How conserved are the conserved 16S-rRNA regions?
Identifieur interne : 000D59 ( Main/Exploration ); précédent : 000D58; suivant : 000D60How conserved are the conserved 16S-rRNA regions?
Auteurs : Marcel Martinez-Porchas [Mexique] ; Enrique Villalpando-Canchola [Mexique] ; Luis Enrique Ortiz Suarez [Mexique] ; Francisco Vargas-Albores [Mexique]Source :
- PeerJ [ 2167-8359 ] ; 2017.
Abstract
The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
Url:
DOI: 10.7717/peerj.3036
PubMed: 28265511
PubMed Central: 5333541
Affiliations:
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Porchas, Marcel" sort="Martinez Porchas, Marcel" uniqKey="Martinez Porchas M" first="Marcel" last="Martinez-Porchas">Marcel Martinez-Porchas</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Centro de Investigación en Alimentación y Desarrollo, A.C.</institution>,<city>Hermosillo</city>,<state>Sonora</state>,<country>Mexico</country></nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Villalpando Canchola, Enrique" sort="Villalpando Canchola, Enrique" uniqKey="Villalpando Canchola E" first="Enrique" last="Villalpando-Canchola">Enrique Villalpando-Canchola</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Centro de Investigación en Alimentación y Desarrollo, A.C.</institution>,<city>Hermosillo</city>,<state>Sonora</state>,<country>Mexico</country></nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ortiz Suarez, Luis Enrique" sort="Ortiz Suarez, Luis Enrique" uniqKey="Ortiz Suarez L" first="Luis Enrique" last="Ortiz Suarez">Luis Enrique Ortiz Suarez</name><affiliation wicri:level="1"><nlm:aff id="aff-2"><institution>Instituto Tecnológico de Morelia</institution>,<city>Morelia</city>,<state>Michoacán</state>,<country>Mexico</country></nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Vargas Albores, Francisco" sort="Vargas Albores, Francisco" uniqKey="Vargas Albores F" first="Francisco" last="Vargas-Albores">Francisco Vargas-Albores</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Centro de Investigación en Alimentación y Desarrollo, A.C.</institution>,<city>Hermosillo</city>,<state>Sonora</state>,<country>Mexico</country></nlm:aff><country xml:lang="fr">Mexique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="eISSN">2167-8359</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Albertsen, M" uniqKey="Albertsen M">M Albertsen</name></author><author><name sortKey="Karst, Sm" uniqKey="Karst S">SM Karst</name></author><author><name sortKey="Ziegler, As" uniqKey="Ziegler A">AS Ziegler</name></author><author><name sortKey="Kirkegaard, Rh" uniqKey="Kirkegaard R">RH Kirkegaard</name></author><author><name sortKey="Nielsen, Ph" uniqKey="Nielsen P">PH Nielsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amann, Ri" uniqKey="Amann R">RI Amann</name></author><author><name sortKey="Binder, Bj" uniqKey="Binder B">BJ Binder</name></author><author><name sortKey="Olson, Rj" uniqKey="Olson R">RJ Olson</name></author><author><name sortKey="Chisholm, Sw" uniqKey="Chisholm S">SW 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P" uniqKey="Yilmaz P">P Yilmaz</name></author><author><name sortKey="Pruesse, E" uniqKey="Pruesse E">E Pruesse</name></author><author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glockner</name></author><author><name sortKey="Ludwig, W" uniqKey="Ludwig W">W Ludwig</name></author><author><name sortKey="Schleifer, K H" uniqKey="Schleifer K">K-H Schleifer</name></author><author><name sortKey="Whitman, Wb" uniqKey="Whitman W">WB Whitman</name></author><author><name sortKey="Euzeby, J" uniqKey="Euzeby J">J Euzeby</name></author><author><name sortKey="Amann, R" uniqKey="Amann R">R Amann</name></author><author><name sortKey="Rossello Mora, R" uniqKey="Rossello Mora R">R Rossello-Mora</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Youssef, N" uniqKey="Youssef N">N Youssef</name></author><author><name sortKey="Sheik, Cs" uniqKey="Sheik C">CS Sheik</name></author><author><name sortKey="Krumholz, Lr" uniqKey="Krumholz L">LR Krumholz</name></author><author><name sortKey="Najar, Fz" uniqKey="Najar F">FZ Najar</name></author><author><name sortKey="Roe, Ba" uniqKey="Roe B">BA Roe</name></author><author><name sortKey="Elshahed, Ms" uniqKey="Elshahed M">MS Elshahed</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, Z" uniqKey="Yu Z">Z Yu</name></author><author><name sortKey="Morrison, M" uniqKey="Morrison M">M Morrison</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Mexique</li></country></list><tree><country name="Mexique"><noRegion><name sortKey="Martinez Porchas, Marcel" sort="Martinez Porchas, Marcel" uniqKey="Martinez Porchas M" first="Marcel" last="Martinez-Porchas">Marcel Martinez-Porchas</name></noRegion><name sortKey="Ortiz Suarez, Luis Enrique" sort="Ortiz Suarez, Luis Enrique" uniqKey="Ortiz Suarez L" first="Luis Enrique" last="Ortiz Suarez">Luis Enrique Ortiz Suarez</name><name sortKey="Vargas Albores, Francisco" sort="Vargas Albores, Francisco" uniqKey="Vargas Albores F" first="Francisco" last="Vargas-Albores">Francisco Vargas-Albores</name><name sortKey="Villalpando Canchola, Enrique" sort="Villalpando Canchola, Enrique" uniqKey="Villalpando Canchola E" first="Enrique" last="Villalpando-Canchola">Enrique Villalpando-Canchola</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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