@article{881046f867e3421787ba21748892d235,
title = "Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics",
abstract = "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 {\textquoteleft}Candidatus Microthrix parvicella{\textquoteright} 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.",
author = "{Mart{\'i}nez Arbas}, Susana and Shaman Narayanasamy and Malte Herold and Lebrun, {Laura A.} and Hoopmann, {Michael R.} and Sujun Li and Lam, {Tony J.} and Kunath, {Beno{\^i}t J.} and Hicks, {Nathan D.} and Liu, {Cindy M.} and Price, {Lance B.} and Laczny, {Cedric C.} and Gillece, {John D.} and Schupp, {James M.} and Keim, {Paul S.} and Moritz, {Robert L.} and Karoline Faust and Haixu Tang and Yuzhen Ye and Alexander Skupin and Patrick May and Muller, {Emilie E.L.} and Paul Wilmes",
note = "Funding Information: We thank the Luxembourg National Research Fund (FNR) for supporting this work through various funding instruments. Specifically, a PRIDE doctoral training unit grant (no. PRIDE15/10907093), CORE grants (nos. CORE/15/BM/10404093 and CORE/17/ SM/11689322), a European Union ERASysAPP grant (no. INTER/SYSAPP/14/05), a proof-of-concept grant (no. PoC/13/02), a European Union Joint Programming in Neurodegenerative Diseases grant (no. INTER/JPND/12/01) and an ATTRACT grant (no. A09/03) all awarded to P.W., as well as an AFR Ph.D. (PHD-2014-1/7934898) grant to S.N. and a CORE Junior (C15/SR/10404839) grant to E.E.L.M. The project received financial support from the Integrated Biobank of Luxembourg with funds from the Luxembourg Ministry of Higher Education and Research. The work of P.M. was funded by the {\textquoteleft}Plan Technologies de la Sant{\'e} du Gouvernement du Grand-Duch{\'e} de Luxembourg{\textquoteright} through the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. The authors acknowledge the ULHPC for providing and maintaining the computing resources. We thank G. Bissen and G. Di Pentima from the Syndicat Intercommunal a Vocation Ecologique (SIVEC) for access to the Schifflange wastewater treatment plant. Publisher Copyright: {\textcopyright} 2020, The Author(s).",
year = "2021",
month = jan,
doi = "10.1038/s41564-020-00794-8",
language = "English (US)",
volume = "6",
pages = "123--135",
journal = "Nature Microbiology",
issn = "2058-5276",
publisher = "Nature Publishing Group",
number = "1",
}