Search Results - "MESH: Metagenome"

1

Strainberry: automated strain separation in low-complexity metagenomes using long reads

Authors: Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E., Chikhi, Rayan

Contributors: Algorithmes pour les séquences biologiques - Sequence Bioinformatics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Warwick Medical School, University of Warwick [Coventry], Earlham Institute [Norwich], Quadram Institute, iThree Institute, University of Technology Sydney (UTS), R.V. and R.C. are funded by ANR INCEPTION (PIA/ANR-16-CONV-0005) and R.C. by ANR PRAIRIE (ANR-19-P3IA-0001) and ANR SeqDigger (ANR-19-CE45-0008). C.Q. is funded through 'Strain resolved metagenomics for medical microbiology' MRC MR/S037195/1 and the 'CLIMB-BIG-DATA' consortium MR/T030062/1. A.E.D.’s contributions to this research were supported in part by the Australian Government through the Australian Research Council Discovery Projects funding scheme (project DP180101506)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), ANR-19-CE45-0008,SeqDigger,Moteur de recherche de donne´es de se´quenc¸age en ge´nomique environnementale(2019), Institut Pasteur [Paris]-Université Paris Cité (UPCité), Biotechnology and Biological Sciences Research Council (BBSRC)

Source: Nature Communications
Nature Communications, Nature Publishing Group, 2021, 12 (1), pp.4485. ⟨10.1038/s41467-021-24515-9⟩
Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

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https://hal.archives-ouvertes.fr/hal-03412884

2

Microbial dark matter filling the niche in hypersaline microbial mats

Authors: Fraser I. MacLeod, Hon Lun Wong, Brendan P. Burns, Pieter T. Visscher, Richard A. White

Contributors: School of Biotechnology and Biomolecular Sciences, University of New South Wales [Sydney] (UNSW), Australian Centre for Astrobiology, RAW Molecular Systems LLC, Departments of Marine Sciences and Geoscience, University of Connecticut (UCONN), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Source: Microbiome
Microbiome, BioMed Central, 2020, 8 (1), pp.135. ⟨10.1186/s40168-020-00910-0⟩
Microbiome, Vol 8, Iss 1, Pp 1-14 (2020)

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http://europepmc.org/articles/PMC7495880

3

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Authors: Stevenn Volant, Laurence Motreff, Pascal Campagne, Sean Kennedy, Pierre Lechat, Amine Ghozlane, Christophe Malabat, Perrine Woringer

Contributors: Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Institut Pasteur

Source: BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2020, 21 (1), pp.345. ⟨10.1186/s12859-020-03666-4⟩
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020)

Subject Terms: Differential analysis, Metagenomics, Visualization, Web application, MESH: Body Fluids, MESH: Child, Preschool, MESH: Metagenome, MESH: Metagenomics, MESH: Microbiota, MESH: RNA, Ribosomal, 16S, MESH: Software, MESH: Statistics as Topic, MESH: User-Computer Interface, MESH: Workflow, MESH: Classification, MESH: Feces, MESH: Humans, MESH: Internet, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, education, Applied Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Structural Biology, Computer science, 16S ribosomal RNA, Source code, media_common.quotation_subject, media_common, Container (abstract data type), Microbiome, User Friendly, Set (abstract data type), Information retrieval, DNA microarray, lcsh:Computer applications to medicine. Medical informatics, lcsh:R858-859.7, lcsh:Biology (General), lcsh:QH301-705.5, Software

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https://hal-pasteur.archives-ouvertes.fr/pasteur-02951458

4

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Contributors: Joint Genome Institute (JGI), Northwest Institute for Nonferrous Metal Research (NIN), Laboratorio de Turbulencia, Universidad de Santiago de Chile [Santiago] (USACH), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, BioSciences Division [Oak Ridge], UT-Battelle, LLC-UT-Battelle, LLC, Duke University [Durham], Centre d'études de chimie métallurgique (CECM), Centre National de la Recherche Scientifique (CNRS), Kansas State University, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Center for Human Genetics, University of Leuven School of Medicine, SCHOOL of MEDICINE [Louvain], Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Joint Genome Institute ( JGI ), Northwest Institute for Nonferrous Metal Research, Oak Ridge National Laboratory, Duke university [Durham], Centre d'études de chimie métallurgique ( CECM ), Centre National de la Recherche Scientifique ( CNRS ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), UNIVERSITY of LEUVEN SCHOOL of MEDICINE, Institute of Northern Engineering, 455 Duckering Bldg, Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), University of California [Berkeley] (UC Berkeley), University of California (UC), Arizona State University [Tempe] (ASU), Deparment of Plant, Soil and Microbial Sciences, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Goethe-University Frankfurt am Main, Utrecht University [Utrecht], Genomic Science Program, U.S. Department of Energy, Office of Science - Biological and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area at Oak Ridge National Laboratory, U.S. Department of Energy DE-AC05- 00OR22725, DOE Joint Genome Institute by the JGI Community sequencing program 570, Office of Science of the US Department of Energy DE-AC02-05CH11231, EU Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE) ANR-11-LABX-0002-01, University of California [Berkeley], University of California, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Source: Environmental Microbiology, 19(8), 2964. Blackwell Publishing Ltd
Environmental Microbiology
Environmental Microbiology, Wiley-Blackwell, 2017, 19 (8), pp.2964-2983. ⟨10.1111/1462-2920.13669⟩
Environmental microbiology, vol 19, iss 8
Environmental Microbiology, Wiley-Blackwell, 2017, 19 (8), pp.2964-2983. 〈10.1111/1462-2920.13669〉
Environmental Microbiology, 2017, 19 (8), pp.2964-2983. ⟨10.1111/1462-2920.13669⟩
Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2017, 19 (8), pp.2964-2983. ⟨10.1111/1462-2920.13669⟩

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https://doi.org/10.1111/1462-2920.13669

5

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Authors: J. Rodney Brister, Ho Bin Jang, Simon Roux, Dann Turner, Mart Krupovic, Benjamin Bolduc, Matthew B. Sullivan, Andrew M. Kropinski, Olivier Zablocki, Rob Lavigne, Jens H. Kuhn, Evelien M. Adriaenssens

Contributors: Ohio State University [Columbus] (OSU), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), DOE Joint Genome Institute [Walnut Creek], U.S. Department of Energy [Washington] (DOE), Institute of Integrative Biology [Liverpool, UK], University of Liverpool, Quadram Institute, National Center for Biotechnology Information (NCBI), National Institutes of Health [Bethesda] (NIH), Ontario Veterinary College [Univ. Guelph, Canada], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Faculty of BioScience Engineering [KU Leuven, Belgium], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of the West of England [Bristol] (UWE Bristol), High-performance computational support was provided as an award from the Ohio Supercomputer Center to M.B.S. Funding was provided in part by the Department of Energy’s Genome Sciences Program Soil Microbiome Scientific Focus Area award (no. SCW1632) to Lawrence Livermore National Laboratory, NSF Biological Oceanography awards (OCE no. 1536989 and OCE no. 1756314), and a Gordon and Betty Moore Foundation Investigator Award (no. 3790) to M.B.S. Funding was provided to J.R.B. by the Intramural Research Program of the National Institutes of Health (NIH) National Library of Medicine. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231 to S.R. This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I to J.H.K. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors., We thank L. Bollinger, G. Trubl and I. Tolstoy for their comments on improving the manuscript, as well as Z.-Q. You for helping push the network analytics., Biotechnology and Biological Sciences Research Council (BBSRC)

Source: Nature Biotechnology
Nature Biotechnology, Nature Publishing Group, 2019, 37 (6), pp.632-639. ⟨10.1038/s41587-019-0100-8⟩
Nature biotechnology, vol 37, iss 6
Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier; Kuhn, Jens H; Roux, Simon; Adriaenssens, Evelien M; et al.(2019). Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.. Nature biotechnology, 37(6), 632-639. doi: 10.1038/s41587-019-0100-8. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/18v6h17b

Subject Terms: Classification and taxonomy, Computational biology and bioinformatics, Software, MESH: Bacteriophages/genetics, MESH: Classification, MESH: Gene Regulatory Networks/genetics, MESH: Genome, Viral/genetics, MESH: Metagenome/genetics, MESH: Metagenomics, MESH: Phylogeny, MESH: Prokaryotic Cells/virology, MESH: Viruses/classification, MESH: Viruses/genetics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Prokaryotic Cells, Viruses, Bacteriophages, Phylogeny, Genome, Viral, Classification, Gene Regulatory Networks, Metagenome, Metagenomics, MD Multidisciplinary, Biomedical Engineering, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biotechnology, Hierarchical clustering, Biology, RefSeq, Virus classification, Bacterial virus, Computational biology, Human virome, Taxonomy (biology), Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, ARCHAEAL VIRUSES, ICTV BACTERIAL, PHAGE, GENERATION, EVOLUTIONARY, POPULATIONS, ECOGENOMICS, UPDATE, TOOL

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https://hal-pasteur.archives-ouvertes.fr/pasteur-02557180

6

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

Authors: Vincent Lombard, Nir Friedman, Edward A. Bayer, Sarah Moraïs, Bareket Dassa, Itzhak Mizrahi, Lizi Bensoussan, Bernard Henrissat

Contributors: Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Source: Environmental Microbiology
Environmental Microbiology, Wiley-Blackwell, 2017, 19 (1), pp.185-197. 〈10.1111/1462-2920.13561〉
Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2017, 19 (1), pp.185-197. ⟨10.1111/1462-2920.13561⟩
Environmental Microbiology, Wiley-Blackwell, 2017, 19 (1), pp.185-197. ⟨10.1111/1462-2920.13561⟩

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https://hal.archives-ouvertes.fr/hal-01802735

7

Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota

Authors: Romain Koszul, Théo Foutel-Rodier, Agnès Thierry, Martial Marbouty

Contributors: Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Sorbonne Université (SU)

Source: High-Density Sequencing Applications in Microbial Molecular Genetics
High-Density Sequencing Applications in Microbial Molecular Genetics, 612, pp.183-195, 2018, Methods in Enzymology, 978-0-12-815993-4. ⟨10.1016/bs.mie.2018.08.001⟩

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https://hal-pasteur.archives-ouvertes.fr/pasteur-02866616

8

Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity

Authors: Eugene V. Koonin, Mart Krupovic

Contributors: National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], EVK is supported by intramural funds of the US Department of Health and Human Services (to the National Library of Medicine).

Source: Current Opinion in Virology
Current Opinion in Virology, Elsevier, 2017, 25, pp.7-15. ⟨10.1016/j.coviro.2017.06.008⟩

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https://hal-pasteur.archives-ouvertes.fr/pasteur-01977356

9

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data

Authors: Romain Koszul, Martial Marbouty

Contributors: Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding to R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement 260822., European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011)

Source: Trends in Genetics
Trends in Genetics, Elsevier, 2015, 31 (12), pp.673-82. ⟨10.1016/j.tig.2015.10.003⟩

Subject Terms: MESH: Chromosomes, MESH: High-Throughput Screening Assays, MESH: Metagenome, [SDV]Life Sciences [q-bio], [SDV.GEN]Life Sciences [q-bio]/Genetics, Genetics, Plasmid, Biology, Genome, Metagenomics, Computational biology, DNA sequencing, DNA, chemistry.chemical_compound, chemistry, Chromosome, Chromosome conformation capture, Mobile genetic elements, Article

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https://hal-pasteur.archives-ouvertes.fr/pasteur-01419974

10

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

Authors: Jean-François Flot, Hervé Marie-Nelly, Romain Koszul

Contributors: Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding to R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement 260822. J.F.F. is supported by the European Research Council (ERC-2012-AdG 322790)., European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), European Project: 322790,EC:FP7:ERC,ERC-2012-ADG_20120314,XENOTURBELLA(2013)

Source: FEBS Letters
FEBS Letters, Wiley, 2015, 589 (20 PartA), pp.2966-74. ⟨10.1016/j.febslet.2015.04.034⟩
FEBS letters, 589 (20PartA

Subject Terms: Hi-C, Genome assembly, Haplotype phasing, 3C, Contact genomics, Metagenomics, Scaffolding, MESH: Animals, MESH: Chromosomes/physiology, MESH: Sequence Analysis, DNA, MESH: Chromosomes/ultrastructure, MESH: Cluster Analysis, MESH: Epistasis, Genetic, MESH: Gene Regulatory Networks, MESH: Genomics, MESH: Haplotypes, MESH: Humans, MESH: Metagenome, [SDV.GEN]Life Sciences [q-bio]/Genetics, Cell Biology, Genetics, Molecular Biology, Biochemistry, Structural Biology, Biophysics, Computational biology, Hybrid genome assembly, Genomics, Base pair, Comparative genomics, DNA sequencing, Genome, Biology, Sequence assembly, Evolution des espèces, Biologie moléculaire, Océanographie biologique, Systématique des espèces [zoologie], Génétique, cytogénétique

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https://hal-pasteur.archives-ouvertes.fr/pasteur-01419996

11

Immuno-microbiota cross and talk: The new paradigm of metabolic diseases

Authors: Lucile Garidou, Céline Pomié, Rémy Burcelin

Contributors: Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)

Source: Seminars in Immunology
Seminars in Immunology, Elsevier, 2012, 24 (1), pp.67-74. ⟨10.1016/j.smim.2011.11.011⟩

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https://doi.org/10.1016/j.smim.2011.11.011

12

The gut microbiota profile is associated with insulin action in humans

Authors: Eduardo García Fuentes, Matteo Serino, José Manuel Fernández-Real, Rémy Burcelin, Alex Sánchez, Maribel Queipo-Ortuño, Francisco J. Tinahones, José María Moreno-Navarrete

Contributors: Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Diabetes Endocrinology and Nutrition, Instituto de Salud Carlos III [Madrid] (ISC)-CIBER Fisiopatologia Obesidad y Nutricion, Service of Endocrinology and Nutrition, CIBER Fisiopatologia Obesidad y Nutricion-Universitario Virgen de Victoria de Malaga, Statistics Department, University of Barcelona, Institut de Recerca, Vall d'Hebron University Hospital [Barcelona], This work was partially supported by research grants from the Ministerio de Educacio'n y Ciencia (SAF2008-0273) to JMFR, from the Agence Nationale de la Recherche (ANR FLORADIP and FLORINFLAM) to RB, and from Socie'te' Francophone du Diabe'te-Glaxo Smith Kline (SFD-GSK) and the Benjamin Delessert foundation both to MS. Alex Sanchez is supported by the Ministerio de Educacio'n y Ciencia-MTM2008-0064.

Source: Acta Diabetologica
Acta Diabetologica, Springer Verlag, 2013, 50 (5), pp.753-61. ⟨10.1007/s00592-012-0410-5⟩

Subject Terms: Gut microbiota, Obesity, Metabolic diseases, Insulin action, DGGE, MESH: Adult, MESH: Case-Control Studies, MESH: Male, MESH: Metagenome, MESH: Microarray Analysis, MESH: Microbiota, MESH: Middle Aged, MESH: Obesity, MESH: Transcriptome, MESH: DNA, Bacterial, MESH: DNA, Fungal, MESH: Diet, High-Fat, MESH: Female, MESH: Gastrointestinal Tract, MESH: Humans, MESH: Insulin, MESH: Insulin Resistance, [SDV.GEN]Life Sciences [q-bio]/Genetics, digestive system, Original Article, Endocrinology, General Medicine, Endocrinology, Diabetes and Metabolism, Internal Medicine, Transcriptome, Quantitative trait locus, Genetics, Insulin, medicine.medical_treatment, medicine, Gut flora, biology.organism_classification, biology, Metagenomics, Microarray analysis techniques, Microbial DNA, Insulin resistance, medicine.disease

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PDF Full Text

13

Quality control of microbiota metagenomics by k-mer analysis

Authors: Plaza Onate, Florian, Batto, Jean-Michel, Juste, Catherine, Fadlallah, Jehane, Fougeroux, Cyrielle, Gouas, Doriane, Pons, Nicolas, Kennedy, Sean, Levenez, Florence, Dore, Joel, Dusko Ehrlich, S., Gorochov, Guy, Larsen, Martin

Contributors: MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Service d'Immunologie [CHU Pitié-Salpétrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), The study was funded by INSERM, the University Pierre et Marie Curie ËMERGENCE' program, Fondation pour l’Aide a la Recherche sur la Sclerose En Plaques (ARSEP), ARTHRITIS Fondation COURTIN and Agence nationale de la recherché (ANR)., The authors acknowledge the funding agencies and the volunteers providing samples for the study., INRA US1367 MetaGenoPolis, Service d'immunologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Source: BMC Genomics
BMC Genomics, BioMed Central, 2015, 16 (1), pp.183. ⟨10.1186/s12864-015-1406-7⟩
www.biomedcentral.com/bmcgenomics
BMC Genomics 1 (16), 183-193. (2015)
BMC Genomics, 2015, 16 (1), pp.183. ⟨10.1186/s12864-015-1406-7⟩

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https://hal.sorbonne-universite.fr/hal-01143359

14

Shedding light on microbial dark matter: a TM6 bacterium as natural endosymbiont of a free-living amoeba

Authors: Delafont, Vincent, Samba-Louaka, Ascel, Didier Bouchon, Moulin, Laurent, Hechard, Yann

Contributors: Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Ecologie, Evolution, Symbiose (EES), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Clercy-Morel, Sylvie

Source: Environmental Microbiology Reports
Environmental Microbiology Reports, Wiley, 2015, 7 (6), pp.970-8. ⟨10.1111/1758-2229.12343⟩
ResearcherID

Subject Terms: MESH: Amoeba, MESH: Bacteria, MESH: Metagenome, MESH: Metagenomics, MESH: Microbiota, MESH: Phylogeny, MESH: RNA, Ribosomal, MESH: Symbiosis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology

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https://hal.archives-ouvertes.fr/hal-01427409

15

A novel group of diverse Polinton-like viruses discovered by metagenome analysis

Authors: Sofiya Shevchenko, Vladimir V Kapitonov, Eugene V. Koonin, Mart Krupovic, Natalya Yutin

Contributors: National Institutes of Health [Bethesda] (NIH), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Center for Biotechnology Information (NCBI), NY, SS, VK and EVK were supported by intramural funds of the US Department of Health and Human Services (to the National Library of Medicine)., We thank Yuri Wolf for helpful advice on sequence assembly and analysis

Source: BMC Biology
BMC Biology, BioMed Central, 2015, 13 (95), ⟨10.1186/s12915-015-0207-4⟩

Subject Terms: Metagenomic Sequence, Major Capsid Protein, Whole Genome Shotgun, Giant Virus, Algal Genome, MESH: Biological Evolution, MESH: DNA Transposable Elements, MESH: Genome, Viral, MESH: Metagenome, MESH: Phylogeny, MESH: Viruses, [SDV]Life Sciences [q-bio], [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Cell Biology, Developmental Biology, Plant Science, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Physiology, Ecology, Evolution, Behavior and Systematics, Structural Biology, Biotechnology, Viral evolution, Gene, Sequence analysis, Transposable element, Virophage, Genome size, Virophages, Biology, Genome, Genetics, Research Article, Biochemistry, Genetics and Molecular Biology(all), Agricultural and Biological Sciences(all)

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b8ecaefccef9e6b5681460d8627c7c13
https://hal-pasteur.archives-ouvertes.fr/pasteur-01977381

16

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

Authors: Achim Quaiser, Yvan Zivanovic, David Moreira, Purificación López-García

Contributors: Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), ANR-08-GENM-0024,EVOLDEEP,Génomique évolutive et des populations de microorganismes non-cultivables de l'océan profond(2008), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)

Source: ISME Journal
ISME Journal, Nature Publishing Group, 2011, 5 (2), pp.285-304. ⟨10.1038/ismej.2010.113⟩
ISME 13, 13th International Symposium on Microbial Ecology
ISME 13, 13th International Symposium on Microbial Ecology, Aug 2010, Seattle, United States

Subject Terms: Ecology, Evolution, Behavior and Systematics, Microbiology, Plankton, Nitrosopumilus, biology.organism_classification, biology, Archaea, Ecology, Crenarchaeota, Alteromonas macleodii, Thaumarchaeota, Pelagibacter ubique, Planctomycetes, fungi, carbon cycle, sulfate reduction, carbon fixation, ammonia oxidation, anaerobic respiration, deep-sea, MESH: Archaea, MESH: Bacteria, MESH: Eukaryota, MESH: Genes, rRNA, MESH: Geologic Sediments, MESH: Metagenome, MESH: Metagenomics, MESH: Molecular Sequence Data, MESH: Oceans and Seas, MESH: Phylogeny, MESH: Plankton, MESH: Biodiversity, MESH: Enzymes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Original Article

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d8a9ee6ff2a85694c9b951245b13c3f
https://doi.org/10.1038/ismej.2010.113

17

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Authors: Simon Roux, Didier Debroas, Jeremy Tournayre, François Enault, Antoine Mahul

Contributors: Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

Source: BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2014, 15, pp.76. ⟨10.1186/1471-2105-15-76⟩
Europe PubMed Central

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::59fd5758ed5d203d1a1af0c1a8f58e72
https://hal.archives-ouvertes.fr/hal-01017832

18

Metagenome and metabolism: the tissue microbiota hypothesis

Authors: Burcelin, Rémy, Serino, Matteo, Chabo, Chantal, Garidou, Lucile, Pomié, Celine, Courtney, Michael, Amar, Jacques, Bouloumié, Anne

Contributors: Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherche-développement en biotechnologie, Prologue Biotech-Vaiomer-Labège Innopole, Médecine Interne et Hypertension Artérielle, CHU Toulouse [Toulouse]-Hôpital de Rangueil, CHU Toulouse [Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), Prologue Biotech-Labège Innopole-Vaiomer

Source: Diabetes, Obesity and Metabolism
Diabetes, Obesity and Metabolism, Wiley, 2013, 15 Suppl 3, pp.61-70. ⟨10.1111/dom.12157⟩

Subject Terms: diabetes, inflammation, gut, brain axis, obesity, tissue microbiota, MESH: Cell Communication, MESH: Animals, MESH: Host Specificity, MESH: Humans, MESH: Intestines, MESH: Metabolic Diseases, MESH: Metabolism, MESH: Metagenome, MESH: Mice, MESH: Microbiota

Access URL: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::67fcd6702e2e31021b9edfb5ee484550
https://www.hal.inserm.fr/inserm-00995650

19

La dysbiose, une nouvelle entité en médecine ?

Authors: Mathias Chamaillard, Thomas Secher, Sylvain Normand

Contributors: Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Source: médecine/sciences
médecine/sciences, EDP Sciences, 2013, 29 (6-7), pp.586-589. ⟨10.1051/medsci/2013296011⟩

Subject Terms: dysbiose, MESH: Crohn Disease, MESH: Humans, MESH: Immunity, MESH: Metagenome, MESH: Nod2 Signaling Adaptor Protein, [SDV.CAN]Life Sciences [q-bio]/Cancer, ComputingMilieux_MISCELLANEOUS, General Biochemistry, Genetics and Molecular Biology, General Medicine, Gynecology, medicine.medical_specialty, medicine, Biology, Dysbiosis, medicine.disease

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::62192fdf3f4374e3c1088c13876bd4bf
https://hal.archives-ouvertes.fr/hal-02180092

20

Diversity and catalytic potential of PAH-specific ring-hydroxylating dioxygenases from a hydrocarbon-contaminated soil

Authors: Florence Martin, Laure Malagnoux, Fabien Violet, Yves Jouanneau, Jean Jakoncic

Contributors: Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Brookhaven National Laboratory Mational Synchrotron Light Source (BNL NSLS), Brookhaven National Laboratory [Upton, NY] (BNL), U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)

Source: Applied Microbiology and Biotechnology
Applied Microbiology and Biotechnology, Springer Verlag, 2013, 97 (11), pp.5125-35. ⟨10.1007/s00253-012-4335-2⟩
Applied Microbiology and Biotechnology, 2013, 97 (11), pp.5125-35. ⟨10.1007/s00253-012-4335-2⟩

Subject Terms: MESH: Cloning, Molecular, MESH: Cluster Analysis, MESH: Phylogeny, MESH: Polycyclic Hydrocarbons, Aromatic, MESH: Sequence Analysis, DNA, MESH: Sequence Homology, MESH: Soil Microbiology, MESH: Soil Pollutants, MESH: Substrate Specificity, MESH: DNA, Bacterial, MESH: Dioxygenases, MESH: Escherichia coli, MESH: Gene Expression, MESH: Genetic Variation, MESH: Gram-Negative Bacteria, MESH: Metagenome, MESH: Molecular Sequence Data, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Applied Microbiology and Biotechnology, General Medicine, Biotechnology, Sphingomonas, biology.organism_classification, biology, Stable-isotope probing, DNA, chemistry.chemical_compound, chemistry, Biochemistry, Sequence analysis, genomic DNA, Burkholderiales, Bacteria, Soil microbiology, Microbiology

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d06ab34e0f75a3e8131d83a15092af14
https://hal.archives-ouvertes.fr/hal-01063652

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