{"doi":"10.1101/2022.11.11.516204","title":"Core Defense Hotspots within <i>Pseudomonas aeruginosa</i> are a consistent and rich source of anti-phage defense systems","abstract":"ABSTRACT Bacteria use a diverse arsenal of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Identifying the full defense repertoire of a given species is still challenging, however. Here, we developed a computational tool to broadly identify anti-phage systems, which was applied to &gt;180,000 genomes available on NCBI, revealing Pseudomonas aeruginosa to possess the most diverse anti-phage arsenal of any species with &gt;200 sequenced genomes. Using network analysis to identify the common neighbors of anti-phage systems, we surprisingly identified two highly conserved core defense hotspot loci (cDHS1 and cDHS2). Across more than 1,000 P. aeruginosa strains, cDHS1 is up to 224 kb (mean: 34 kb) with varied arrangements of at least 31 immune systems while cDHS2 has 24 distinct systems (mean: 15.4 kb). cDHS1/2 are present in most P. aeruginosa isolates, in contrast to highly variable mobile DHSs. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identification of core gene markers that flank immune islands could be a simple approach for immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":302169,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9569,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":686539,"name":"Eric Laderman","orcid":"0009-0005-7369-7333","position":1,"is_corresponding":false},{"id":471706,"name":"Erin Huiting","orcid":"0000-0002-5454-2679","position":2,"is_corresponding":false},{"id":991213,"name":"Charles Zhang","orcid":"0000-0002-0418-6354","position":3,"is_corresponding":false},{"id":254496,"name":"Alan R. Davidson","orcid":"0000-0002-0744-9199","position":4,"is_corresponding":false},{"id":238123,"name":"Joseph Bondy‐Denomy","orcid":"0000-0002-4909-9481","position":5,"is_corresponding":false},{"id":820555,"name":"Matthew C. Johnson","orcid":"0000-0003-4534-5697","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:32:06.309890Z","pmid":null,"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":[]}