Quality control of microbiota metagenomics by k-mer analysis
Identifieur interne : 001608 ( Main/Exploration ); précédent : 001607; suivant : 001609Quality control of microbiota metagenomics by k-mer analysis
Auteurs : Florian Plaza Onate [France] ; Jean-Michel Batto [France] ; Catherine Juste [France] ; Jehane Fadlallah [France] ; Cyrielle Fougeroux [France] ; Doriane Gouas [France] ; Nicolas Pons [France] ; Sean Kennedy [France] ; Florence Levenez [France] ; Joel Dore [France] ; S Dusko Ehrlich [France] ; Guy Gorochov [France] ; Martin Larsen [France]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Bactéries.
- microbiologie : Fèces, Tube digestif.
- normes : Métagénomique.
- Analyse de regroupements, Bactéries, Contrôle de qualité, Génome bactérien, Humains, Microbiote, Métagénome, Métagénomique, Sensibilité et spécificité.
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.
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.
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.
The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1406-7
PubMed: 25887914
PubMed Central: 4373121
Affiliations:
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<author><name sortKey="Fougeroux, Cyrielle" sort="Fougeroux, Cyrielle" uniqKey="Fougeroux C" first="Cyrielle" last="Fougeroux">Cyrielle Fougeroux</name>
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<author><name sortKey="Pons, Nicolas" sort="Pons, Nicolas" uniqKey="Pons N" first="Nicolas" last="Pons">Nicolas Pons</name>
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<country xml:lang="fr">France</country>
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<author><name sortKey="Kennedy, Sean" sort="Kennedy, Sean" uniqKey="Kennedy S" first="Sean" last="Kennedy">Sean Kennedy</name>
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<author><name sortKey="Levenez, Florence" sort="Levenez, Florence" uniqKey="Levenez F" first="Florence" last="Levenez">Florence Levenez</name>
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<country xml:lang="fr">France</country>
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<settlement type="city">Jouy en Josas</settlement>
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<author><name sortKey="Dore, Joel" sort="Dore, Joel" uniqKey="Dore J" first="Joel" last="Dore">Joel Dore</name>
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<country xml:lang="fr">France</country>
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<placeName><region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Jouy en Josas</settlement>
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<affiliation wicri:level="1"><nlm:aff id="Aff2">UMR1319 Micalis, INRA, Jouy-en-Josas, France</nlm:aff>
<country xml:lang="fr">France</country>
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</author>
<author><name sortKey="Ehrlich, S Dusko" sort="Ehrlich, S Dusko" uniqKey="Ehrlich S" first="S Dusko" last="Ehrlich">S Dusko Ehrlich</name>
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<country xml:lang="fr">France</country>
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<settlement type="city">Jouy en Josas</settlement>
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<wicri:regionArea>UMR1319 Micalis, INRA, Jouy-en-Josas</wicri:regionArea>
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<author><name sortKey="Gorochov, Guy" sort="Gorochov, Guy" uniqKey="Gorochov G" first="Guy" last="Gorochov">Guy Gorochov</name>
<affiliation wicri:level="3"><nlm:aff id="Aff3">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</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>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</wicri:regionArea>
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<affiliation wicri:level="3"><nlm:aff id="Aff4">Département d’Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013 Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Département d’Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013 Paris</wicri:regionArea>
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<affiliation wicri:level="3"><nlm:aff id="Aff5">Inserm UMR-S1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013 Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Inserm UMR-S1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013 Paris</wicri:regionArea>
<placeName><region type="region" nuts="2">Île-de-France</region>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Larsen, Martin" sort="Larsen, Martin" uniqKey="Larsen M" first="Martin" last="Larsen">Martin Larsen</name>
<affiliation wicri:level="3"><nlm:aff id="Aff3">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</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>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</wicri:regionArea>
<placeName><region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="Aff4">Département d’Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013 Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Département d’Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013 Paris</wicri:regionArea>
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<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="Aff5">Inserm UMR-S1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013 Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Inserm UMR-S1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013 Paris</wicri:regionArea>
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<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2015">2015</date>
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<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="KwdFr" xml:lang="fr"><term>Analyse de regroupements</term>
<term>Bactéries ()</term>
<term>Bactéries (génétique)</term>
<term>Contrôle de qualité</term>
<term>Fèces (microbiologie)</term>
<term>Génome bactérien</term>
<term>Humains</term>
<term>Microbiote</term>
<term>Métagénome</term>
<term>Métagénomique ()</term>
<term>Métagénomique (normes)</term>
<term>Sensibilité et spécificité</term>
<term>Tube digestif (microbiologie)</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="génétique" xml:lang="fr"><term>Bactéries</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Fèces</term>
<term>Tube digestif</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Feces</term>
<term>Gastrointestinal Tract</term>
</keywords>
<keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Métagénomique</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>
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<term>Contrôle de qualité</term>
<term>Génome bactérien</term>
<term>Humains</term>
<term>Microbiote</term>
<term>Métagénome</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Results</title>
<p>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.</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<author><name sortKey="Duncan, A" uniqKey="Duncan A">A Duncan</name>
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<author><name sortKey="Olson, R" uniqKey="Olson R">R Olson</name>
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<author><name sortKey="Disz, T" uniqKey="Disz T">T Disz</name>
</author>
<author><name sortKey="Pusch, Gd" uniqKey="Pusch G">GD Pusch</name>
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<author><name sortKey="Vonstein, V" uniqKey="Vonstein V">V Vonstein</name>
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<author><name sortKey="Stevens, R" uniqKey="Stevens R">R Stevens</name>
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</analytic>
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</analytic>
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</author>
<author><name sortKey="Trimble, Wl" uniqKey="Trimble W">WL Trimble</name>
</author>
<author><name sortKey="Shilts, M" uniqKey="Shilts M">M Shilts</name>
</author>
<author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Ochman, H" uniqKey="Ochman H">H Ochman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gao, L" uniqKey="Gao L">L Gao</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Shannon, Ce" uniqKey="Shannon C">CE Shannon</name>
</author>
</analytic>
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<author><name sortKey="Kreil, Dp" uniqKey="Kreil D">DP Kreil</name>
</author>
<author><name sortKey="Beauvallet, C" uniqKey="Beauvallet C">C Beauvallet</name>
</author>
<author><name sortKey="Guillot, A" uniqKey="Guillot A">A Guillot</name>
</author>
<author><name sortKey="Vaca, S" uniqKey="Vaca S">S Vaca</name>
</author>
<author><name sortKey="Carapito, C" uniqKey="Carapito C">C Carapito</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Zumstein, E" uniqKey="Zumstein E">E Zumstein</name>
</author>
<author><name sortKey="Dabert, P" uniqKey="Dabert P">P Dabert</name>
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<author><name sortKey="Habouzit, F" uniqKey="Habouzit F">F Habouzit</name>
</author>
<author><name sortKey="Moletta, R" uniqKey="Moletta R">R Moletta</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mardis, Er" uniqKey="Mardis E">ER Mardis</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name>
</author>
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</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Rau, A" uniqKey="Rau A">A Rau</name>
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<author><name sortKey="Aubert, J" uniqKey="Aubert J">J Aubert</name>
</author>
<author><name sortKey="Hennequet Antier, C" uniqKey="Hennequet Antier C">C Hennequet-Antier</name>
</author>
<author><name sortKey="Jeanmougin, M" uniqKey="Jeanmougin M">M Jeanmougin</name>
</author>
<author><name sortKey="Servant, N" uniqKey="Servant N">N Servant</name>
</author>
</analytic>
</biblStruct>
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</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Peng, Y" uniqKey="Peng Y">Y Peng</name>
</author>
<author><name sortKey="Leung, Hc" uniqKey="Leung H">HC Leung</name>
</author>
<author><name sortKey="Yiu, Sm" uniqKey="Yiu S">SM Yiu</name>
</author>
<author><name sortKey="Chen, Jc" uniqKey="Chen J">JC Chen</name>
</author>
<author><name sortKey="Chin, Fy" uniqKey="Chin F">FY Chin</name>
</author>
</analytic>
</biblStruct>
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</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, J" uniqKey="Li J">J Li</name>
</author>
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<author><name sortKey="Cai, X" uniqKey="Cai X">X Cai</name>
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<author><name sortKey="Zhong, H" uniqKey="Zhong H">H Zhong</name>
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<author><name sortKey="Feng, Q" uniqKey="Feng Q">Q Feng</name>
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<author><name sortKey="Sunagawa, S" uniqKey="Sunagawa S">S Sunagawa</name>
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</analytic>
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</TEI>
<affiliations><list><country><li>France</li>
</country>
<region><li>Île-de-France</li>
</region>
<settlement><li>Jouy en Josas</li>
<li>Paris</li>
</settlement>
</list>
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<name sortKey="Batto, Jean Michel" sort="Batto, Jean Michel" uniqKey="Batto J" first="Jean-Michel" last="Batto">Jean-Michel Batto</name>
<name sortKey="Dore, Joel" sort="Dore, Joel" uniqKey="Dore J" first="Joel" last="Dore">Joel Dore</name>
<name sortKey="Dore, Joel" sort="Dore, Joel" uniqKey="Dore J" first="Joel" last="Dore">Joel Dore</name>
<name sortKey="Ehrlich, S Dusko" sort="Ehrlich, S Dusko" uniqKey="Ehrlich S" first="S Dusko" last="Ehrlich">S Dusko Ehrlich</name>
<name sortKey="Ehrlich, S Dusko" sort="Ehrlich, S Dusko" uniqKey="Ehrlich S" first="S Dusko" last="Ehrlich">S Dusko Ehrlich</name>
<name sortKey="Fadlallah, Jehane" sort="Fadlallah, Jehane" uniqKey="Fadlallah J" first="Jehane" last="Fadlallah">Jehane Fadlallah</name>
<name sortKey="Fadlallah, Jehane" sort="Fadlallah, Jehane" uniqKey="Fadlallah J" first="Jehane" last="Fadlallah">Jehane Fadlallah</name>
<name sortKey="Fougeroux, Cyrielle" sort="Fougeroux, Cyrielle" uniqKey="Fougeroux C" first="Cyrielle" last="Fougeroux">Cyrielle Fougeroux</name>
<name sortKey="Gorochov, Guy" sort="Gorochov, Guy" uniqKey="Gorochov G" first="Guy" last="Gorochov">Guy Gorochov</name>
<name sortKey="Gorochov, Guy" sort="Gorochov, Guy" uniqKey="Gorochov G" first="Guy" last="Gorochov">Guy Gorochov</name>
<name sortKey="Gorochov, Guy" sort="Gorochov, Guy" uniqKey="Gorochov G" first="Guy" last="Gorochov">Guy Gorochov</name>
<name sortKey="Gouas, Doriane" sort="Gouas, Doriane" uniqKey="Gouas D" first="Doriane" last="Gouas">Doriane Gouas</name>
<name sortKey="Gouas, Doriane" sort="Gouas, Doriane" uniqKey="Gouas D" first="Doriane" last="Gouas">Doriane Gouas</name>
<name sortKey="Juste, Catherine" sort="Juste, Catherine" uniqKey="Juste C" first="Catherine" last="Juste">Catherine Juste</name>
<name sortKey="Juste, Catherine" sort="Juste, Catherine" uniqKey="Juste C" first="Catherine" last="Juste">Catherine Juste</name>
<name sortKey="Kennedy, Sean" sort="Kennedy, Sean" uniqKey="Kennedy S" first="Sean" last="Kennedy">Sean Kennedy</name>
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<name sortKey="Pons, Nicolas" sort="Pons, Nicolas" uniqKey="Pons N" first="Nicolas" last="Pons">Nicolas Pons</name>
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</affiliations>
</record>
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