Quality control of microbiota metagenomics by k-mer analysis.
Identifieur interne : 001642 ( PubMed/Corpus ); précédent : 001641; suivant : 001643Quality control of microbiota metagenomics by k-mer analysis.
Auteurs : Florian Plaza Onate ; Jean-Michel Batto ; Catherine Juste ; Jehane Fadlallah ; Cyrielle Fougeroux ; Doriane Gouas ; Nicolas Pons ; Sean Kennedy ; Florence Levenez ; Joel Dore ; S Dusko Ehrlich ; Guy Gorochov ; Martin LarsenSource :
- BMC genomics [ 1471-2164 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- classification : Bacteria.
- genetics : Bacteria.
- methods : Metagenomics.
- microbiology : Feces, Gastrointestinal Tract.
- standards : Metagenomics.
- Cluster Analysis, Genome, Bacterial, Humans, Metagenome, Microbiota, Quality Control, Sensitivity and Specificity.
Abstract
The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case-control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue.
DOI: 10.1186/s12864-015-1406-7
PubMed: 25887914
Links to Exploration step
pubmed:25887914Le document en format XML
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Martin.Larsen@upmc.fr.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25887914</idno><idno type="pmid">25887914</idno><idno type="doi">10.1186/s12864-015-1406-7</idno><idno type="wicri:Area/PubMed/Corpus">001642</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001642</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Quality control of microbiota metagenomics by k-mer analysis.</title><author><name sortKey="Plaza Onate, Florian" sort="Plaza Onate, Florian" uniqKey="Plaza Onate F" first="Florian" last="Plaza Onate">Florian Plaza Onate</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. florian.plaza@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Batto, Jean Michel" sort="Batto, Jean Michel" uniqKey="Batto J" first="Jean-Michel" last="Batto">Jean-Michel Batto</name><affiliation><nlm:affiliation>UMR1319 Micalis, INRA, Jouy-en-Josas, France. jean-michel.batto@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Juste, Catherine" sort="Juste, Catherine" uniqKey="Juste C" first="Catherine" last="Juste">Catherine Juste</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. catherine.juste@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Fadlallah, Jehane" sort="Fadlallah, Jehane" uniqKey="Fadlallah J" first="Jehane" last="Fadlallah">Jehane Fadlallah</name><affiliation><nlm:affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. jehane_fad@yahoo.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Fougeroux, Cyrielle" sort="Fougeroux, Cyrielle" uniqKey="Fougeroux C" first="Cyrielle" last="Fougeroux">Cyrielle Fougeroux</name><affiliation><nlm:affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. cyrielle.fougeroux@yahoo.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Gouas, Doriane" sort="Gouas, Doriane" uniqKey="Gouas D" first="Doriane" last="Gouas">Doriane Gouas</name><affiliation><nlm:affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. dorianegouas@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Pons, Nicolas" sort="Pons, Nicolas" uniqKey="Pons N" first="Nicolas" last="Pons">Nicolas Pons</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. nicolas.pons@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Kennedy, Sean" sort="Kennedy, Sean" uniqKey="Kennedy S" first="Sean" last="Kennedy">Sean Kennedy</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. skennedy@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Levenez, Florence" sort="Levenez, Florence" uniqKey="Levenez F" first="Florence" last="Levenez">Florence Levenez</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. florence.levenez@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Dore, Joel" sort="Dore, Joel" uniqKey="Dore J" first="Joel" last="Dore">Joel Dore</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. joel.dore@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Ehrlich, S Dusko" sort="Ehrlich, S Dusko" uniqKey="Ehrlich S" first="S Dusko" last="Ehrlich">S Dusko Ehrlich</name><affiliation><nlm:affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. dusko.ehrlich@jouy.inra.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Gorochov, Guy" sort="Gorochov, Guy" uniqKey="Gorochov G" first="Guy" last="Gorochov">Guy Gorochov</name><affiliation><nlm:affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. guy.gorochov@upmc.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Larsen, Martin" sort="Larsen, Martin" uniqKey="Larsen M" first="Martin" last="Larsen">Martin Larsen</name><affiliation><nlm:affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. Martin.Larsen@upmc.fr.</nlm:affiliation></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (classification)</term><term>Bacteria (genetics)</term><term>Cluster Analysis</term><term>Feces (microbiology)</term><term>Gastrointestinal Tract (microbiology)</term><term>Genome, Bacterial</term><term>Humans</term><term>Metagenome</term><term>Metagenomics (methods)</term><term>Metagenomics (standards)</term><term>Microbiota</term><term>Quality Control</term><term>Sensitivity and Specificity</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Feces</term><term>Gastrointestinal Tract</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Metagenomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Genome, Bacterial</term><term>Humans</term><term>Metagenome</term><term>Microbiota</term><term>Quality Control</term><term>Sensitivity and Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case-control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25887914</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><PubDate><Year>2015</Year><Month>Mar</Month><Day>14</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Quality control of microbiota metagenomics by k-mer analysis.</ArticleTitle><Pagination><MedlinePgn>183</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-1406-7</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case-control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from "empty" ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Plaza Onate</LastName><ForeName>Florian</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. florian.plaza@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Batto</LastName><ForeName>Jean-Michel</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>UMR1319 Micalis, INRA, Jouy-en-Josas, France. jean-michel.batto@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Juste</LastName><ForeName>Catherine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. catherine.juste@jouy.inra.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UMR1319 Micalis, INRA, Jouy-en-Josas, France. catherine.juste@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fadlallah</LastName><ForeName>Jehane</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. jehane_fad@yahoo.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. jehane_fad@yahoo.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fougeroux</LastName><ForeName>Cyrielle</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. cyrielle.fougeroux@yahoo.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gouas</LastName><ForeName>Doriane</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. dorianegouas@gmail.com.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France. dorianegouas@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pons</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. nicolas.pons@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kennedy</LastName><ForeName>Sean</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. skennedy@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Levenez</LastName><ForeName>Florence</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. florence.levenez@jouy.inra.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UMR1319 Micalis, INRA, Jouy-en-Josas, France. florence.levenez@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dore</LastName><ForeName>Joel</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. joel.dore@jouy.inra.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UMR1319 Micalis, INRA, Jouy-en-Josas, France. joel.dore@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ehrlich</LastName><ForeName>S Dusko</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. dusko.ehrlich@jouy.inra.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UMR1319 Micalis, INRA, Jouy-en-Josas, France. dusko.ehrlich@jouy.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gorochov</LastName><ForeName>Guy</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. guy.gorochov@upmc.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. guy.gorochov@upmc.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France. guy.gorochov@upmc.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Larsen</LastName><ForeName>Martin</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. Martin.Larsen@upmc.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. Martin.Larsen@upmc.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France. Martin.Larsen@upmc.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>03</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName 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