{"doi":"10.1093/nar/gkae814","title":"Phage defence loci of <i>Streptococcus thermophilus—</i>tip of the anti-phage iceberg?","abstract":"Bacteria possess (bacterio)phage defence systems to ensure their survival. The thermophilic lactic acid bacterium, Streptococcus thermophilus, which is used in dairy fermentations, harbours multiple CRISPR-Cas and restriction and modification (R/M) systems to protect itself against phage attack, with limited reports on other types of phage-resistance. Here, we describe the systematic identification and functional analysis of the phage resistome of S. thermophilus using a collection of 27 strains as representatives of the species. In addition to CRISPR-Cas and R/M systems, we uncover nine distinct phage-resistance systems including homologues of Kiwa, Gabija, Dodola, defence-associated sirtuins and classical lactococcal/streptococcal abortive infection systems. The genes encoding several of these newly identified S. thermophilus antiphage systems are located in proximity to the genetic determinants of CRISPR-Cas systems thus constituting apparent Phage Defence Islands. Other phage-resistance systems whose encoding genes are not co-located with genes specifying CRISPR-Cas systems may represent anchors to identify additional Defence Islands harbouring, as yet, uncharacterised phage defence systems. We estimate that up to 2.5% of the genetic material of the analysed strains is dedicated to phage defence, highlighting that phage-host antagonism plays an important role in driving the evolution and shaping the composition of dairy streptococcal genomes.","journal":"Nucleic Acids Research","year":2024,"id":433334,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9483,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1238599,"name":"Guillermo Ortíz Charneco","orcid":"0000-0003-1601-6173","position":1,"is_corresponding":false},{"id":1238600,"name":"Zoe Kampff","orcid":"0000-0002-8399-1465","position":2,"is_corresponding":false},{"id":821609,"name":"Natalia Díaz‐Garrido","orcid":"0000-0003-1220-015X","position":3,"is_corresponding":false},{"id":1238601,"name":"Francesca Bottacini","orcid":"0000-0002-0142-2956","position":4,"is_corresponding":false},{"id":1221724,"name":"Brian McDonnell","orcid":"0000-0003-1704-8759","position":5,"is_corresponding":false},{"id":1238602,"name":"Gabriele Andrea Lugli","orcid":"0000-0002-3024-0537","position":6,"is_corresponding":false},{"id":1238603,"name":"Marco Ventura","orcid":"0000-0002-4875-4560","position":7,"is_corresponding":false},{"id":432177,"name":"Alexey Fomenkov","orcid":"0000-0002-2463-5946","position":8,"is_corresponding":false},{"id":1239064,"name":"Pascal Quénée","orcid":null,"position":9,"is_corresponding":false},{"id":1139040,"name":"Saulius Kulakauskas","orcid":"0000-0002-3466-8266","position":10,"is_corresponding":false},{"id":1239065,"name":"Paul de Waal","orcid":null,"position":11,"is_corresponding":false},{"id":1221726,"name":"Noël N. M. E. van Peij","orcid":"0009-0002-3946-4067","position":12,"is_corresponding":false},{"id":705143,"name":"Christian Cambillau","orcid":"0000-0001-5502-4729","position":13,"is_corresponding":false},{"id":4076,"name":"Richard J. Roberts","orcid":"0000-0002-4348-0169","position":14,"is_corresponding":false},{"id":124924,"name":"Douwe van Sinderen","orcid":null,"position":15,"is_corresponding":false},{"id":901807,"name":"Jennifer Mahony","orcid":"0000-0001-5846-6303","position":16,"is_corresponding":false},{"id":1221723,"name":"Philip Kelleher","orcid":"0000-0003-3423-7930","position":0,"is_corresponding":true}],"reference_count":70,"raw_metadata":null,"created_at":"2026-07-19T01:59:44.444627Z","pmid":"39315705","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}