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1. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Author

Nielsen, H.B., Almeida, M., Sierakowska Juncker, A., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D.R., Gautier, L., Pedersen, A.G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J.M., Quintanilha dos Santos, M.B., Blom, N., Borruel, N., Burgdorf, K.S., Boumezbeur, F., Casellas, F., Doré, J., Dworzynski, P., Guarner, F., Hansen, T., Hildebrand, F., Kaas, R.S., Kennedy, S., Kristiansen, K., Kultima, J.R., Leonard, P., Levenez, F., Lund, O., Moumen, B., Le Paslier, D., Pons, N., Pedersen, O., Prifti, E., Qin, J., Raes, J., Sørensen, S., Tap, J., Tims, S., Ussery, D.W., Yamada, T., Jamet, A., Mérieux, A., Cultrone, A., Torrejon, A., Quinquis, B., Brechot, C., Delorme, C., M'Rini, C., de Vos, W.M., Maguin, E., Varela, E., Guedon, E., Gwen, F., Haimet, F., Artiguenave, F., Vandemeulebrouck, G., Denariaz, G., Khaci, G., Blottière, H., Knol, J., Weissenbach, J., van Hylckama Vlieg, J.E., Torben, J., Parkhil, J., Turner, K., van de Guchte, M., Antolin, M., Rescigno, M., Kleerebezem, M., Derrien, M., Galleron, N., Sanchez, N., Grarup, N., Veiga, P., Oozeer, R., Dervyn, R., Layec, S., Bruls, T., Winogradski, Y., Zoetendal, E.G., Renault, D., Sicheritz-Ponten, Bork, P., Wang, J., Brunak, S., Ehrlich, S.D., Center for Biological Sequence Analysis, Technical University of Denmark [Lyngby] (DTU), Novo Nordisk Foundation Center for Biosustainability, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Computer Science [Baltimore], Johns Hopkins University (JHU), BGI Hong Kong Researche Institute, BGI Shenzhen, School of Bioscience and Biotechnology, Southern University of Science and Technology [Shenzhen] (SUSTech), European Molecular Biology Laboratory, US 1367 MetaGénoPolis, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-MetaGénoPolis (MGP), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-Université Paris-Saclay, Université d'Évry-Val-d'Essonne (UEVE), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Digestive System Research Unit, Vall d'Hebron University Hospital [Barcelona], Faculty of Health Sciences, University of Southern Denmark (SDU), Department of Structural Biology, Flanders Institute for Biotechnology, Department of Bioscience Engineering, Vrije Universiteit [Brussels] (VUB), 8National Food Institute - Division for Epidemiology and Microbial Genomics, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], Hagedorn Research Institute, Faculty of Health, Aarhus University [Aarhus], BGI Hong Kong research Institute, Rega Institute - Department of Microbiology and Immunology, Université Catholique de Louvain (UCL), VIB Center for the Biology of Disease, Section of Microbiology [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], Laboratory of Microbiology, Wageningen University and Research Centre [Wageningen] (WUR), Department of Biological Information, Tokyo Institute of Technology [Tokyo] (TITECH), Max-Delbrück Center for Molecular Medicine, Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, King‘s College London, Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA), European Community's Seventh Framework Programme [FP7-HEALTH-F4-2007-201052, FP7-HEALTH-2010-261376], OpenGPU FUI collaborative research projects, DGCIS, Instituto de Salud Carlos III (Spain), Ministere de la Recherche et de l'Education Nationale (France), [ANR-11-DPBS-0001], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Beijing Genomics Institute [Shenzhen] (BGI), Southern University of Science and Technology (SUSTech), MetaGenoPolis, Université Paris-Saclay-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), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Vrije Universiteit Brussel (VUB), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], Wageningen University and Research [Wageningen] (WUR), Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, European Project: 201052,EC:FP7:HEALTH,FP7-HEALTH-2007-A,METAHIT(2008), Department of Systems Biology, Center for Biological Sequence Analysis, Ctr Biol Sequence Anal, National University of Singapore (NUS), European Molecular Biology Laboratory [Heidelberg] (EMBL), Department of Mathematics and Computer Science [Odense] (IMADA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Vall d’Hebron Research Institute (VHIR), Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen = Københavns Universitet (KU), INRA US1367 MetaGenoPolis, European Molecular Biology Laboratory [Grenoble] (EMBL), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP], Center for Biological Sequence Analysis [Lyngby], Chinese Academy of Agricultural Mechanization Sciences (CCCME), 1Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, and Department of Bio-engineering Sciences

Subjects
Cellular immunity, polypeptide, [SDV]Life Sciences [q-bio], SHORT READ ALIGNMENT SEQUENCES SYSTEMS ALGORITHMS MICROBIOTA PROTEIN LIFE SETS TREE TOOL, complex metagenomic sample, Applied Microbiology and Biotechnology, Genome, Microbiologie, Databases, Genetic, genetic element, Cluster Analysis, sets, short read alignment, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, tool, metagenomic, tree, Lactococcus lactis, IL-12, Molecular Medicine, Biotechnology, life, Microbial Genomes, antigen specific immune response, Biomedical Engineering, Bioengineering, Computational biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, cellular immunity, Biology, algorithms, Microbiology, 03 medical and health sciences, Genetic variation, microbiota, Microbiome, Gene, genome, 030304 developmental biology, adjuvant activity, VLAG, 030306 microbiology, Metagenomics, WIAS, Microbial genetics, sequences, systems, protein
Abstract

Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

Published
2014
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2. Enterotypes of the human gut microbiome

Author

Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, Takuji, Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J. M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H. B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E. G., Wang, J., Guarner, F., Pedersen, O., de Vos, W. M., Brunak, S., Dor�, J., Antol匤, M., Artiguenave, F., Blottiere, H. M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K. U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., M駻ieux, A., Melo Minardi, R., M'rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S. D., Bork, P., Consortium, MetaHIT, Microbiota Interaction with Human and Animal (MIHA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Molecular Biology Laboratory [Heidelberg] (EMBL), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Center for Biological Sequence Analysis [Lyngby], Technical University of Denmark [Lyngby] (DTU), Digestive System Research Unit, Vall d'Hebron University Hospital [Barcelona], Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Centre Interlangues - Texte, Image, Langage (TIL), Université de Bourgogne (UB), Hagedorn Research Institute, Faculty of Health Sciences, University of Southern Denmark (SDU), NIZO [Ede, Netherlands], Institut National de la Recherche Agronomique (INRA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Beijing Genomics Institute [Shenzhen] (BGI), Laboratory of Microbiology, Wageningen University and Research [Wageningen] (WUR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCAMP), Novo Nordisk Foundation, International Science and Technology Cooperation Project in China [0806], Agence Nationale de la Recherche (ANR), Institute for the encouragement of Scientific Research and Innovation of Brussels (ISRIB), Fund for Scientific Research Flanders (FWO), European Project: 201052,EC:FP7:HEALTH,FP7-HEALTH-2007-A,METAHIT(2008), 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)-Université Paris-Saclay, NIZO FOOD RESEARCH (NIZO), Nizo food research, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Wageningen University and Research Centre [Wageningen] (WUR), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, intestinal microbiota, catalog, obesity, [SDV]Life Sciences [q-bio], pathways, Biodiversity, Biology, Microbiology, Article, diversity, 03 medical and health sciences, Feces, Human gut, mucin, Phylogenetics, Microbiologie, Humans, bacterial, Microbiome, genes, Phylogeny, 030304 developmental biology, VLAG, 2. Zero hunger, 0303 health sciences, metagenomics, Multidisciplinary, Bacteria, colon, 030306 microbiology, Host (biology), Ecology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Bacterial Typing Techniques, Europe, Intestines, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary biology, Metagenomics, Metagenome, Enterotype, Biological Markers, Female, Biomarkers, Human Microbiome Project
Abstract

International audience; Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

Published
2011
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5. Genome sequence of the probiotic strain Bifidobacterium animalis subsp. lactis CNCM I-2494.

Author

Chervaux C, Grimaldi C, Bolotin A, Quinquis B, Legrain-Raspaud S, van Hylckama Vlieg JE, Denariaz G, and Smokvina T

Subjects
Molecular Sequence Data, Bifidobacterium genetics, Genome, Bacterial genetics, Probiotics
Abstract

Bifidobacterium animalis subsp. lactis CNCM I-2494 is part of a commercialized fermented dairy product with documented health benefits revealed by multiple randomized placebo-controlled clinical trials. Here we report the complete genome sequence of this strain, which has a circular genome of 1,943,113 bp with 1,660 open reading frames and 4 ribosomal operons.

Published
2011
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6. Enterotypes of the human gut microbiome.

Author

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, and Bork P

Subjects
Bacteria genetics, Bacterial Typing Techniques, Biodiversity, Biomarkers analysis, Europe, Feces microbiology, Female, Humans, Male, Metagenomics, Phylogeny, Bacteria classification, Intestines microbiology, Metagenome
Abstract

Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

Published
2011
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7. Modulation of proliferation, second messenger levels, and morphotype expression of the rat intestinal epithelial cell line IEC-6 by fermented milk.

Author

Thoreux K, Senegas-Balas F, Bernard-Perrone F, Giannarelli S, Denariaz G, Bouley C, and Balas D

Subjects
Animals, Bifidobacterium metabolism, Cell Line, Cyclic AMP metabolism, DNA biosynthesis, Epithelial Cells, Epithelium metabolism, Intestinal Mucosa metabolism, Lactobacillus metabolism, Milk microbiology, Rats, Thymidine analogs & derivatives, Thymidine metabolism, Yogurt, Cell Division, Fermentation, Intestines cytology, Milk physiology, Second Messenger Systems
Abstract

Trophic effects of milk fermented with Lactobacillus helveticus, Lactobacillus paracasei ssp. paracasei, Bifidobacterium sp., or the combination of Lactobacillus bulgaricus and Streptococcus thermophilus (yogurt) were studied on the IEC-6 intestinal epithelial cell line. Incorporation of [methyl-3H]thymidine, mitochondrial dehydrogenase activities, cyclic AMP production, and differentiation of levels of the IEC-6 strain were evaluated between the 15th and 30th passage in culture. All fermented and unfermented milks enhanced trophic responses of IEC-6 cells in a dose-dependent manner. Compared with the corresponding milks, supernatant fractions were more effective in stimulating mitochondrial dehydrogenase response. Fermented milk supernatants were also more effective than the corresponding unfermented fractions. Increases in DNA synthesis and cyclic AMP confirmed the activation observed with mitochondrial dehydrogenase. Yogurt induced the more trophic response with an increased number of the more differentiated cell morphotype. Fermentation with L. casei also demonstrated an important trophic adaptation of IEC-6 cells. Milk processing by lactic acid bacteria enhanced trophic and proliferation responses of intestinal epithelial cell line IEC-6. These results suggested that IEC-6 cells could represent an accurate and easy in vitro model for testing the trophic quality of various nutrients and for an optimization of physiological digestive functions.

Published
1996
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8. NMR and EPR studies on a monoheme cytochrome c550 isolated from Bacillus halodenitrificans.

Author

Saraiva LM, Denariaz G, Liu MY, Payne WJ, Le Gall J, and Moura I

Subjects
Amino Acid Sequence, Bacillus, Cytochrome c Group genetics, Cytochrome c Group isolation & purification, Heme chemistry, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidation-Reduction, Sequence Homology, Nucleic Acid, Cytochrome c Group chemistry, Electron Spin Resonance Spectroscopy, Magnetic Resonance Spectroscopy
Abstract

A c-type monoheme ferricytochrome c550 (9.6 kDa) was isolated from cells of Bacillus halodenitrificans sp.nov., grown anaerobically as a denitrifier. The visible absorption spectrum indicates the presence of a band at 695 nm characteristic of heme-methionine coordination. The midpoint redox potential was determined at several pH values by visible spectroscopy. The redox potential at pH 7.6 is 138 mV. When studied by 1H-NMR spectroscopy as a function of pH, the spectrum shows a pH dependence with pKa values of 6.0 and 11.0. According to these pKa values, three forms designated as I, II and III can be attributed to cytochrome c550. The first pKa is probably associated with protonation of the propionate groups. The second pKa value introduces a larger effect in the 1H-NMR spectrum and is probably due to the ionisation of the axial histidine. Studies of temperature variation of the 1H-NMR spectra for both the ferrous and ferri forms of the cytochrome were performed. Heme meso protons, the heme methyl groups, the thioether protons, two protons from a propionate and the methylene protons from the axial methionine were identified in the reduced form. The heme methyl resonances of the ferri form were also assigned. EPR spectroscopy was also used to probe the ferric heme environment. A signal at gmax approximately 3.5 at pH 7.5 was observed indicating an almost axial heme environment. At higher pH values the signal at gmax approximately 3.5 converts mainly to a signal at g approximately 2.96. The pKa associated with this change is around 11.3. The N-terminal sequence of this cytochrome was determined and compared with known amino acid sequences of other cytochromes.

Published
1992
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