VIRAME project 2017-2023

In situ characterization of the genomic content of VIRuses of MEthanogenic Archaea in organic waste fermentation bioprocesses

Publications

Tools

You can find the bioinformatics pipeline developed during the project, for shotgun metagenome and metavirome analysis, on the gitlab repository: https://forgemia.inra.fr/cedric.midoux/workflow_metagenomics

Publications

pre-print. Hoang Ngo, Maximilien Sotomski, Angeline Guenne, Mahendra Mariadassou, Mart Krupovic, François Enault, Ariane Bize. Viral DNA SIP: the isotopic composition of virions is correlated with that of the substrate used for host growth. bioRxiv, 10.15.512377 (2022). https://doi.org/10.1101/2022.10.15.512377

Hoang Ngo, François Enault, Cédric Midoux, Mahendra Mariadassou, Olivier Chapleur, Laurent Mazéas, Valentin Loux, Théodore Bouchez, Mart Krupovic, Ariane Bize. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomic. Environmental Microbiology 1-16 (2022). https://doi.org/10.1111/1462-2920.16120

Not directly financed by the ANR VIRAME project, but still connected to viral ecology: Jean-Jacques Godon, Ariane Bize, Hoang Ngo, Laurent Cauquil, Mathieu Almeida, Marie-Agnès Petit, Olivier Zemb. Bacterial consumption of T4 phages. Microorganisms 9(9), 1852 (2021). https://doi.org/10.3390/microorganisms9091852

Ariane Bize, Cédric Midoux, Mahendra Mariadassou, Sophie Schbath, Patrick Forterre, Violette Da Cunha. Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history. BMC Genomics 22, 186 (2021). https://doi.org/10.1186/s12864-021-07471-y

Oral communications

April, 20, 2023: presentation by Marion Covès et al, Characterization of virus-host dynamics in anaerobic digesters under abiotic stress, Journées des doctorant.e.s ABIES 2023 (AgroParisTech, Palaiseau, France, https://jddabies.wixsite.com/website-2/blank)

Ariane Bize et al, Diversity of novel viruses infecting methanogenic archaea, discovered through coupling of stable isotope probing and metagenomics, oral presentation, Phages in Paris (Paris, France, annual conference of the French network Phages.fr, https://phages2022.sciencesconf.org/ , https://site.phages.fr/explorer-ressources/colloques/)

Marion Covès et al, Characterization of virus-host dynamics in anaerobic digesters under abiotic stress, oral presentation, MICROBES 2022, 17th congress of the French Society of Microbiology (Société Française de Microbiologie, SFM, October, 4, 2022, Montpellier, France, https://www.alphavisa.com/sfm/2022/fr/)

Ariane Bize et al, Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics, poster + pitch presentation, 18th International Symposium on Microbial Ecology (August, 15, 2022, #ISME18, Lausanne, Switzerland, https://isme18.isme-microbes.org/)

Ariane Bize et al, Exploration de la diversité des virus d’archées méthanogènes dans les procédés de digestion anaérobie, par des approches isotopiques et métagénomiques, oral presentation, 10^ème congrès de l’Association Francophone d’Ecologie Microbienne, AFEM (November, 15, 2021, virtual congress, France, https://afem-10.sciencesconf.org/)

Hoang Ngo et al, Characterization of the diversity of viruses infecting methanogens in anaerobic digestion processes by shotgun sequencing metagenomics, oral presentation, 16^th Congrès National de la Société Française de Microbiologie, SFM (September, 24, 2021, Nantes, France, https://www.alphavisa.com/sfm/2021/fr/index.php)

Ariane Bize et al, Stable Isotope Probing in microbial ecology and VIRAME project, oral presentation, “Phage ecology” meeting of the French network Phages.fr (March, 27, 2019, Lyon, France, http://phages.fr/workshops/)

Ariane Bize et al, K-mer profiles in cell, virus and plasmid genomes from the domain Archaea, oral presentation, “Phages in Bordeaux” 2018 (September 24, 2018, Bordeaux, France, annual conference of the French network phages.fr, http://phages.fr/colloques/)

Ariane Bize et al, K-mer profiles in cell, virus and plasmid genomes from the domain Archaea, oral presentation, Viruses of Microbes 2018 (July 12, 2018, Wroclaw, Poland, http://meetings.embo.org/event/18-virus-microbe)