{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Dion MB"],"funding":["Natural Sciences and Engineering Research Council of Canada","Novo Nordisk Foundation","Canada First Research Excellence Fund","Tier 1 Canada Research Chair in Bacteriophages","Intestinal Microbiomics, Institute of Nutrition, Metabolism, and Diabetes","Faculty of Health and Medical Sciences, University of Copenhagen","Danish Agency for Science and Higher Education","Canadian Institutes of Health Research","CIHR","Calcul Québec","Fonds de Recherche du Québec-Nature et Technologies","BRIDGE–Translational Excellence Programme","Joint Programming Initiative “Healthy Diet for a Healthy Life,”","Digital Research Alliance of Canada","Novo Nordisk Fonden"],"pagination":["wrae005"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10910852"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["18(1)"],"pubmed_abstract":["CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active."],"journal":["The ISME journal"],"pubmed_title":["Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages."],"pmcid":["PMC10910852"],"funding_grant_id":["2019-05183","950-232136","NNF20OC0061029","143924","259257","NNF18SA0034956"],"pubmed_authors":["Shah SA","Thorsen J","Dion MB","Krogfelt KA","Allard A","Petit MA","Stokholm J","Deng L","Schjorring S","Horvath P","Nielsen DS","Moineau S"],"additional_accession":[]},"is_claimable":false,"name":"Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages.","description":"CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Jan","modification":"2026-06-28T03:08:20.006Z","creation":"2025-04-05T11:38:33.779Z"},"accession":"S-EPMC10910852","cross_references":{"pubmed":["38366192"],"doi":["10.1093/ismejo/wrae005"]}}