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9 results on '"MESH: Bacteria/genetics"'

1. Prediction of the intestinal resistome by a three-dimensional structure-based method

Author

Willem van Schaik, Kevin Weiszer, Nicolas Maziers, Hervé M. Blottière, Luis Máiz, Nicolas Pons, Fernando Baquero, S. Dusko Ehrlich, Bruno Fantin, José L. Martínez, Amine Ghozlane, Julien Tap, Malbert R. C. Rogers, Pierre Leonard, Rob J. L. Willems, Anne-Sophie Alvarez, Florence Haimet, Etienne Ruppé, Sara Hernando-Amado, Victoire de Lastours, Alexandre G. de Brevern, Tiphaine Goulenok, Ingrid Wieder, Xinglin Zhang, Antoine Andremont, Trinidad Cuesta, Véronique Léjard, Jean-Michel Batto, Aline Letur, Nawal Amor, Joël Doré, Val F. Lanza, Teresa M. Coque, Florence Levenez, Irene Clares, Sean Kennedy, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biomics, Centre de Recherche et Innovation Technologique (CITECH), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Instituto Ramon y Cajal de Investigacion Sanitaria [Madrid, Spain] (IRYCIS), Universidad de Alcalá - University of Alcalá (UAH), CIBER de Epidemiología y Salud Pública (CIBERESP), Hospital Universitario Ramón y Cajal [Madrid], Service de Médecine Interne [AP-HP, CHU Beaujon], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Beaujon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire de Bactériologie [AP-HP Hôpital Bichat-Claude Bernard], AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University Medical Center [Utrecht], University of Birmingham [Birmingham], Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), King‘s College London, The project was funded in part by the European Union Seventh Framework Programme (FP7-HEALTH-2011-single-stage) under grant agreement number 282004, EvoTAR. IRYCIS authors acknowledge the European Development Regional Fund ‘A way to achieve Europe’ for co-founding the Spanish R&D National Plan 2012–2019 Work (PI15-0512), CIBER (CIBERESP, CB06/02/0053) and the Government of Madrid (InGeMICS- B2017/BMD-3691). V.F.L. was further funded by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases., The authors are grateful to the GENOTOUL (Toulouse, France), GENOUEST (Rennes, France), ABIMS (Roscoff, France), MIGALE (Jouy-en-Josas) and TGCC-GENCI (Institut Curie) calculation clusters. The authors also thank B. Perichon (Institut Pasteur, Paris, France) for providing ARD sequences from Acinetobacter baumannii, P. Siguier (CNRS, Toulouse, France) for helping the search of insertion sequences with ISfinder, J. Guglielmini (Institut Pasteur, Paris, France) for his assistance in finding conjugative elements, S. Volant (Institut Pasteur, Paris, France) for the design of the statistical model in SHAMAN, T. Jové (University of Limoges, France) for his assistance in finding integrons, M. Petitjean (IAME Research Center, Paris, France) for her assistance in bioinformatic analyses, and F. Plaza-Oñate and M. Almeida for their help with MSPs., European Project: 282004,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,EVOTAR(2011), European Commission, Instituto de Salud Carlos III, Comunidad de Madrid, European Society of Clinical Microbiology and Infectious Diseases, Kennedy, Sean, Evolution and Transfer of Antibiotic Resistance - EVOTAR - - EC:FP7:HEALTH2011-10-01 - 2015-09-30 - 282004 - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Institut Pasteur [Paris], Biocomputing Unit [Madrid], and Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP)

Subjects
ARDS, Protein Conformation, microbiome, Drug resistance, Antimicrobial resistance, Applied Microbiology and Biotechnology, MESH: Anti-Bacterial Agents/pharmacology, MESH: Intestines/microbiology, bacteria, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics, MESH: Protein Conformation, 0303 health sciences, antibiotic-resistance genes, MESH: Gastrointestinal Microbiome/genetics, tool, alignment, Anti-Bacterial Agents, 3. Good health, MESH: Bacteria/drug effects, Intestines, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Enterotype, reveals, MESH: Bacterial Proteins/chemistry, Microbiology (medical), reservoir, Immunology, MESH: Bacteria/genetics, Biology, MESH: beta-Lactamases/chemistry, MESH: Bacterial Proteins/genetics, Microbiology, beta-Lactamases, web, Bacterial genetics, 03 medical and health sciences, models, Antibiotic resistance, Bacterial Proteins, Drug Resistance, Bacterial, medicine, Microbiome, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 030304 developmental biology, 030306 microbiology, Cell Biology, medicine.disease, Gastrointestinal Microbiome, Resistome, Computational biology and bioinformatics, MESH: beta-Lactamases/genetics, MESH: Drug Resistance, Bacterial/genetics, MESH: Bacteria/classification, identification, Mobile genetic elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens., The project was funded in part by the European Union Seventh Framework Programme (FP7-HEALTH-2011-single-stage) under grant agreement number 282004, EvoTAR. IRYCIS authors acknowledge the European Development Regional Fund ‘A way to achieve Europe’ for co-founding the Spanish R&D National Plan 2012–2019 Work (PI15-0512), CIBER (CIBERESP; CB06/02/0053) and the Government of Madrid (InGeMICS- B2017/BMD-3691). V.F.L. was further funded by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases.

Published
2019

2. Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

Author

Lun Cui, Enno R. Oldewurtel, Sven van Teeffelen, Antoine Vigouroux, David Bikard, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris] (IP), Morphogénèse et Croissance microbiennes / Microbial Morphogenesis and Growth, This work was supported by the European Research Council (ERC) under the Europe Union's Horizon 2020 research and innovation program [Grant Agreement No. (677823) to DB and No. (679980) to SvT], the French Government's Investissement d'Avenir program Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR‐10‐LABX‐62‐IBEID) to SvT, DB, and AV, the Marie de Paris 'Emergence(s)' program and the Volkswagen Foundation to SvT, and the Pasteur‐Weizmann consortium to DB., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), European Project: 679980,H2020,ERC-2015-STG,RCSB(2016), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, MESH: CRISPR-Cas Systems, Cell morphology, single‐cell, MESH: RNA, Guide/genetics, chemistry.chemical_compound, Transcription (biology), RNA polymerase, Gene expression, Gene Knockdown Techniques, Guide RNA, Promoter Regions, Genetic, Quantitative Biology & Dynamical Systems, Gene knockdown, gene-expression noise, MESH: Gene Expression Regulation, Bacterial, Applied Mathematics, Articles, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Computational Theory and Mathematics, MESH: Genes, Bacterial, General Agricultural and Biological Sciences, Transcription, RNA, Guide, Kinetoplastida, Information Systems, Transcriptional Activation, gene‐expression noise, MESH: Bacteria/genetics, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, CRISPR‐dCas9, 03 medical and health sciences, MESH: Promoter Regions, Genetic, Gene, Bacteria, General Immunology and Microbiology, CRISPR-dCas9, CRISPRi, Gene Expression Regulation, Bacterial, single-cell, MESH: Gene Knockdown Techniques, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, peptidoglycan cell wall, 030104 developmental biology, chemistry, Genes, Bacterial, MESH: Transcriptional Activation, CRISPR-Cas Systems, Synthetic Biology & Biotechnology
Abstract

International audience; Over the past few years, tools that make use of the Cas9 nuclease have led to many breakthroughs, including in the control of gene expression. The catalytically dead variant of Cas9 known as dCas9 can be guided by small RNAs to block transcription of target genes, in a strategy also known as CRISPRi. Here, we reveal that the level of complementarity between the guide RNA and the target controls the rate at which RNA polymerase "kicks out" dCas9 from the target and completes transcription. We use this mechanism to precisely and robustly reduce gene expression by defined relative amounts. Alternatively, tuning repression by changing dCas9 concentration is noisy and promoter-strength dependent. We demonstrate broad applicability of this method to the study of genetic regulation and cellular physiology. First, we characterize feedback strength of a model auto-repressor. Second, we study the impact of amount variations of cell-wall synthesizing enzymes on cell morphology. Finally, we multiplex the system to obtain any combination of fractional repression of two genes.

Published
2018

3. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Author

Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Enzyme complex, MESH: Genome, Archaeal, LUCA, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, Genome, Corrections, chemistry.chemical_compound, Genome, Archaeal, MESH: Multienzyme Complexes/genetics, methanogens, Phylogeny, MESH: Phylogeny, Genetics, Carbon Monoxide, Multidisciplinary, Last universal ancestor, Carbon fixation, Acetyl-CoA, MESH: Carbon Cycle, Aldehyde Oxidoreductases, Biological Evolution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PNAS Plus, MESH: Bacteria/enzymology, Wood–Ljungdahl pathway, Wood-Ljungdahl pathway, MESH: Aldehyde Oxidoreductases/metabolism, Carbon monoxide dehydrogenase, 030106 microbiology, MESH: Bacteria/genetics, Acetate-CoA Ligase, Bacterial genome size, Biology, MESH: Biological Evolution, MESH: Aldehyde Oxidoreductases/genetics, Carbon Cycle, 03 medical and health sciences, MESH: Carbon Monoxide/metabolism, Multienzyme Complexes, MESH: Archaea/genetics, evolution, MESH: Acetate-CoA Ligase/metabolism, MESH: Multienzyme Complexes/metabolism, MESH: Archaea/enzymology, Bacteria, MESH: Acetate-CoA Ligase/genetics, Archaea, acetogens, 030104 developmental biology, chemistry, biology.protein, Genome, Bacterial
Abstract

Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.

Published
2018

4. 'Bacterial Toxins' Section in the Journal Toxins: A Fantastic Multidisciplinary Interplay between Bacterial Pathogenicity Mechanisms, Physiological Processes, Genomic Evolution, and Subsequent Development of Identification Methods, Efficient Treatment, and Prevention of Toxigenic Bacteria

Author

Michel R. Popoff, Bactéries anaérobies et Toxines, Institut Pasteur [Paris], and Institut Pasteur [Paris] (IP)

Subjects
0301 basic medicine, Identification methods, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Bacterial Toxins, MathematicsofComputing_GENERAL, MESH: Bacteria/genetics, lcsh:Medicine, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Toxicology, Bacterial Physiological Phenomena, GeneralLiterature_MISCELLANEOUS, Microbiology, 03 medical and health sciences, InformationSystems_GENERAL, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], MESH: Bacterial Toxins, Organism, ComputingMilieux_MISCELLANEOUS, Microbial toxins, Bacteria, Host (biology), MESH: Genomics, lcsh:R, fungi, MESH: Bacteria/pathogenicity, Pathogenicity, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, n/a, 030104 developmental biology, Editorial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Bacterial Physiological Phenomena
Abstract

Toxins are powerful pathogenicity factors produced by certain bacteria, fungi, animals, and plants which mediate drastic interactions of these pathogens on the organism host[...].

Published
2018

5. An integrated overview of the midgut bacterial flora composition of Phlebotomus perniciosus, a vector of zoonotic visceral leishmaniasis in the Western Mediterranean Basin

Author

Elyes Zhioua, Franck Dorkeld, Walid Barhoumi, Marcelo Ramalho-Ortigao, Saifedine Cherni, Pascale Perrin, Imed Sbissi, Maher Gtari, Denis Sereno, Ifhem Chelbi, Wael Fraihi, Ravi Durvasula, Wasfi Fares, Laboratory of Vector Ecology, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Laboratory of Microorganisms and Active Biomolecules, Université de Tunis El Manar (UTM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), The University of New Mexico [Albuquerque], Uniformed Services University of the Health Sciences (USUHS), The authors received no specific funding for this work., Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Tunis El Manar (UTM), Sereno, Denis, and Zhioua, Elyes

Subjects
0301 basic medicine, MESH: Sequence Analysis, DNA, MESH: Bacteria/genetics, Bacillus, MESH: Bacteriological Techniques, Disease Vectors, Pathology and Laboratory Medicine, phlebotome, Database and Informatics Methods, 0302 clinical medicine, MESH: Mediterranean Region, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine and Health Sciences, MESH: Animals, Bacillus Cereus, biology, Ecology, Mediterranean Region, lcsh:Public aspects of medicine, Genomics, Bacterial Pathogens, Insects, Bacillus Subtilis, Infectious Diseases, Experimental Organism Systems, Medical Microbiology, Prokaryotic Models, Seasons, Leishmania infantum, Lutzomyia, MESH: Metagenomics, Pathogens, Sequence Analysis, Symbiotic bacteria, Research Article, lcsh:Arctic medicine. Tropical medicine, Arthropoda, Phlebotominae, lcsh:RC955-962, Bioinformatics, 030231 tropical medicine, Sequence Databases, Microbial Genomics, Research and Analysis Methods, Microbiology, bassin méditerranéen, 03 medical and health sciences, leishmania, MESH: Gastrointestinal Microbiome, vecteur de maladie, parasitic diseases, Genetics, Animals, Psychodidae, Microbial Pathogens, Bacteriological Techniques, Bacteria, Diptera, fungi, Public Health, Environmental and Occupational Health, Organisms, Species diversity, Biology and Life Sciences, Midgut, lcsh:RA1-1270, Sequence Analysis, DNA, biology.organism_classification, MESH: Insect Vectors, Invertebrates, Gastrointestinal Microbiome, Insect Vectors, Sand Flies, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Species Interactions, 030104 developmental biology, Biological Databases, Phlebotomus, Species richness, MESH: Phlebotomus/microbiology, Metagenomics, Microbiome, flore bactérienne, MESH: Bacteria/classification, MESH: Seasons, MESH: Bacteria/isolation & purification
Abstract

Background The Leishmania developmental life cycle within its sand fly vector occurs exclusively in the lumen of the insect’s digestive tract in the presence of symbiotic bacteria. The composition of the gut microbiota and the factors that influence its composition are currently poorly understood. A set of factors, including the host and its environment, may influence this composition. It has been demonstrated that the insect gut microbiota influences the development of several human pathogens, such as Plasmodium falciparum. For sand flies and Leishmania, understanding the interactions between the parasite and the microbial environment of the vector midgut can provide new tools to control Leishmania transmission. Methodology/Principal findings The midguts of female Phlebotomus perniciosus from laboratory colonies or from the field were collected during the months of July, September and October 2011 and dissected. The midguts were analyzed by culture-dependent and culture-independent methods. A total of 441 and 115 cultivable isolates were assigned to 30 and 11 phylotypes from field-collected and colonized P. perniciosus, respectively. Analysis of monthly variations in microbiota composition shows a species diversity decline in October, which is to the end of the Leishmania infantum transmission period. In parallel, a compilation and a meta-analysis of all available data concerning the microbiota of two Psychodidae genera, namely Phlebotomus and Lutzomyia, was performed and compared to P. perniciosus, data obtained herein. This integrated analysis did not reveal any substantial divergences between Old and New world sand flies with regards to the midgut bacterial phyla and genera diversity. But clearly, most bacterial species (>76%) are sparsely distributed between Phlebotominae species. Conclusion/Significance Our results pinpoint the need for a more exhaustive understanding of the bacterial richness and abundance at the species level in Phlebotominae sand flies in order to capture the role of midgut bacteria during Leishmania development and transmission. The occurrence of Bacillus subtilis in P. perniciosus and at least two other sand fly species studied so far suggests that this bacterial species is a potential candidate for paratransgenic or biolological approaches for the control of sand fly populations in order to prevent Leishmania transmission., Author summary The use of conventional microbiological methods gave us the opportunity to investigate the richness of symbiotic bacteria that inhabit the gut of P. perniciosus during its main period of activity. Our results were subsequently analyzed in the framework of what has been done on sand flies microbiota in order to validate our results and to address the question of the definition of the core bacterial microbiota of sand flies. A meta-analysis on the respective gut microbiota of Old and New World sand flies shows that the majority of bacterial species is observed only in one host whereas less than 8% are shared by more than two hosts. Our results pinpoint the need for a more exhaustive understanding of the microbiota composition and dynamic in phlebotominae, with the aim to implement new biological approaches for the control of sand fly populations in order to prevent Leishmania transmission.

Published
2016

6. Quality control of microbiota metagenomics by k-mer analysis

Author

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, INRA US1367 MetaGenoPolis, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Service d'immunologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Centre d'Immunologie et de Maladies Infectieuses (CIMI), 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), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), 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 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., Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Administateur, HAL Sorbonne Université

Subjects
Sample size limits, Quality control, Sampling bias, Metagenomics, Next generation sequencing, MESH: Bacteria/genetics, MESH: Quality Control, Médecine humaine et pathologie, MESH: Metagenomics/standards, MESH: Genome, Bacterial, Sensitivity and Specificity, Feces, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Cluster Analysis, Humans, MESH: Gastrointestinal Tract/microbiology, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, MESH: Humans, Bacteria, Methodology Article, Microbiota, MESH: Feces/microbiology, MESH: Metagenome, MESH: Microbiota, MESH: Cluster Analysis, MESH: Sensitivity and Specificity, MESH: Metagenomics/methods, Gastrointestinal Tract, MESH: Bacteria/classification, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Metagenome, Human health and pathology, Genome, Bacterial, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Biotechnology
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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.

Published
2015

7. COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists

Author

Emilie Camiade, Clément Brehier, Marc Monot, Mickael Orgeur, Bruno Dupuy, Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris], Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by Institut Pasteur and Grant ERA-PTG/SAU/0002/2008 (ERA-NET PathoGenoMics) for Bruno Dupuy and Marc Monot., European Project: 109584,FCT::,ERA-PTG/2008,ERA-PTG/SAU/0002/2008(2009), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), Institut Pasteur [Paris] (IP), and Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT)

Subjects
MESH: Web Browser, Computer science, Interface (computing), MESH: Bacteria/genetics, Genomics, Web Browser, computer.software_genre, Login, Biochemistry, 03 medical and health sciences, MESH: Software, Software, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Databases, Genetic, Genetics, MESH: Computational Biology/methods, Molecular Biology, MESH: High-Throughput Nucleotide Sequencing, MESH: Databases, Genetic, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Internet, Bacteria, 030306 microbiology, business.industry, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Original Articles, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Visualization, MESH: Reproducibility of Results, MESH: Genomics/methods, MESH: Internet, Data analysis, Molecular Medicine, The Internet, Data mining, User interface, business, computer, Biotechnology
Abstract

International audience; COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/. This website is free and open to users without any login requirement.

Published
2014

8. The type II secretion system – a dynamic fiber assembly nanomachine

Author

Olivera Francetic, David A. Cisneros, Mangayarkarasi Nivaskumar, Manuel Campos, Génétique Moléculaire, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), The study of protein secretion in our team has been funded by the Institut Pasteur grant PTR339 and by the ANR grant SecPath. MC was a scholar of the French Ministry of Science and Education, MN is the recipient of the Pasteur-Paris University (PPU) International PhD program fellowship and DAC was funded by EMBO long term and Roux fellowships., We are grateful to our collaborators Michaël Nilges, Guillaume Bouvier, Peter J. Bond, Gérard Péhau-Arnaudet, Nadia Izadi-Pruneyre, Gisèle Amorim, Daniel Ladant and Gouzel Karimova for their contributions to the pseudopilus project. We are grateful to all members of the Molecular Genetics Unit for many stimulating discussions. We thank Tony Pugsley for generous support and for the critical reading of the manuscript., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Bacterial Secretion Systems, MESH: Fimbriae, Bacterial/metabolism, Pilus assembly, MESH: Cell Membrane/genetics, MESH: Protein Transport, MESH: Bacteria/genetics, MESH: Bacteria/metabolism, Biology, Flagellum, MESH: Cell Membrane/metabolism, MESH: Bacterial Proteins/genetics, Microbiology, Pilus, MESH: Bacterial Proteins/metabolism, MESH: Fimbriae, Bacterial/genetics, 03 medical and health sciences, Bacterial Proteins, Pseudopilins, Type IV pili, Secretion, Bacterial Secretion Systems, Molecular Biology, 030304 developmental biology, 0303 health sciences, Type II protein secretion, Bacteria, Type II secretion system, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030306 microbiology, Cell Membrane, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Periplasmic space, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cell biology, Protein Transport, Secretory protein, Fimbriae, Bacterial, Biogenesis
Abstract

International audience; Type II secretion systems (T2SSs) share common origins and structure with archaeal flagella (archaella) and pili, bacterial competence systems and type IV pili. All of these systems use a conserved ATP-powered machinery to assemble helical fibers that are anchored in the plasma membrane. The T2SSs assemble pseudopili, periplasmic filaments that promote extracellular secretion of folded periplasmic proteins. Comparative analysis of T2SSs and related fiber assembly nanomachines might provide important clues on their functional specificities and dynamics. This review focuses on recent developments in the study of pseudopilus structure and biogenesis, and discusses mechanistic models of pseudopilus function in protein secretion.

Published
2013

9. Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments

Author

David Halter, Florence Goulhen-Chollet, Audrey Cordi, Fabienne Séby, Christophe Pagnout, Christine Schaeffer, Philippe N. Bertin, Sebastien Gallien, Simonetta Gribaldo, Didier Montaut, Florence Arsène-Ploetze, Pascale Bauda, Alain Van Dorsselaer, Christine Carapito, Audrey Heinrich-Salmeron, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Interactions Ecotoxicologie, Biodiversité, Ecosystèmes (LIEBE), Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Ultra Traces Analyses Aquitaine (UT2A), Ultra Traces Analyses Aquitaine, Audrey Cordi was supported by grants from the French Ministry of Research and the 'Zone Atelier Moselle' (ZAM) project. Audrey Heinrich-Salmeron, David Halter and Sebastien Gallien were supported by grants from the French Ministry of Research and the Université de Strasbourg. Florence Goulhen-Chollet was supported by the Agence Nationale de la Recherche (ANR), RARE project (Reactivity of an Arsenic-Rich Ecosystem). This study was financed by the EC2CO program (Institut National des Sciences de l’Univers, CNRS) and BRG., This work was performed in the framework of the Groupement de Recherche 'Métabolisme de l’Arsenic chez les micro-organismes: de la résistance à la détoxication' (GDR2909-CNRS)., ANR-07-BLAN-0118,RARE,Reactivity of an arsenic-rich ecosystem: an integrated genomics approach(2007), Institut Pasteur [Paris], Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Geologic Sediments, Thaumarchaeota, MESH: Archaea/metabolism, MESH: Environmental Pollutants/metabolism, [SDV]Life Sciences [q-bio], MESH: Bacteria/genetics, MESH: Archaea/classification, Polymerase Chain Reaction, MESH: DNA, Archaeal/analysis, RNA, Ribosomal, 16S, MESH: Archaea/isolation & purification, MESH: Ecosystem, MESH: Geologic Sediments/microbiology, MESH: Phylogeny, Phylogeny, 0303 health sciences, biology, Ecology, Planctomycetes, MESH: Microbial Consortia/physiology, General Medicine, Biodiversity, Adaptation, Physiological, DNA, Archaeal, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Arsenic/metabolism, Environmental Pollutants, France, Proteobacteria, MESH: Archaea/genetics, MESH: Bacteria/metabolism, DNA, Bacterial, MESH: Rivers/microbiology, MESH: RNA, Ribosomal, 16S/analysis, Gene Transfer, Horizontal, Microbial Consortia, Environmental genomics, Microbiology, Mining, MESH: Biodiversity, Arsenic, 03 medical and health sciences, Rivers, Metaproteomics, MESH: DNA, Bacterial/analysis, Molecular Biology, Ecosystem, 030304 developmental biology, MESH: Proteomics, Bacteria, 030306 microbiology, Phylum, Bacteroidetes, Prokaryote, MESH: Polymerase Chain Reaction, biology.organism_classification, Archaea, MESH: Adaptation, Physiological, MESH: RNA, Ribosomal, 16S/genetics, MESH: Gene Transfer, Horizontal, MESH: DNA, Bacterial/genetics, MESH: France, Metagenomics, MESH: DNA, Archaeal/genetics, MESH: Bacteria/classification, human activities, Acidobacteria, MESH: Bacteria/isolation & purification
Abstract

International audience; Arsenic-resistant prokaryote diversity is far from being exhaustively explored. In this study, the arsenic-adapted prokaryotic community present in a moderately arsenic-contaminated site near Sainte-Marie-aux-Mines (France) was characterized, using metaproteomic and 16S rRNA-encoding gene amplification. High prokaryotic diversity was observed, with a majority of Proteobacteria, Acidobacteria and Bacter-oidetes, and a large archaeal community comprising Euryarchaeaota and Thaumarchaeota. Metaproteomic analysis revealed that Proteobacteria, Planctomycetes and Cyanobacteria are among the active bacteria in this ecosystem. Taken together, these results highlight the unsuspected high diversity of the arsenic-adapted prokaryotic community, with some phyla never having been described in highly arsenic-exposed sites.

Published
2011

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