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1. Unveiling Crucivirus Diversity by Mining Metagenomic Data

Author: Ignacio de la Higuera, George W. Kasun, Ellis L. Torrance, Alyssa A. Pratt, Amberlee Maluenda, Jonathan Colombet, Maxime Bisseux, Viviane Ravet, Anisha Dayaram, Daisy Stainton, Simona Kraberger, Peyman Zawar-Reza, Sharyn Goldstien, James V. Briskie, Robyn White, Helen Taylor, Christopher Gomez, David G. Ainley, Jon S. Harding, Rafaela S. Fontenele, Joshua Schreck, Simone G. Ribeiro, Stephen A. Oswald, Jennifer M. Arnold, François Enault, Arvind Varsani, and Kenneth M. Stedman
Subjects: crucivirus, CRESS-DNA viruses, gene transfer, recombination, virus evolution, environmental virology, Microbiology, QR1-502
Abstract: ABSTRACT The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.
Published: 2020
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2. Discovery of High Abundances of Aster-Like Nanoparticles in Pelagic Environments: Characterization and Dynamics

Author: Jonathan Colombet, Hermine Billard, Bernard Viguès, Stéphanie Balor, Christelle Boulé, Lucie Geay, Karim Benzerara, Nicolas Menguy, Guy Ilango, Maxime Fuster, François Enault, Corinne Bardot, Véronique Gautier, Angia Sriram Pradeep Ram, and Télesphore Sime-Ngando
Subjects: pleomorphic nanoparticles, femtoplankton, femtoplanktonic diversity, aquatic ecosystems, aquatic ecology, Microbiology, QR1-502
Abstract: This study reports the discovery of Aster-Like Nanoparticles (ALNs) in pelagic environments. ALNs are pleomorphic, with three dominant morphotypes which do not fit into any previously defined environmental entities [i.e., ultramicro-prokaryotes, controversed nanobes, and non-living particles (biomimetic mineralo-organic particles, natural nanoparticles or viruses)] of similar size. Elemental composition and selected-area electron diffraction patterns suggested that the organic nature of ALNs may prevail over the possibility of crystal structures. Likewise, recorded changes in ALN numbers in the absence of cells are at odds with an affiliation to until now described viral particles. ALN abundances showed marked seasonal dynamics in the lakewater, with maximal values (up to 9.0 ± 0.5 × 107 particles·mL−1) reaching eight times those obtained for prokaryotes, and representing up to about 40% of the abundances of virus-like particles. We conclude that (i) aquatic ecosystems are reservoirs of novel, abundant, and dynamic aster-like nanoparticles, (ii) not all virus-like particles observed in aquatic systems are necessarily viruses, and (iii) there may be several types of other ultra-small particles in natural waters that are currently unknown but potentially ecologically important.
Published: 2019
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3. Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

Author: Simon Roux, Mart Krupovic, Didier Debroas, Patrick Forterre, and François Enault
Subjects: phages, viruses, metagenomics, functional potential, Biology (General), QH301-705.5
Abstract: Although the importance of viruses in natural ecosystems is widely acknowledged, the functional potential of viral communities is yet to be determined. Viral genomes are traditionally believed to carry only those genes that are directly pertinent to the viral life cycle, though this view was challenged by the discovery of metabolism genes in several phage genomes. Metagenomic approaches extended these analyses to a community scale, and several studies concluded that microbial and viral communities encompass similar functional potentials. However, these conclusions could originate from the presence of cellular DNA within viral metagenomes. We developed a computational method to estimate the proportion and origin of cellular sequences in a set of 67 published viromes. A quarter of the datasets were found to contain a substantial amount of sequences originating from cellular genomes. When considering only viromes with no cellular DNA detected, the functional potential of viral and microbial communities was found to be fundamentally different—a conclusion more consistent with the actual picture drawn from known viruses. Yet a significant number of cellular metabolism genes was still retrieved in these viromes, suggesting that the presence of auxiliary genes involved in various metabolic pathways within viral genomes is a general trend in the virosphere.
Published: 2013
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4. Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.

Author: Simon Roux, Mart Krupovic, Axel Poulet, Didier Debroas, and François Enault
Subjects: Medicine, Science
Abstract: Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Published: 2012
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5. Clouds boost microbial activity in the atmosphere

Author: Pierre Amato, Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, Jean-Luc Baray, Laurent Deguillaume, François Enault, Institut de Chimie de Clermont-Ferrand (ICCF), SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Physique (LaMP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), and ANR-17-MPGA-0013,MOBIDIC,Modeling biologically-driven processes in clouds(2017)
Subjects: [SDE]Environmental Sciences
Abstract: International audience; The atmosphere transports biological material including living microorganisms. Whereas their survival is impaired during atmospheric transport due to desiccation and UV notably, certain organisms maintain metabolic activity and interact with physicochemical processes. This has especially been studied in clouds for its potential impacts on chemical processes such as the degradation of organic compounds and the oxidant capacity. However, it is still unknown whether the functioning of airborne microorganisms in clouds is specific and differs from the rest of the atmosphere; this question was investigated here. We developed a metagenomic/metratranscriptomic approach to investigate the in-situ functioning of airborne microbial communities and decipher its environmental drivers, notably the impacts of the presence of condensed water in clouds. Aerosol and clouds samples were collected from puy de Dôme mountain summit (1465 m asl, France) using series of high flow rate impingers, into a fixative agent to preserve nucleic acids (DNA and RNA), i.e. the identity and instantaneous functional signature of organisms. A bioinformatics pipeline was developed specifically to analyze these unprecedented and complex datasets. Comparative analyses revealed that clouds are genuine oases for living microorganisms in the atmosphere: although their microbial biodiversity is similar as that during clear atmospheric situations, droplets provide shelters especially against oxidative stress, which is found to characterize the metabolic functioning of airborne microbes in dry aerosols. The presence of condensed water boosts many biological functions, and functions related with starvation toward carbon and nitrogen notably indicate increased biological needs and evidence the existence of numerous interactions with chemical processes and atmospheric biogeochemical cycles. Regarding microbial ecology, the reactivation of metabolic functions in airborne microorganisms transiting through clouds could facilitate their settlement in their new environment.
Published: 2023
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6. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Dann Turner, Andrey N. Shkoporov, Cédric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J Rodney Brister, Nina Chanisvili, Rob A. Edwards, François Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtböke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Muñoz, Jānis Rūmnieks, BL Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens, UCL - SST/ELI/ELIM - Applied Microbiology, University of the West of England [Bristol] (UWE Bristol), University College Cork (UCC), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Leicester, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of the Western Cape (UWC), Cairo University, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Guelph, Adam Mickiewicz University in Poznań (UAM), National Center for Biotechnology Information (NCBI), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Flinders Accelerator for Microbiome Exploration [Adelaide, Australia], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Novi Sad, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of the Sunshine Coast (USC), D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), University of Gdańsk (UG), Center for Biologics Evaluation and Research, U.S. Food and Drug Administration (FDA), Institute of Biochemistry and Biophysics [Warsaw] (IBB), University of Oldenburg, Pontificia Universidad Católica de Chile (UC), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Makerere University [Kampala, Ouganda] (MAK), Universidad de los Andes [Bogota] (UNIANDES), Latvian Biomedical Research and Study Center (BMC), National Institute of Cholera and Enteric Diseases, Ohio State University [Columbus] (OSU), Okayama University, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Beijing University of Chemical Technology, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship funded by the German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 Research and Innovation Program, under the Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF). Work by J.R.B. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health. R.A.E was supported by an award from the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institute of Health RC2DK116713 and an award from the Australian Research Council, DP220102915. R.L. is supported by the research grant PHAGEFORCE from the KU Leuven. C.L. is supported by the Research Foundation - Flanders (FWO Grant 12D8623N) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2051 – Project-ID 390713860. V.M. is supported by the Russian state-funded project For ICBFM SB RAS, Grant 121031300043-8. H.M.O. was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre Finland, Instruct-ERIC. M.M.P. acknowledges funding from the Sigrid Jusélius Foundation and the Academy of Finland (grant 331627). A.N.S is supported by a Wellcome Trust Research Career Development Fellowship [220646/Z/20/Z] and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No 101001684). E.M.A. gratefully acknowledges funding by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), and European Project: 101001684,ERC-2020-COG,PHAGENET(2021)
Subjects: Science & Technology, [SDV]Life Sciences [q-bio], Virology, General Medicine, Life Sciences & Biomedicine
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023
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7. Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages

Author: Eric Olo Ndela, Simon Roux, Christian Henke, Alexander Sczyrba, Télesphore Sime Ngando, Arvind Varsani, and François Enault
Subjects: Virology, Microbiology
Abstract: Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991–3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses—amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.
Published: 2022
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8. Viral DNA SIP: the isotopic composition of virions is correlated with that of the substrate used for host growth

Author: Vuong Quoc Hoang Ngo, Maximilien Sotomski, Angeline Guenne, Mahendra Mariadassou, Mart Krupovic, François Enault, and Ariane Bize
Abstract: DNA Stable Isotope Probing is emerging as a powerful tool to study host-virus interactions. Indeed, since all viruses depend on a host for virion production, a link between the isotopic compositions of hosts and the virions they produce is expected. However, stable isotope probing applied to viral DNA has never been evaluated on simple biological models. Here, this method was tested on the bacteriophage T4 and its hostEscherichia coli. To validate that E. coli cells cultivated using a substrate enriched in13C isotope were resulting on the production of 13C-labeled T4 DNA.T4 DNA buoyant density in CsCl gradient was overall higher than the values predicted by a previously established empirical model, highlighting the need to adapt this type of models when analysing modified viral DNA. Moreover, our results show a strong correlation between the proportion of13C6-D-glucose in the substrate used for host growth and the buoyant density of T4 DNA, validating the use of DNA SIP in viral ecology, to identify viruses infecting hosts with a specific metabolism.
Published: 2022
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9. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Author: Vuong Quoc Hoang Ngo, François Enault, Cédric Midoux, Mahendra Mariadassou, Olivier Chapleur, Laurent Mazéas, Valentin Loux, Théodore Bouchez, Mart Krupovic, Ariane Bize, Procédés biotechnologiques au service de l'environnement (UR PROSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE05-0011,VIRAME,Caractérisation in situ du contenu génomique de virus d'archées méthanogènes au sein de bioprocédés de fermentation de déchets organiques(2017), and ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020)
Subjects: Archaeal Viruses, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Formates, Isotopes, Methanobacterium, Viruses, Genome, Viral, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Archaea, Microbiology, Carbon, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
Published: 2022
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10. WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs.

Author: Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, and Johannes Söding
Published: 2017
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11. Annotation of bacterial genomes using improved phylogenomic profiles.

Author: François Enault, Karsten Suhre, Chantal Abergel, Olivier Poirot, and Jean-Michel Claverie
Published: 2003

12. Rainfalls sprinkle cloud bacterial diversity while scavenging biomass

Author: Florent Rossi, Jean-Luc Baray, Raphaëlle Péguilhan, Laurent Deguillaume, Pierre Amato, Ludovic Besaury, François Enault, Laboratoire de Météorologie Physique (LaMP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Clermont-Ferrand (ICCF), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), and ANR-17-MPGA-0013,MOBIDIC,Modeling biologically-driven processes in clouds(2017)
Subjects: 010504 meteorology & atmospheric sciences, Biodiversity, Precipitation, Bioaerosol dispersal, Biology, Atmospheric sciences, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, complex mixtures, 03 medical and health sciences, Ecosystem, Biomass, Scavenging, 030304 developmental biology, 0105 earth and related environmental sciences, 2. Zero hunger, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Biomass (ecology), Ecology, Bacteria, Atmosphere, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Vegetation, 15. Life on land, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Epiphytic bacteria, Species richness, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Cloud
Abstract: Bacteria circulate in the atmosphere, through clouds and precipitation to surface ecosystems. Here, we conducted a coordinated study of bacteria assemblages in clouds and precipitation at two sites distant of ∼800 m in elevation in a rural vegetated area around puy de Dôme Mountain, France, and analysed them in regard to meteorological, chemical and air masses’ history data. In both clouds and precipitation, bacteria generally associated with vegetation or soil dominated. Elevated ATP-to-cell ratio in clouds compared with precipitation suggested a higher proportion of viable cells and/or specific biological processes. The increase of bacterial cell concentration from clouds to precipitation indicated strong below-cloud scavenging. Using ions as tracers, we derive that 0.2 to 25.5% of the 1.1 × 107 to 6.6 × 108 bacteria cell/m2/h1 deposited with precipitation originated from the source clouds. Yet, the relative species richness decreased with the proportion of inputs from clouds, pointing them as sources of distant microbial diversity. Biodiversity profiles, thus, differed between clouds and precipitation in relation with distant/local influencing sources, and potentially with bacterial phenotypic traits. Notably Undibacterium, Bacillus and Staphylococcus were more represented in clouds, while epiphytic bacteria such as Massilia, Sphingomonas, Rhodococcus and Pseudomonas were enriched in precipitation.
Published: 2021
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13. Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis.

Author: François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, and Jean-Michel Claverie
Published: 2004
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14. Unveiling Crucivirus Diversity by Mining Metagenomic Data

Author: Simona Kraberger, Alyssa A. Pratt, Jennifer M. Arnold, Anisha Dayaram, Kenneth M. Stedman, James V. Briskie, Amberlee Maluenda, François Enault, Maxime Bisseux, George W. Kasun, Simone G. Ribeiro, Peyman Zawar-Reza, Robyn White, Stephen A. Oswald, Viviane Ravet, David G. Ainley, Jon S. Harding, Ellis L. Torrance, Ignacio de la Higuera, Arvind Varsani, Helen R. Taylor, Joshua Schreck, Sharyn J. Goldstien, Jonathan Colombet, Christopher Gomez, Rafaela S. Fontenele, Daisy Stainton, 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), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), IGNACIO DE LA HIGUERA, PORTLAND STATE UNIVERSITUY, USA, GEORGE W. KASUN, PORTLAND STATE UNIVERSITY, USA, ELLIS L. TORRANCE, PORTLAND STATE UNIVERSITY, USA, ALYSSA A. PRATT, PORTLAND STATE UNIVERSITY, USA, AMBERLEE MALUENDA, PORTLAND STATE UNIVERSITY, USA, JONATHAN COLOMBET, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, MAXIME BISSEUX, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, VIVIANE RAVET, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, ANISHA DAYARAM, CHARITÉ-UNIVERSITÄTSMEDIZIN, GERMANY, DAISY STAINTON, UNIVERSITY OF ARKANSAS SYSTEM, USA, SIMONA KRABERGER, ARIZONA STATE UNIVERSITY, USA, PEYMAN SAWAR-REZA, UNIVERSITY OF CANTERBURY, NEW ZEALAND, SHARYN GOLDSTIEN, UNIVERSITY OF CANTERBURY, NEW ZEALAND, JAMES V. BRISKIE, UNIVERSITY OF CANTERBURY, NEW ZEALAND, ROBYN WHITE, UNIVERSITY OF CANTERBURY, NEW ZEALAND, HELEN TAYLOR, UNIVERSITY OF OTAGO, NEW ZEALAND, CHRISTOPHER GOMEZ, KOBE UNIVERSITY, JAPAN, DAVID G. AINLEY, HT HARVEY AND AZZOCIATES, USA, JON S. HARDING, UNIVERSITY OF CANTERBURY, NEW ZEALAND, RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, JOSHUA SCHRECK, ARIZONA STATE UNIVERSITY, USA, SIMONE DA GRACA RIBEIRO, Cenargen, STEPHEN A. OSWALD, PENNSYLVANIA STATE UNIVERSITY, USA, JENNIFER M. ARNOLD, PENNSYLVANIA STATE UNIVERSITY, USA, FRANÇOIS ENAULT, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA, and KENNETH M. STEDMAN, PORTLAND STATE UNIVERSITY, USA.
Subjects: environmental virology, [SDV]Life Sciences [q-bio], viruses, Protein domain, Sequence assembly, Genome, Viral, Ecological and Evolutionary Science, Computational biology, Genetic recombination, Genome, Microbiology, crucivirus, 03 medical and health sciences, chemistry.chemical_compound, Tombusviridae, Virology, Data Mining, RNA Viruses, gene transfer, Gene transfer, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, virus evolution, 0303 health sciences, biology, 030306 microbiology, DNA Viruses, Crucivirus, RNA, Environmental virology, biology.organism_classification, Virus evolution, recombination, Recombination, QR1-502, CRESS-DNA viruses, chemistry, Evolutionary biology, Viral evolution, Horizontal gene transfer, Metagenome, Capsid Proteins, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], DNA, Research Article
Abstract: Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability., The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.
Published: 2020
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15. Hundreds of viral families in the healthy infant gut

Author: Anders Pedersen, Morten Arendt Rasmussen, Jakob Stokholm, Jonathan Thorsen, Gisle Vestergaard, Josue Castro-Meija, Sylvain Moineau, Moïra B. Dion, François Enault, Romain Sausset, Ling Deng, Fie Olsen Romme, Marie-Agnès Petit, Eric Olo Ndela, Dennis Sandris Nielsen, Søren J. Sørensen, Tamsin Redgwell, Shiraz A. Shah, Yichang Zhang, Mathis Hjort Hjelmsø, Ronalds Silins, and Hans Bisgaard
Subjects: Genetics, Bacteriophage, biology, viruses, Clostridiales, Virulence, Human virome, biology.organism_classification, Clade, Feces, CRISPR Spacers, Bifidobacterium
Abstract: The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic inflammatory diseases later in life. Bacteriophages (phages) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. We uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clades. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers, including those in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 Caudoviricetes families, including 32 families that were found to be virulent, while 117 were temperate. Virulent phage families were more abundant but temperate ones were more diverse and widespread. Together, the viral families found in this study represent a major expansion of existing bacteriophage taxonomy.
Published: 2021
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16. Hundreds of viral families in the healthy infant gut

Author: Yichang Zhang, Fie Olsen Romme, Marie-Agnès Petit, Sylvain Moineau, Ronalds Silins, Anders Pedersen, Gisle Vestergaard, Dennis Sandris Nielsen, Jonathan Thorsen, Ling Deng, Romain Sausset, François Enault, Josué L. Castro-Mejía, Moïra B. Dion, Shiraz A. Shah, Morten Arendt Rasmussen, Mathis Hjemlsø, Hans Bisgaard, Jakob Stokholm, Eric Olo Ndela, Søren J. Sørensen, and Tamsin Redgwell
Subjects: Genetics, Bacteriophage, Temperateness, Homogeneous, viruses, Clostridiales, Virulence, Human virome, Biology, biology.organism_classification, CRISPR Spacers, Feces
Abstract: The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic inflammatory diseases later in life. Bacteriophages (phages) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. We uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clades. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers, including those in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 Caudoviricetes families, including 32 families that were found to be virulent, while 117 were temperate. Virulent phage families were more abundant but temperate ones were more diverse and widespread. Together, the viral families found in this study represent a major expansion of existing bacteriophage taxonomy.
Published: 2021
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17. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author: Jakub Barylski, Hanna M. Oksanen, Johannes Wittmann, Annika Gillis, Peter Simmonds, Evelien M. Adriaenssens, Bas E. Dutilh, Robert Edwards, Petar Knezevic, Jochen Klumpp, Andrew M. Kropinski, Matthew B. Sullivan, Jens H. Kuhn, J. Rodney Brister, Rob Lavigne, Margo B.P. Schuller, François Enault, Pakorn Aiewsakun, Igor Tolstoy, Ho Bin Jang, Mart Krupovic, UCL - SST/ELI/ELIM - Applied Microbiology, Adam Mickiewicz University in Poznań (UAM), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], San Diego State University (SDSU), Université Catholique de Louvain = Catholic University of Louvain (UCL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of Novi Sad, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Ohio State University [Columbus] (OSU), University of Oxford, Mahidol University [Bangkok], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), University of Guelph, University of Liverpool, This work was supported by the National Science Centre, Poland (2016/23/D/NZ2/00435) to J.B., the Netherlands Organization for Scientific Research (NWO) (Vidi 864.14.004) to B.E.D. (MBPS and BED), the US National Science Foundation (DUE-132809 and MCB-1330800) to R.A.E., the University of Helsinki and Academy of Finland funding for Instruct-FI to H.M.O., the Chargé de Recherches fellowship from the National Fund for Scientific Research, FNRS, Belgium to A.G., the EUed Horizon 2020 Framework Programme for Research and Innovation, ‘Virus-X’ (685778) to F.E., the Gordon and Betty Moore Foundation Investigator Award (GBMF#3790) to M.B.S., the Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) (Contract number HHSN272200700016I) to J.H.K., the GOA grant ‘Phage Biosystems’ of the KULeuven to R.L. the Intramural Research Program of the NIH, National Library of Medicine to J.R.B. and I.T., and by the Biotechnology and Biological Sciences Research Council Institute Strategic Programme in Gut Microbes and Health BB/R012490/1 and its constituent project BBS/E/F/000PR10353 to E.M.A. 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., European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Institut Pasteur [Paris], University of Helsinki, and University of Oxford [Oxford]
Subjects: 0301 basic medicine, Evolution, viruses, 030106 microbiology, BACTERIOPHAGES, Caudovirales, Herelleviridae, phylogenetics, phylogenomics, spounavirus, virus classification, virus taxonomy, Myoviridae, Genome, Viral, SOFTWARE, CLASSIFICATION, Siphoviridae, 03 medical and health sciences, Podoviridae, Behavior and Systematics, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Genetics, ALGORITHM, Phylogeny, Ecology, Evolution, Behavior and Systematics, Virus classification, 11832 Microbiology and virology, SERVER, Evolutionary Biology, Science & Technology, Ecology, biology, Archaeal Viruses, Classification, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Bacillus Phage, ORTHOLOGOUS GROUPS, 030104 developmental biology, Evolutionary biology, ICTV BACTERIAL, UPDATE, Spounavirinae, Life Sciences & Biomedicine, GENOMICS, Regular Articles
Abstract: Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order., Systematic Biology, 69 (1), ISSN:1063-5157, ISSN:1076-836X
Published: 2019
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18. PHROG: families of prokaryotic virus proteins clustered using remote homology

Author: Rubén Enrique Pérez Bucio, Julien Lossouarn, Eric Olo Ndela, Clovis Galiez, François Enault, Robin Mom, Marie-Agnès Petit, Paul Terzian, Ariane Toussaint, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Université libre de Bruxelles (ULB), H2020 European Research Council685778INRAE, Statistique pour le Vivant et l’Homme (SVH), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut de Biologie et de Médecine Moléculaires [Gosselies] (ULB/IBMM), Faculté des Sciences [Bruxelles] (ULB), and Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB)
Subjects: AcademicSubjects/SCI01140, AcademicSubjects/SCI01060, Protein family, Viral protein, Ecology (disciplines), AcademicSubjects/SCI00030, Standard Article, Computational biology, Biology, AcademicSubjects/SCI01180, medicine.disease_cause, 03 medical and health sciences, Annotation, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Homology (anthropology), Cluster analysis, 030304 developmental biology, Sequence (medicine), 0303 health sciences, prokaryotic virus proteins, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], MOBILE GENETIC ELEMENTS, 030302 biochemistry & molecular biology, homology, Classification, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, AcademicSubjects/SCI00980, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], PHROG, Reference genome
Abstract: Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number of different protein families encountered and in the sequence heterogeneity of each protein family. The recent increase in sequenced viral genomes constitutes a great opportunity to gain new insights into this diversity and consequently urges the development of annotation resources to help functional and comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), a library of viral protein families generated using a new clustering approach based on remote homology detection by HMM profile-profile comparisons. Considering 17 473 reference (pro)viruses of prokaryotes, 868 340 of the total 938 864 proteins were grouped into 38 880 clusters that proved to be a 2-fold deeper clustering than using a classical strategy based on BLAST-like similarity searches, and yet to remain homogeneous. Manual inspection of similarities to various reference sequence databases led to the annotation of 5108 clusters (containing 50.6 % of the total protein dataset) with 705 different annotation terms, included in 9 functional categories, specifically designed for viruses. Hopefully, PHROG will be a useful tool to better annotate future prokaryotic viral sequences thus helping the scientific community to better understand the evolution and ecology of these entities.
Published: 2021
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19. Going to extremes – a metagenomic journey into the dark matter of life

Author: Alexandra Helleux, Håkon Dahle, Alexander Sczyrba, Karolina Kwiatkowska-Semrau, Anders Svensson, Ruoshi Zhang, Paul Terzian, Olesia Werbowy, Edda Olgudóttir, Gudmundur O. Hreggvidsson, Jonathan Vincent, Andrius Jasilionis, David Prangishvili, Thibaud Mas, Ehmke Pohl, Javier A. Linares-Pastén, Tobias Lutterman, Olafur H. Fridjonsson, Agata Jurczak-Kurek, Martin Steinegger, Arnthor Aevarsson, Justine Vanhalst, Mart Krupovic, Elisabet E. Gudmundsdottir, Sigurlaug Skirnisdottir, Milot Mirdita, Tadeusz Kaczorowski, Monika Szadkowska, Joanna Lange, Magdalena Plotka, Hildegard Watzlawick, François Enault, Magdalena Cichowicz-Cieślak, Sigmar K. Stefansson, Björn Walse, Jessica Louise Ray, Steffen A Lorentsen, Jörn Kalinowski, Slawomir Dabrowski, Josefin Ahlqvist, William Merre, Eric Olo Ndela, Lei Wang, Salam Al-Karadaghi, Sebastian Dorawa, Martin Welin, Francine Perler, Cathrine Pedersen, Tara Róbertsdóttir, Stefanie Freitag-Pohl, Anna-Karina Kaczorowska, Ruth-Anne Sandaa, Jérémy Courtin, Ilmur Jónsdóttir, Ewa Wons, Bjorn T. Adalsteinsson, Úlfur Áugúst Átlasson, Birkir Reynisson, Katrine Stange Overå, Christian Henke, Maria Håkansson, Julien Lebrat, Annika Jochheim, Mathilde Tourigny, Bas Vroling, Ying Liu, Eirin Glomsaker, Olav Lanes, Sigrídur Hjörleifdóttir, Sólveig K Pétursdóttir, Lukasz P. Kozlowski, Bernd Striberny, David Brandt, Agnieszka Morzywolek, Mickael Guérin, Julia Dusaucy, Ida Helene Steen, Clovis Galiez, Sigurd E Gundesø, J. Altenbuchner, Lilja Björk Jónsdóttir, Jørn Remi Henriksen, Katy A. S. Cornish, Tom van den Bergh, Eva Nordberg Karlsson, Johannes Söding, Hördur Gudmundsson, Hasan Arsin, Anita-Elin Fedøy, Emma J Tarrant, Samia Djeffane, Terese Solstad, Matis ohf [Reykjavík], University of Gdańsk (UG), Lund University [Lund], SARomics Biostructures [Lund, Sweden], Universität Stuttgart [Stuttgart], University of Bergen (UiB), Universität Bielefeld = Bielefeld University, Durham University, A&A Biotechnology [Gdansk, Poland], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Max-Planck-Institut für Biophysikalische Chemie - Max Planck Institute for Biophysical Chemistry [Göttingen], Max-Planck-Gesellschaft, ArcticZymes Technologies [Tromsø, Norway], University of Iceland [Reykjavik], University of Warsaw (UW), Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris] (IP), Bio-Prodict [Nijmegen The Netherlands], Perls of Wisdom Biotech Consulting [Brookline, MA], NORCE Norwegian Research Center, University of Stuttgart, Funding was provided by the Europan Union's Horizon 2020 Research and Innovation Programme Virus-X project: Viral Metagenomics for Innovation Value (grant no. 685778). This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B)., and European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016)
Subjects: Engineering, Exploit, archaea, bioprospecting, Genome, Viral, virus, Microbiology, Viral gene, 03 medical and health sciences, Viral Proteins, Hydrothermal Vents, Databases, Genetic, Genetics, Functional studies, Molecular Biology, 030304 developmental biology, virosphere, 0303 health sciences, Bioprospecting, metagenomics, 030306 microbiology, business.industry, Virome, Scale (chemistry), Computational Biology, Data science, Europe, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metagenomics, Viruses, Ecosystem dynamics, business, thermophiles
Abstract: The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life. © The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.
Published: 2021
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20. Assemblages of anoxygenic phototrophic bacteria in tank bromeliads exhibit a host‐specific signature

Author: Anne‐hélène Le Jeune, Régis Céréghino, Christian Jeanthon, François Enault, Corinne Bardot, Anne-Catherine Lehours, Vincent Darbot, Antoine Vergne, Jean-François Carrias, Eric Giraud, Bruno Corbara, Isabelle Mary, Céline Leroy, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)
Subjects: Assembly rules, [SDV]Life Sciences [q-bio], Plant Science, 03 medical and health sciences, Nitrogen fixation, Dominance (ecology), Plant–bacteria interactions, Ecology, Evolution, Behavior and Systematics, Phylogenetic analyses, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Ecology, biology, Phototroph, 030306 microbiology, Illumina sequencing, 15. Life on land, biology.organism_classification, Anoxygenic photosynthesis, Rhodobacterales, Burkholderiales, [SDE]Environmental Sciences, Biological dispersal, Evolutionary ecology
Abstract: International audience; Anoxygenic phototrophic bacteria (APB) are a very significant metabolic functional group in the phytotelmata of tank-forming Bromeliaceae plants. Considering the close relationships existing between the bromeliad and its tank microbiota, the dominance of APB raises the question of their role in the ecology and evolution of these plants. Here, using pufM gene sequencing for taxonomic profiling, we investigated the structure of APB communities in the tanks of five bromeliad species exhibiting different habitat characteristics (i.e. physicochemical factors associated with the host), and occurring in different localities of French Guiana. We found that APB assemblages were specific to plant species and were less dependent on location or on bromeliad habitat characteristics. This convergence suggests that the identity of the bromeliad species per se is more important than habitat filtering or dispersal to control specific assembly rules for APB. The pufM OTUs were affiliated with five orders of Alpha- and Beta-proteobacteria (Rhodobacterales, Sphingomonadales, Rhizobiales, Burkholderiales and Rhodospirillales), and we assume that they may be major components of the core microbiota of plant-held waters. Our findings also revealed that up to 79% of the sequences were affiliated with APB clades possessing nitrogen-fixing genes suggesting that this metabolic capability is widespread within the APB community inhabiting tank bromeliads. We hypothesized that bromeliads may benefit nutritionally from associations with free-living APB capable to fix atmospheric nitrogen. Synthesis. Understanding the dominance of APB in tank bromeliads and determining whether a potential interplay exists between these partners is an intriguing aspect of possible mutualistic and coevolving interactions between the two existing forms of chlorophototrophy (i.e. bacteriochlorophyll-based anoxygenic and chlorophyll-based oxygenic phototrophy). In the present study, we found that bromeliad species was the main factor that explained variance in APB community composition. These findings suggest that APB and tank bromeliads may have a close, mutualistic relationship and we hypothesize according to our genomic analyses that APB may promote the bromeliad growth by provisioning essential nutrients like nitrogen.
Published: 2021
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21. Author response for 'Assemblages of anoxygenic phototrophic bacteria in tank bromeliads exhibit a host‐specific signature'

Author: Jean-François Carrias, Anne-Hélène Le Jeune, Régis Céréghino, Eric Giraud, Corinne Bardot, Christian Jeanthon, François Enault, Bruno Corbara, Céline Leroy, Isabelle Mary, Vincent Darbot, Anne-Catherine Lehours, and Antoine Vergne
Subjects: Phototroph, biology, Ecology, biology.organism_classification, Signature (topology), Anoxygenic photosynthesis, Host specific, Bacteria
Published: 2021
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22. Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes.

Author: François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, and Jean-Michel Claverie
Published: 2003
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23. Metagenomics applied to environmental viral communities

Author: Simon, Roux, Didier, Debroas, and François, Enault
Abstract: Viruses are the most abundant biological entities observed in environmental samples. They display an extraordinary morphological and genetic richness. In addition to their pathogenicity, viruses are now considered as of major influence on biogeochemical cycles, microorganisms' population regulation and more generally on the evolution of cellular genomes throughout the history of life. Viral metagenomics, i.e. the random sequencing of encapsidated nucleic acids in samples, has provided important new insights into viral diversity. These data reveals an overwhelming genetic diversity in the biosphere's viral communities sampled so far, especially in marine environments. Generally, the type of biome or environmental niche from which samples were obtained seems to be the main determinant of its composition. In addition, virome sequences obtained are generally quite distant from the reference sequences available in databases. This fact leads to the inescapable conclusion that nearly all of the virosphere's vast population is currently unknown to science, and emphasizes the need for pushing efforts toward surveying and characterizing the viral diversity.
Published: 2020

24. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author: Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. 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 no. DE-AC02-05CH11231. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
Subjects: [SDV]Life Sciences [q-bio], Microbiología, 2.2 Factors relating to physical environment, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, Databases, Genetic, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], phage, Viral, 0303 health sciences, Genetic Databases, Environmental microbiology, pipeline, Genome project, dynamics, Genomics, annotation, Viruses, Molecular Medicine, tacomony, Infection, Genetic databases, Biotechnology, Virus Cultivation, In silico, Biomedical Engineering, Phage biology, Bioengineering, Computational biology, Genome, Viral, Biology, Virus, dna viruses, Article, Uncultivated virus genomes, Databases, 03 medical and health sciences, Annotation, Genetic, Virology, MD Multidisciplinary, Genetics, 030304 developmental biology, Human Genome, Biological classification, commitee, prediction, Metagenomics, Minimum Information about any (x) Sequence (MIxS), 030217 neurology & neurosurgery, discovery
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156
Published: 2018
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25. Metavir: a web server dedicated to virome analysis.

Author: Simon Roux, Michaël Faubladier, Antoine Mahul, Nils Paulhe, Aurélien Bernard, Didier Debroas, and François Enault
Published: 2011
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26. Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.

Author: Simon Roux, Jeremy Tournayre, Antoine Mahul, Didier Debroas, and François Enault
Published: 2014
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27. Discovery of High Abundances of Aster-Like Nanoparticles in Pelagic Environments: Characterization and Dynamics

Author: Bernard Viguès, Télesphore Sime-Ngando, Angia Sriram Pradeep Ram, Lucie Geay, Nicolas Menguy, Guy Ilango, Karim Benzerara, Corinne Bardot, Christelle Boulé, Hermine Billard, Maxime Fuster, Jonathan Colombet, François Enault, Stephanie Balor, Véronique Gautier, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), FE was supported by the EUed Horizon 2020 Framework Programme for Research and Innovation (Virus-X, project no. 685778). This study is a contribution to the C NO LIMIT project funded by the Interdisciplinary Mission of the French National Center of Scientific Research (CNRS) Program X-life, 2018 edition. Funding for sampling at Halong Bay was obtained through the French-Vietnamese Hubert Curien Partnership (Contract No. 23971TK) and the Ministry of Science and Technology of Vietnam (Contract No. 46/2012/HD-NDT)., Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
Subjects: Microbiology (medical), pleomorphic nanoparticles, lcsh:QR1-502, Nanoparticle, Microbiology, lcsh:Microbiology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, aquatic ecology, femtoplankton, femtoplanktonic diversity, 14. Life underwater, Aster (genus), Original Research, 030304 developmental biology, aquatic ecosystems, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Elemental composition, biology, 030306 microbiology, Chemistry, Natural water, Aquatic ecosystem, Pelagic zone, biology.organism_classification, Characterization (materials science), Environmental chemistry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; This study reports the discovery of Aster-Like Nanoparticles (ALNs) in pelagic environments. ALNs are pleomorphic, with three dominant morphotypes which do not fit into any previously defined environmental entities [i.e., ultramicro-prokaryotes, controversed nanobes, and non-living particles (biomimetic mineralo-organic particles, natural nanoparticles or viruses)] of similar size. Elemental composition and selected-area electron diffraction patterns suggested that the organic nature of ALNs may prevail over the possibility of crystal structures. Likewise, recorded changes in ALN numbers in the absence of cells are at odds with an affiliation to until now described viral particles. ALN abundances showed marked seasonal dynamics in the lakewater, with maximal values (up to 9.0 ± 0.5 × 10 7 particles·mL −1) reaching eight times those obtained for prokaryotes, and representing up to about 40% of the abundances of virus-like particles. We conclude that (i) aquatic ecosystems are reservoirs of novel, abundant, and dynamic aster-like nanoparticles, (ii) not all virus-like particles observed in aquatic systems are necessarily viruses, and (iii) there may be several types of other ultra-small particles in natural waters that are currently unknown but potentially ecologically important.
Published: 2019
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28. Alvira: comparative genomics of viral strains.

Author: François Enault, Romain Fremez, Eric Baranowski, and Thomas Faraut
Published: 2007
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29. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting

Author: David Robertson, Mark P. Zwart, Bas E. Dutilh, Dino P. McMahon, François Enault, Brett E. Pickett, Ksenia Arkhipova, Philippe Lemey, Alexander Schönhuth, Anne Kupczok, Arthur Gruber, Bashar Ibrahim, Manja Marz, Richard H. Scheuermann, Susana Posada-Céspedes, Arno C. Andeweg, Eugene V. Koonin, Alexandra Zhernakova, Alice C. McHardy, Pediatric Surgery, Virology, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Erasmus University Medical Center [Rotterdam] (Erasmus MC), European Virus Bioinformatics Center [Jena], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of São Paulo (USP), National Center for Biotechnology Information (NCBI), Kiel University, Free University of Berlin (FU), BAM Federal Institute for Materials Research and Testing, Federal Institute for Materials Research and Testing - Bundesanstalt für Materialforschung und -prüfung (BAM), J. Craig Venter Institute, University of Edinburgh, University Medical Center Groningen [Groningen] (UMCG), Netherlands Institute of Ecology (NIOO-KNAW), Life Sciences [Amsterdam] (MAC4), Centrum Wiskunde & Informatica (CWI), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Universitätsklinikum Friedrich-Schiller-University (FSU), Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Leibniz Association, Université de Lausanne = University of Lausanne (UNIL), Universidade de São Paulo = University of São Paulo (USP), Sub Bioinformatics, Theoretical Biology and Bioinformatics, Microbial Ecology (ME), BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany., Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Translational Immunology Groningen (TRIGR)
Subjects: 0301 basic medicine, Societies, Scientific, DYNAMICS, PREDICTION, Best practice, Ecology (disciplines), Genomic data, [SDV]Life Sciences [q-bio], Research Support, Bioinformatics, viruses, software, virology, bioinformatics, METAGENOMICS, PLOTS, 03 medical and health sciences, Political science, ddc:6, Humans, Center (algebra and category theory), ddc:610, Non-U.S. Gov't, Congresses, Ecology, SEQUENCES, Research Support, Non-U.S. Gov't, article, DNA Viruses, Computational Biology, Conference Report, Genomics, Congresses as Topic, Research findings, Virology, EVOLUTION, 3. Good health, 030104 developmental biology, Infectious Diseases, international, VÍRUS, GENOMIC DATA, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.
Published: 2018
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30. Taxonomy proposal: To create one (1) new family, Herelleviridae, in the order Caudovirales

Author: Jakub Barylski, François Enault, Dutilh, Bas E., Schuller, Margo B. P., Edwards, Robert A., Annika Gillis, Jochen Klumpp, Petar Knezevic, Mart Krupovic, Kuhn, Jens H., Rob Lavigne, Hanna Oksanen, Sullivan, Matthew B., Ho Bin Jang, Peter Simmonds, Pakorn Aiewsakun, Johannes Wittmann, Igor Tolstoy, Rodney Brister, J., Kropinski, Andrew M., Adriaenssens, Evelien M., Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, and Faculty of Biological and Environmental Sciences
Subjects: 1183 Plant biology, microbiology, virology
Published: 2018

31. Phydbac 'Gene Function Predictor' : a gene annotation tool based on genomic context analysis.

Author: François Enault, Karsten Suhre, and Jean-Michel Claverie
Published: 2005
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32. Analysis of metagenomic data reveals common features of halophilic viral communities across continents

Author: Jean-Christophe Auguet, Patrick Forterre, David Prangishvili, Viviane Ravet, Thierry Bouvier, Simon Roux, François Enault, Didier Debroas, Yvan Bettarel, Soizick Lucas-Staat, Télesphore Sime-Ngando, Jonathan Colombet, and Agnès Vellet
Subjects: 0301 basic medicine, Genetic diversity, biology, Ecology, biology.organism_classification, Microbiology, Halophile, 03 medical and health sciences, 030104 developmental biology, Caudovirales, Metagenomics, Genetic variation, Clade, Gene, Ecology, Evolution, Behavior and Systematics, Archaea
Abstract: Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.
Published: 2015
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33. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages

Author: Jochen Klumpp, Evelien M. Adriaenssens, Igor Tolstoy, Hanna M. Oksanen, Annika Gillis, Petar Knezevic, Bas E. Dutilh, Jens H. Kuhn, Matthew B. Sullivan, François Enault, Andrew M. Kropinski, Jakub Barylski, Margo B.P. Schuller, Rob Lavigne, Mart Krupovic, Robert Edwards, Johannes Wittmann, and J. Rodney Brister
Subjects: 0303 health sciences, Subfamily, biology, Phylogenetic tree, 030306 microbiology, Myoviridae, biology.organism_classification, Siphoviridae, 03 medical and health sciences, Podoviridae, Caudovirales, Evolutionary biology, Spounavirinae, Clade, 030304 developmental biology
Abstract: It is almost a cliché that tailed bacteriophages of the order Caudovirales are the most abundant and diverse viruses in the world. Yet, their taxonomy still consists of a single order with just three families: Myoviridae, Siphoviridae, and Podoviridae. Thousands of newly discovered phage genomes have recently challenged this morphology-based classification, revealing that tailed bacteriophages are genomically even more diverse than once thought. Here, we evaluate a range of methods for bacteriophage taxonomy by using a particularly challenging group as an example, the Bacillus phage SPO1-related viruses of the myovirid subfamily Spounavirinae. Exhaustive phylogenetic and phylogenomic analyses indicate that the spounavirins are consistent with the taxonomic rank of family and should be divided into at least five subfamilies. This work is a case study for virus genomic taxonomy and the first step in an impending massive reorganization of the tailed bacteriophage taxonomy.
Published: 2017
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34. Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

Author: Arnaud Briet, Matthew B. Sullivan, François Enault, Marie-Agnès Petit, Simon Roux, Léa Bouteille, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Technology, Drug Resistance, Genome, Viral, Biology, medicine.disease_cause, Microbiology, Genome, Viral Proteins, 03 medical and health sciences, Transduction (genetics), Antibiotic resistance, Drug Resistance, Bacterial, Escherichia coli, medicine, Bacteriophages, Human virome, Viral, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, 030306 microbiology, Bacterial conjugation, Bacterial, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Anti-Bacterial Agents, 030104 developmental biology, Metagenomics, Horizontal gene transfer, Metagenome, Original Article, Environmental Sciences
Abstract: Antibiotic resistance genes (ARG) are pervasive in gut microbiota, but it remains unclear how often ARG are transferred, particularly to pathogens. Traditionally, ARG spread is attributed to horizontal transfer mediated either by DNA transformation, bacterial conjugation or generalized transduction. However, recent viral metagenome (virome) analyses suggest that ARG are frequently carried by phages, which is inconsistent with the traditional view that phage genomes rarely encode ARG. Here we used exploratory and conservative bioinformatic strategies found in the literature to detect ARG in phage genomes, and experimentally assessed a subset of ARG predicted using exploratory thresholds. ARG abundances in 1,181 phage genomes were vastly over-estimated using exploratory thresholds (421 predicted vs 2 known), due to low similarities and matches to protein unrelated to antibiotic resistance. Consistent with this, 4 ARG predicted using exploratory thresholds were experimentally evaluated and failed to confer antibiotic resistance in Escherichia coli. Re-analysis of available human-or mouse-associated viromes for ARG and their genomic context suggested that bona fide ARG attributed to phages in viromes were previously over-estimated. These findings provide guidance for documentation of ARG in viromes, and re-assert that ARG are rarely encoded in phages.
Published: 2017
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35. Qualité des données NGS : de la séquence aux bases de données

Author: Pierre Peyret, Julie Aubert, Vincent Breton, François Enault, Line Le Gall, Denis Le Paslier, Tiphaine Martin, Guy Perriere, Eric Peyretaillade, Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Inconnu, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: base de données, [SDV]Life Sciences [q-bio], séquence, données NGS
Abstract: Qualité des données NGS : de la séquence aux bases de données
Published: 2016

36. Study of Prokaryotes and Viruses in Aquatic Ecosystems by Metagenetic and Metagenomic Approaches

Author: Didier Debroas, Mylène Hugoni, Isabelle Jouan-Dufournel, Viviane Ravet, Gisèle Bronner, Najwa Taib, François Enault, Isabelle Mary, and Simon Roux
Subjects: 0301 basic medicine, Viral metagenomics, Thaumarchaeota, Phylum, 030106 microbiology, Biology, biology.organism_classification, 03 medical and health sciences, 030104 developmental biology, Caudovirales, Metagenomics, Phylogenetics, Evolutionary biology, Human virome, Archaea
Abstract: High-throughput sequencing methods have revolutionized the study of microbial communities in ecosytems. In this chapter, we present the use of metagenetics, targeted metagenomics and viral metagenomics to depict the diversity and the role of Bacteria, Archaea and viruses in the mixolimnion of the lake Pavin. Actinobacteria dominated the bacterial community and was represented by two typical clades: acI and acIV. Focusing on this phylum, we describe its genomic properties characterized by a low GC content (42–52 %) and high substitution rates. Phylogeny based on both SSU rRNA gene and concatenated proteins showed that these clades represented different ecotypes. Archaea was a minor but active component among prokaryotes. The Thaumarchaeota Marine Group I, already known to play an important role in ammonia oxidation dominated the archaeal assemblage in surface waters but surprisingly the Miscellaneous Euryarchaeotic Group (MEG) was the most active in particular zones such as the oxycline. Finally, the analysis of viral particles by a metagenomic approach in the lake Pavin was the first study published about freshwater temperate lakes. Among aquatic datasets, genetic richness of marine viromes was higher in average than that of freshwater ones. The viral community was composed of viruses from families of double-stranded (Caudovirales) and single-stranded (Microviridae, Circoviridae, Nanoviridae) DNA viruses. The phylogeny of the complete Microviridae genomes from the Lake Pavin virome led to the description of a new group, the Pichovirinae, and new “chimeric” genomes could be assembled, challenging the established view of ancient viral evolutionary history.
Published: 2016
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37. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages

Author: Viviane Ravet, François Enault, Olivier Pereira, Simon Roux, Matthew B. Sullivan, Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, 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), Department of Ecology and Evolutionary Biology, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: Genetics, Microbiology (medical), Viral metagenomics, Phylogenetic tree, freshwater ecology, lcsh:QR1-502, Sequence assembly, Biology, biology.organism_classification, Genome, Microbiology, 6. Clean water, lcsh:Microbiology, capsid proteins, viral genomes, T4 phages, Caudovirales, Metagenomics, [SDE]Environmental Sciences, Sequence space (evolution), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Clade, Original Research
Abstract: International audience; Viral metagenomics (viromics) is a tremendous tool to reveal viral taxonomic and functional diversity across ecosystems ranging from the human gut to the world's oceans. As with microbes however, there appear vast swaths of "dark matter" yet to be documented for viruses, even among relatively well-studied viral types. Here, we use viromics to explore the "Far-T4 phages" sequence space, a neighbor clade from the well-studied T4-like phages that was first detected through PCR study in seawater and subsequently identified in freshwater lakes through 454-sequenced viromes. To advance the description of these viruses beyond this single marker gene, we explore Far-T4 genome fragments assembled from two deeply-sequenced freshwater viromes. Single gene phylogenetic trees confirm that the Far-T4 phages are divergent from the T4-like phages, genome fragments reveal largely collinear genome organizations, and both data led to the delineation of five Far-T4 clades. Three-dimensional models of major capsid proteins are consistent with a T4-like structure, and highlight a highly conserved core flanked by variable insertions. Finally, we contextualize these now better characterized Far-T4 phages by re-analyzing 196 previously published viromes. These suggest that Far-T4 are common in freshwater and seawater as only four of 82 aquatic viromes lacked Far-T4-like sequences. Variability in representation across the five newly identified clades suggests clade-specific niche differentiation may be occurring across the different biomes, though the underlying mechanism remains unidentified. While complete genome assembly from complex communities and the lack of host linkage information still bottleneck virus discovery through viromes, these findings exemplify the power of metagenomics approaches to assess the diversity, evolutionary history, and genomic characteristics of novel uncultivated phages.
Published: 2015
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38. VirSorter: mining viral signal from microbial genomic data

Author: François Enault, Matthew B. Sullivan, Bonnie L. Hurwitz, Simon Roux, Laboratoire Microorganismes : Génome et Environnement (LMGE), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)
Subjects: Viral metagenomics, Bioinformatics, lcsh:Medicine, Computational biology, Microbiology, Genome, General Biochemistry, Genetics and Molecular Biology, Bacteriophage, Transduction (genetics), Virology, Human virome, Prophage, Genetics, biology, General Neuroscience, lcsh:R, Genomics, General Medicine, crAssphage, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Virus, Single-cell amplified genome, Metagenomics, General Agricultural and Biological Sciences
Abstract: International audience; Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter's prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in "reverse" to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.
Published: 2015
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39. Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

Author: Mart Krupovic, François Enault, Daniel Vaulot, Gisèle Bronner, Simon Roux, Patrick Forterre, 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), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]
Subjects: viruses, General Physics and Astronomy, DNA, Single-Stranded, Genome, Viral, Genome, General Biochemistry, Genetics and Molecular Biology, Virus, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, RNA Viruses, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Geminiviridae, Gene, Phylogeny, 030304 developmental biology, Gene Library, Genetics, Recombination, Genetic, 0303 health sciences, Multidisciplinary, biology, 030306 microbiology, DNA Viruses, RNA virus, General Chemistry, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, DNA, Viral, Nanoviridae, Capsid Proteins, Circoviridae, Metagenomics, DNA
Abstract: Metagenomic studies have uncovered an astonishing diversity of ssDNA viruses encoding replication proteins (Reps) related to those of eukaryotic Circoviridae, Geminiviridae or Nanoviridae; however, exact evolutionary relationships among these viruses remain obscure. Recently, a unique chimeric virus (CHIV) genome, which has apparently emerged via recombination between ssRNA and ssDNA viruses, has been discovered. Here we report on the assembly of 13 new CHIV genomes recovered from various environments. Our results indicate a single event of capsid protein (CP) gene capture from an RNA virus in the history of this virus group. The domestication of the CP gene was followed by an unprecedented recurrent replacement of the Rep genes in CHIVs with distant counterparts from diverse ssDNA viruses. We suggest that parasitic and symbiotic interactions between unicellular eukaryotes were central for the emergence of CHIVs and that such turbulent evolution was primarily dictated by incongruence between the CP and Rep proteins.
Published: 2013
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40. Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes

Author: Olivier Poirot, Chantal Abergel, Jean-Michel Claverie, Karsten Suhre, François Enault, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, and Helmholtz Zentrum München = German Research Center for Environmental Health
Subjects: Computational biology, Bacterial genome size, Biology, Genome, Evolution, Molecular, Open Reading Frames, User-Computer Interface, 03 medical and health sciences, Annotation, 0302 clinical medicine, Protein sequencing, Bacterial Proteins, Sequence Analysis, Protein, Phylogenetics, Genetics, ORFS, Gene, Phylogeny, 030304 developmental biology, Internet, 0303 health sciences, Escherichia coli Proteins, Articles, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Open reading frame, Genes, Bacterial, 030220 oncology & carcinogenesis, Genome, Bacterial, Software
Abstract: International audience; Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.
Published: 2003
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41. Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads

Author: Mart Krupovic, François Enault, Didier Debroas, Axel Poulet, Simon Roux, 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), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]
Subjects: Microvirus, Genes, Viral, Microviridae, Genome, Genome Databases, Environmental Microbiology, Genome Sequencing, Genome Evolution, Conserved Sequence, Phylogeny, Genetics, 0303 health sciences, Multidisciplinary, biology, Phylogenetic tree, Genomics, Horizontal gene transfer, Medicine, Sequence Analysis, Research Article, Gene Transfer, Horizontal, Science, Sequence Databases, Genome, Viral, Viral Structure, Microbiology, Viral Evolution, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Virology, Gokushovirinae, Humans, Human virome, Biology, 030304 developmental biology, Evolutionary Biology, Base Sequence, 030306 microbiology, Computational Biology, Genetic Variation, Genomic Evolution, Sequence Analysis, DNA, Comparative Genomics, biology.organism_classification, Metagenome, Capsid Proteins, Metagenomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Published: 2012
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42. Assessing the diversity and specificity of two freshwater viral communities through metagenomics

Author: Sébastien Personnic, Simon Roux, Sébastien Theil, Jonathan Colombet, Didier Debroas, Agnès Robin, François Enault, Viviane Ravet, Télesphore Sime-Ngando, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: Ecological Metrics, Science, Fresh Water, Genome, Viral, Microbiology, 03 medical and health sciences, Caudovirales, Species Specificity, Virology, Sequence Homology, Nucleic Acid, Cluster Analysis, Human virome, Marine ecosystem, Evolutionary Systematics, 14. Life underwater, Biology, Phylogeny, 030304 developmental biology, 0303 health sciences, Evolutionary Biology, Likelihood Functions, Freshwater Viral Communities, Multidisciplinary, biology, Community, Ecology, Base Sequence, 030306 microbiology, Aquatic ecosystem, Species diversity, Computational Biology, Genetic Variation, Genomics, biology.organism_classification, 6. Clean water, Lakes, Viral Classification, Metagenomics, M40 - Écologie aquatique, Viruses, Medicine, Species richness, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Research Article
Abstract: International audience; Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.
Published: 2012
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43. Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems

Author: Simon Roux, Gisèle Bronner, François Enault, Didier Debroas, 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), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: Microbial diversity, Archaeal Proteins, RNA, Archaeal, Biology, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Microbiology, Genome, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, RNA, Ribosomal, 16S, Molecular marker, Operon, 14. Life underwater, Internal transcribed spacer, 16S rRNA, Phylogeny, DNA Primers, 030304 developmental biology, Genetics, 0303 health sciences, Bacteria, Ecology, 030306 microbiology, Biodiversity, Ribosomal RNA, 16S ribosomal RNA, Archaea, Housekeeping gene, RNA, Bacterial, chemistry, Metagenomics, Metagenome, RRNA Operon, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Microbiology
Abstract: International audience; PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.
Published: 2011
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44. Metagenomic Approach Studying the Taxonomic and Functional Diversity of the Bacterial Community in a Lacustrine Ecosystem

Author: Gisèele Bronner, Didier Debroas, Isabelle Jouan-Dufournel, Jean-François Humbert, and François Enault
Subjects: Functional diversity, Ecology, Metagenomics, Ecosystem, Biology
Published: 2011
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45. Metavir: a web server dedicated to virome analysis

Author: Michael Faubladier, Didier Debroas, François Enault, Nils Paulhe, Antoine Mahul, Aurélien Bernard, Simon Roux, 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), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and 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)
Subjects: Statistics and Probability, Web server, Computational biology, Genome, Viral, Biology, computer.software_genre, Biochemistry, MESH: Viruses, 03 medical and health sciences, Taxonomic composition, MESH: Software, Viral sequence, Human virome, MESH: Phylogeny, Molecular Biology, Phylogeny, 030304 developmental biology, Supplementary data, 0303 health sciences, Internet, 030306 microbiology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Computer Science Applications, Computational Mathematics, MESH: Internet, Computational Theory and Mathematics, Viruses, Data mining, Metagenomics, MESH: Genome, Viral, MESH: Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: Summary: Metavir is a web server dedicated to the analysis of viral metagenomes (viromes). In addition to classical approaches for analyzing metagenomes (general sequence characteristics, taxonomic composition), new tools developed specifically for viral sequence analysis make it possible to: (i) explore viral diversity through automatically constructed phylogenies for selected marker genes, (ii) estimate gene richness through rarefaction curves and (iii) perform cross-comparison against other viromes using sequence similarities. Metavir is thus unique as a platform that allows a comprehensive virome analysis. Availability: Metavir is freely available online at: http://metavir-meb.univ-bpclermont.fr Contact: simon.roux@univ-bpclermont.fr Supplementary Information: Supplementary data are available at Bioinformatics online.
Published: 2011
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46. Alvira: comparative genomics of viral strains

Author: Thomas Faraut, François Enault, Romain Fremez, Eric Baranowski, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), and ProdInra, Migration
Subjects: MESH: Sequence Analysis, DNA, [SDV]Life Sciences [q-bio], MESH: Base Sequence, Biochemistry, Genome, Viral quasispecies, User-Computer Interface, Génétique, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, Multiple sequence alignment, BIOINFORMATICS, 030302 biochemistry & molecular biology, Chromosome Mapping, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENOMIQUE, Computer Science Applications, [SDV] Life Sciences [q-bio], Computational Mathematics, Computational Theory and Mathematics, Viral genomes, Viruses, VIRUS, Graph (abstract data type), MESH: Computer Graphics, MESH: Genome, Viral, Algorithms, COMPARATIVE GENOMICS, Statistics and Probability, Multiple alignment, Molecular Sequence Data, MESH: Sequence Alignment, ComputerApplications_COMPUTERSINOTHERSYSTEMS, MESH: Algorithms, Computational biology, Genome, Viral, Biology, MESH: Viruses, 03 medical and health sciences, MESH: Software, Computer Graphics, Genomes, Molecular Biology, Alignment-free sequence analysis, 030304 developmental biology, MESH: User-Computer Interface, Comparative genomics, MESH: Molecular Sequence Data, Base Sequence, Sequence Analysis, DNA, General purpose, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Chromosome Mapping, GENOMICS, Sequence Alignment, Software
Abstract: Motivation: The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution.Availability: The Alvira software is available at: http://bioinfo.genopole-toulouse.prd.fr/AlviraContact: fenault@toulouse.inra.frSupplementary information: A tutorial is available at Alvira's homepage.
Published: 2007
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47. Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis

Author: Olivier Poirot, Chantal Abergel, Karsten Suhre, François Enault, Jean-Michel Claverie, Information génomique et structurale (IGS), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genomics, Computational biology, Bacterial genome size, Biology, Genome, 03 medical and health sciences, 0302 clinical medicine, Cog, Phylogenetics, Genetics, KEGG, ComputingMilieux_MISCELLANEOUS, Phylogeny, 030304 developmental biology, 0303 health sciences, Internet, Chromosome Mapping, Artificial Gene Fusion, Articles, Chromosomes, Bacterial, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genes, Bacterial, Pairwise comparison, 030217 neurology & neurosurgery, Genome, Bacterial, Software
Abstract: International audience; Phydbac (phylogenomic display of bacterial genes) implemented a method of phylogenomic profiling using a distance measure based on normalized BLAST scores. This method was able to increase the predictive power of phylogenomic profiling by about 25% when compared to the classical approach based on Hamming distances. Here we present a major extension of Phydbac (named here Phydbac2), that extends both the concept and the functionality of the original web-service. While phylogenomic profiles remain the central focus of Phydbac2, it now integrates chromosomal proximity and gene fusion analyses as two additional non-similarity-based indicators for inferring pairwise gene functional relationships. Moreover, all presently available (January 2004) fully sequenced bacterial genomes and those of three lower eukaryotes are now included in the profiling process, thus increasing the initial number of reference genomes (71 in Phydbac) to 150 in Phydbac2. Using the KEGG metabolic pathway database as a benchmark, we show that the predictive power of Phydbac2 is improved by 27% over the previous version. This gain is accounted for on one hand, by the increased number of reference genomes (11%) and on the other hand, as a result of including chromosomal proximity into the distance measure (16%). The expanded functionality of Phydbac2 now allows the user to query more than 50 different genomes, including at least one member of each major bacterial group, most major pathogens and potential bio-terrorism agents. The search for co-evolving genes based on consensus profiles from multiple organisms, the display of Phydbac2 profiles side by side with COG information, the inclusion of KEGG metabolic pathway maps the production of chromosomal proximity maps, and the possibility of collecting and processing results from different Phydbac queries in a common shopping cart are the main new features of Phydbac2. The Phydbac2 web server is available at http://igs-server.cnrs-mrs.fr/phydbac/.
Published: 2004
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48. Annotation of bacterial genomes using improved phylogenomic profiles

Author: Chantal Abergel, Karsten Suhre, François Enault, Olivier Poirot, Jean-Michel Claverie, Enault, François, Information génomique et structurale (IGS), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Statistics and Probability, Normalization (statistics), Proteome, Documentation, Computational biology, Bacterial genome size, Biology, computer.software_genre, Biochemistry, Evolution, Molecular, 03 medical and health sciences, Annotation, Binary form, Bacterial Proteins, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gene Expression Profiling, 030302 biochemistry & molecular biology, Chromosome Mapping, Gene Expression Regulation, Bacterial, Gene Annotation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], EcoCyc, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Pairwise comparison, Data mining, computer, Algorithms, Genome, Bacterial
Abstract: Motivation: Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al. (1999). Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between bacteria, the definition of a phylogenomic neighborhood based on continuous pairwise distances between genes and an original annotation procedure including the computation of a p-value for each functional assignment. Results: The method presented here increases the number of Ecocyc enzymes identified as being evolutionarily related by about 25% with respect to the original binary form (absent/present) method. The fraction of ‘false’ positives is shown to be smaller than 20%. Based on their phylogenomic relationships, genes of unknown function can then be automatically related to annotated genes. Each gene annotation predicted is associated with a p-value, i.e. its probability to be obtained by chance. The validity of this method was extensively tested on a large set of genes of known function using the MultiFun database. We find that 50% of 3122 function attributions that can be made at a p-value level of 10−11 correspond to the actual gene annotation. The method can be readily applied to any newly sequenced microbial genome. In contrast to earlier work on the same topic, our approach avoids the use of arbitrary cut-off values, and provides a reliability estimate of the functional predictions in form of p-values. Contact: enault@igs.cnrs-mrs.fr Keywords: phylogenomics, functional prediction, automated annotation, bacteria, evolution. *To whom correspondence should be addressed.
Published: 2003

49. Fouilles de Pirak - Baluchistan

Author: Jean-François Enault and Jean-François Jarrige
Subjects: Cultural Studies, Visual Arts and Performing Arts
Abstract: Situation geographique et historique du site decouvert par R. Raikes en 1960 qui recueillit un materiel de surface (poterie a la main decoree de motifs geometriques peints| associee a des lames de silex. Sondages de Jean-Marie Casal 1967-1968: couches d'habitation de la seconde moitie du II millenaire et de la premiere moitie du I| trace d'une premiere occupation contemporaine des cultures du Balouchistan au III millenaire et de la civilisation de Harappa| hiatus important entre les traces d'un etablissement ancien qui remonterait au III millenaire et l'occupation "Pirak" de la seconde moitie du II. Elements de cette culture etrangers aux traditions (taureau qui n'apparait que sous forme de figurines en terre crue, en revanche, cheval et chameau a deux bosses souvent atteste| cavalier a tete d'animal). Paralleles avec l'Asie Centrale. Poterie grise tournee de Pirak III remplacant la poterie peinte faite a la main.
Published: 1976

50. Les fouilles du Mont-Beuvray : rapport biennal 1984-1985

Author: jean-Paul, Françoise Beck, Jean-Louis Bruneau, Alain Duval, Olivier Buchsenschutz, Jean-François Enault, Katherine Gruel, Christian Peyre, Jean-Paul Saint-Aubin, Guillaumet, Jean-Paul, Archéologie, Terre, Histoire, Sociétés [Dijon] (ARTeHiS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Ministère de la Culture et de la Communication (MCC), Musée d'Archéologie Nationale (Saint-Germain-en-Laye, FRANCE), Archéologie et Philologie d'Orient et d'Occident (AOROC), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Musée des Antiquités Nationales, MUSEES DE FRANCE-MUSEES DE FRANCE, Ministère de la Culture et de la Communication, and Ministère de la Culture et de la Communication (MCC)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 1987

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