligonucleotide Probes, RNA, Ribosomal, 16S.
- chemical , metabolism : Sulfates.
- classification : Sulfur-Reducing Bacteria.
- genetics : Sulfur-Reducing Bacteria.
- metabolism : Sulfur-Reducing Bacteria.
- methods : Oligonucleotide Array Sequence Analysis.
- microbiology : Tooth.
- Nucleic Acid Hybridization, Phylogeny, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, DNA.
Abstract
For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).
DOI: 10.1128/aem.68.10.5064-5081.2002
PubMed: 12324358
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002492
- to stream PubMed, to step Curation: 002492
- to stream PubMed, to step Checkpoint: 002360
- to stream Ncbi, to step Merge: 000154
- to stream Ncbi, to step Curation: 000154
- to stream Ncbi, to step Checkpoint: 000154
- to stream Main, to step Merge: 003357
- to stream Main, to step Curation: 003321
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.</title><author><name sortKey="Loy, Alexander" sort="Loy, Alexander" uniqKey="Loy A" first="Alexander" last="Loy">Alexander Loy</name><affiliation wicri:level="4"><nlm:affiliation>Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising</wicri:regionArea><wicri:noRegion>85350 Freising</wicri:noRegion><orgName type="university">Université technique de Munich</orgName><placeName><settlement type="city">Munich</settlement><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region></placeName></affiliation></author><author><name sortKey="Lehner, Angelika" sort="Lehner, Angelika" uniqKey="Lehner A" first="Angelika" last="Lehner">Angelika Lehner</name></author><author><name sortKey="Lee, Natuschka" sort="Lee, Natuschka" uniqKey="Lee N" first="Natuschka" last="Lee">Natuschka Lee</name></author><author><name sortKey="Adamczyk, Justyna" sort="Adamczyk, Justyna" uniqKey="Adamczyk J" first="Justyna" last="Adamczyk">Justyna Adamczyk</name></author><author><name sortKey="Meier, Harald" sort="Meier, Harald" uniqKey="Meier H" first="Harald" last="Meier">Harald Meier</name></author><author><name sortKey="Ernst, Jens" sort="Ernst, Jens" uniqKey="Ernst J" first="Jens" last="Ernst">Jens Ernst</name></author><author><name sortKey="Schleifer, Karl Heinz" sort="Schleifer, Karl Heinz" uniqKey="Schleifer K" first="Karl-Heinz" last="Schleifer">Karl-Heinz Schleifer</name></author><author><name sortKey="Wagner, Michael" sort="Wagner, Michael" uniqKey="Wagner M" first="Michael" last="Wagner">Michael Wagner</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2002">2002</date><idno type="RBID">pubmed:12324358</idno><idno type="pmid">12324358</idno><idno type="doi">10.1128/aem.68.10.5064-5081.2002</idno><idno type="wicri:Area/PubMed/Corpus">002492</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002492</idno><idno type="wicri:Area/PubMed/Curation">002492</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002492</idno><idno type="wicri:Area/PubMed/Checkpoint">002360</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002360</idno><idno type="wicri:Area/Ncbi/Merge">000154</idno><idno type="wicri:Area/Ncbi/Curation">000154</idno><idno type="wicri:Area/Ncbi/Checkpoint">000154</idno><idno type="wicri:doubleKey">0099-2240:2002:Loy A:oligonucleotide:microarray:for</idno><idno type="wicri:Area/Main/Merge">003357</idno><idno type="wicri:Area/Main/Curation">003321</idno><idno type="wicri:Area/Main/Exploration">003321</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.</title><author><name sortKey="Loy, Alexander" sort="Loy, Alexander" uniqKey="Loy A" first="Alexander" last="Loy">Alexander Loy</name><affiliation wicri:level="4"><nlm:affiliation>Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising</wicri:regionArea><wicri:noRegion>85350 Freising</wicri:noRegion><orgName type="university">Université technique de Munich</orgName><placeName><settlement type="city">Munich</settlement><region type="land" nuts="1">Bavière</region><region type="district" nuts="2">District de Haute-Bavière</region></placeName></affiliation></author><author><name sortKey="Lehner, Angelika" sort="Lehner, Angelika" uniqKey="Lehner A" first="Angelika" last="Lehner">Angelika Lehner</name></author><author><name sortKey="Lee, Natuschka" sort="Lee, Natuschka" uniqKey="Lee N" first="Natuschka" last="Lee">Natuschka Lee</name></author><author><name sortKey="Adamczyk, Justyna" sort="Adamczyk, Justyna" uniqKey="Adamczyk J" first="Justyna" last="Adamczyk">Justyna Adamczyk</name></author><author><name sortKey="Meier, Harald" sort="Meier, Harald" uniqKey="Meier H" first="Harald" last="Meier">Harald Meier</name></author><author><name sortKey="Ernst, Jens" sort="Ernst, Jens" uniqKey="Ernst J" first="Jens" last="Ernst">Jens Ernst</name></author><author><name sortKey="Schleifer, Karl Heinz" sort="Schleifer, Karl Heinz" uniqKey="Schleifer K" first="Karl-Heinz" last="Schleifer">Karl-Heinz Schleifer</name></author><author><name sortKey="Wagner, Michael" sort="Wagner, Michael" uniqKey="Wagner M" first="Michael" last="Wagner">Michael Wagner</name></author></analytic><series><title level="j">Applied and environmental microbiology</title><idno type="ISSN">0099-2240</idno><imprint><date when="2002" type="published">2002</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotide Probes (genetics)</term><term>Phylogeny</term><term>RNA, Bacterial (chemistry)</term><term>RNA, Ribosomal, 16S (analysis)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Reproducibility of Results</term><term>Sensitivity and Specificity</term><term>Sequence Analysis, DNA</term><term>Sulfates (metabolism)</term><term>Sulfur-Reducing Bacteria (classification)</term><term>Sulfur-Reducing Bacteria (genetics)</term><term>Sulfur-Reducing Bacteria (metabolism)</term><term>Tooth (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN bactérien ()</term><term>ARN ribosomique 16S (analyse)</term><term>ARN ribosomique 16S (génétique)</term><term>Analyse de séquence d'ADN</term><term>Bactéries sulfato-réductrices ()</term><term>Bactéries sulfato-réductrices (génétique)</term><term>Bactéries sulfato-réductrices (métabolisme)</term><term>Dent (microbiologie)</term><term>Hybridation d'acides nucléiques</term><term>Phylogénie</term><term>Reproductibilité des résultats</term><term>Sensibilité et spécificité</term><term>Sondes oligonucléotidiques (génétique)</term><term>Sulfates (métabolisme)</term><term>Séquençage par oligonucléotides en batterie ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotide Probes</term><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Sulfates</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ARN ribosomique 16S</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Sulfur-Reducing Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Sulfur-Reducing Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN ribosomique 16S</term><term>Bactéries sulfato-réductrices</term><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Sulfur-Reducing Bacteria</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Dent</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Tooth</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bactéries sulfato-réductrices</term><term>Sulfates</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Nucleic Acid Hybridization</term><term>Phylogeny</term><term>Reproducibility of Results</term><term>Sensitivity and Specificity</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN bactérien</term><term>Analyse de séquence d'ADN</term><term>Bactéries sulfato-réductrices</term><term>Hybridation d'acides nucléiques</term><term>Phylogénie</term><term>Reproductibilité des résultats</term><term>Sensibilité et spécificité</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).</div></front></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Bavière</li><li>District de Haute-Bavière</li></region><settlement><li>Munich</li></settlement><orgName><li>Université technique de Munich</li></orgName></list><tree><noCountry><name sortKey="Adamczyk, Justyna" sort="Adamczyk, Justyna" uniqKey="Adamczyk J" first="Justyna" last="Adamczyk">Justyna Adamczyk</name><name sortKey="Ernst, Jens" sort="Ernst, Jens" uniqKey="Ernst J" first="Jens" last="Ernst">Jens Ernst</name><name sortKey="Lee, Natuschka" sort="Lee, Natuschka" uniqKey="Lee N" first="Natuschka" last="Lee">Natuschka Lee</name><name sortKey="Lehner, Angelika" sort="Lehner, Angelika" uniqKey="Lehner A" first="Angelika" last="Lehner">Angelika Lehner</name><name sortKey="Meier, Harald" sort="Meier, Harald" uniqKey="Meier H" first="Harald" last="Meier">Harald Meier</name><name sortKey="Schleifer, Karl Heinz" sort="Schleifer, Karl Heinz" uniqKey="Schleifer K" first="Karl-Heinz" last="Schleifer">Karl-Heinz Schleifer</name><name sortKey="Wagner, Michael" sort="Wagner, Michael" uniqKey="Wagner M" first="Michael" last="Wagner">Michael Wagner</name></noCountry><country name="Allemagne"><region name="Bavière"><name sortKey="Loy, Alexander" sort="Loy, Alexander" uniqKey="Loy A" first="Alexander" last="Loy">Alexander Loy</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003321 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003321 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:12324358
|texte= Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:12324358" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |