title: Quality control of microbiota metagenomics by k-mer analysis.
abstract: 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.
  
  
  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.
  
  
  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.
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. florian.plaza@jouy.inra.fr.
authors.forename: Florian
authors.initials: F
authors.lastname: Plaza Onate
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France. jean-michel.batto@jouy.inra.fr.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Batto
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. catherine.juste@jouy.inra.fr.|UMR1319 Micalis, INRA, Jouy-en-Josas, France. catherine.juste@jouy.inra.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Juste
authors.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.|Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. jehane_fad@yahoo.fr.
authors.forename: Jehane
authors.initials: J
authors.lastname: Fadlallah
authors.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.
authors.forename: Cyrielle
authors.initials: C
authors.lastname: Fougeroux
authors.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.|Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France. dorianegouas@gmail.com.
authors.forename: Doriane
authors.initials: D
authors.lastname: Gouas
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. nicolas.pons@jouy.inra.fr.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pons
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. skennedy@jouy.inra.fr.
authors.forename: Sean
authors.initials: S
authors.lastname: Kennedy
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. florence.levenez@jouy.inra.fr.|UMR1319 Micalis, INRA, Jouy-en-Josas, France. florence.levenez@jouy.inra.fr.
authors.forename: Florence
authors.initials: F
authors.lastname: Levenez
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. joel.dore@jouy.inra.fr.|UMR1319 Micalis, INRA, Jouy-en-Josas, France. joel.dore@jouy.inra.fr.
authors.forename: Joel
authors.initials: J
authors.lastname: Dore
authors.affiliation: INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. dusko.ehrlich@jouy.inra.fr.|UMR1319 Micalis, INRA, Jouy-en-Josas, France. dusko.ehrlich@jouy.inra.fr.
authors.forename: S Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.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.|Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. guy.gorochov@upmc.fr.|Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France. guy.gorochov@upmc.fr.
authors.forename: Guy
authors.initials: G
authors.lastname: Gorochov
authors.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.|Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. Martin.Larsen@upmc.fr.|Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France. Martin.Larsen@upmc.fr.
authors.forename: Martin
authors.initials: M
authors.lastname: Larsen
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D016000:Cluster Analysis; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology; D016680:Genome, Bacterial; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods* / Q000592:standards; D064307:Microbiota; D011786:Quality Control; D012680:Sensitivity and Specificity