Reference : Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics...

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Microbiology
	To cite this reference:	http://hdl.handle.net/10993/45371

Title :	Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
Language :	English
Author, co-author :	Martinez Arbas, Susana* [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Narayanasamy, Shaman* [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > > > > ; Megeno S.A]
	Herold, Malte [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)]
	Lebrun, Laura [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Hoopmann, Michael R. [Institute for Systems Biology, Washington, USA]
	Li, Sujun [School of Informatics, Computing and Engineering, Indiana University, USA]
	Lam, Tony J. [School of Informatics, Computing and Engineering, Indiana University, USA]
	Kunath, Benoît [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Hicks, Nathan D. [TGen North, USA > > > ; Harvard T.H. Chan, School of Public Health, USA]
	Liu, Cindy M. [TGen North, USA > > > ; Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, USA]
	Price, Lance B. [TGen North, USA > > > ; Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, USA]
	Laczny, Cedric Christian [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Gillece, John D. [TGen North, USA]
	Schupp, James M. [TGen North, USA]
	Keim, Paul S. [TGen North, USA > > > ; The Pathogen and Microbiome Institute, Northern Arizona University, USA]
	Moritz, Robert L. [Institute for Systems Biology, Washington, USA]
	Faust, Karoline [Laboratory of Molecular Bacteriology, KU Leuven, Belgium]
	Tang, Haixu [School of Informatics, Computing and Engineering, Indiana University, USA]
	Ye, Yuzhen [School of Informatics, Computing and Engineering, Indiana University, USA]
	Skupin, Alexander [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Integrative Cell Signalling >]
	May, Patrick [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core >]
	Muller, Emilie E. L. [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > > > > ; Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France]
	Wilmes, Paul [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	* These authors have contributed equally to this work.
Publication date :	2-Nov-2020
Journal title :	Nature Microbiology
Publisher :	Nature Publishing Group
Peer reviewed :	Yes (verified by ORBilu)
e-ISSN :	2058-5276
City :	London
Country :	United Kingdom
Keywords :	[en] CRISPR ; metagenomics ; activated sludge ; metatranscriptomics ; phages ; plasmids ; wastewater ; time series ; multi-omics
Abstract :	[en] Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
Permalink :	http://hdl.handle.net/10993/45371

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