{"id":"https://openalex.org/W7220472893","doi":"https://doi.org/10.64898/2026.10.04.756616","title":"Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus","display_name":"Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus","publication_year":2026,"publication_date":"2026-10-05","ids":{"openalex":"https://openalex.org/W7220472893","doi":"https://doi.org/10.64898/2026.10.04.756616"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.04.756616","doi":"https://doi.org/10.64898/2026.10.04.756616","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.04.756616","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/05/2026.10.04.756616.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/05/2026.10.04.756616.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080326955","display_name":"Audrey Leprince","orcid":"https://orcid.org/0000-0002-8068-1365","observed_orcids":["https://orcid.org/0000-0002-8068-1365"]},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Audrey Leprince","raw_affiliation_strings":["D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020172304","display_name":"Vincent Somerville","orcid":"https://orcid.org/0000-0002-1256-6058","observed_orcids":["https://orcid.org/0000-0002-1256-6058"]},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Vincent Somerville","raw_affiliation_strings":["D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016803235","display_name":"Justine Lefran\u00e7ois","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Justine Lefran\u00e7ois","raw_affiliation_strings":["D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075517792","display_name":"Genevi\u00e8ve M. Rousseau","orcid":"https://orcid.org/0000-0002-1792-626X","observed_orcids":["https://orcid.org/0000-0002-1792-626X"]},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Genevi\u00e8ve M. Rousseau","raw_affiliation_strings":["D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011363917","display_name":"Anne M. Millen","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anne M. Millen","raw_affiliation_strings":["IFF, 3329 Agriculture Dr., Madison, WI, USA 53716"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IFF, 3329 Agriculture Dr., Madison, WI, USA 53716","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027526408","display_name":"Damian Magill","orcid":"https://orcid.org/0000-0002-2162-2074","observed_orcids":["https://orcid.org/0000-0002-2162-2074"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Damian Magill","raw_affiliation_strings":["IFF, CS 10010, Dang\u00e9-Saint-Romain 86220, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IFF, CS 10010, Dang\u00e9-Saint-Romain 86220, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008191157","display_name":"Philippe Horvath","orcid":"https://orcid.org/0000-0003-2015-8123","observed_orcids":["https://orcid.org/0000-0003-2015-8123"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Philippe Horvath","raw_affiliation_strings":["IFF, CS 10010, Dang\u00e9-Saint-Romain 86220, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IFF, CS 10010, Dang\u00e9-Saint-Romain 86220, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023997675","display_name":"Dennis A. Romero","orcid":"https://orcid.org/0000-0002-8222-5574","observed_orcids":["https://orcid.org/0000-0002-8222-5574"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dennis A. Romero","raw_affiliation_strings":["IFF, 3329 Agriculture Dr., Madison, WI, USA 53716"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IFF, 3329 Agriculture Dr., Madison, WI, USA 53716","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079257651","display_name":"Sylvain Moineau","orcid":"https://orcid.org/0000-0002-2832-5101","observed_orcids":["https://orcid.org/0000-0002-2832-5101"]},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sylvain Moineau","raw_affiliation_strings":["D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de biochimie, de microbiologie et de bio-informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada. Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Pavillon Charles-Eug\u00e8ne-Marchand, Universit\u00e9 Laval, Qu\u00e9bec City, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5080326955"],"corresponding_institution_ids":["https://openalex.org/I43406934"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/streptococcus-thermophilus","display_name":"Streptococcus thermophilus","score":0.8920000195503235},{"id":"https://openalex.org/keywords/genomic-islands","display_name":"genomic islands","score":0.7139999866485596},{"id":"https://openalex.org/keywords/bacterial-immunity","display_name":"bacterial immunity","score":0.7789999842643738},{"id":"https://openalex.org/keywords/antiviral-defense","display_name":"antiviral defense","score":0.7039999961853027},{"id":"https://openalex.org/keywords/accessory-genes","display_name":"accessory genes","score":0.8379999995231628},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.8370000123977661},{"id":"https://openalex.org/keywords/guilt-by-association","display_name":"guilt by association","score":0.703000009059906}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8023999929428101},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6114000082015991},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6037999987602234},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.5652999877929688},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5371999740600586},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5299999713897705},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4837999939918518},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47780001163482666},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.45170000195503235},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.40849998593330383},{"id":"https://openalex.org/C2777276588","wikidata":"https://www.wikidata.org/wiki/Q1041276","display_name":"Streptococcus thermophilus","level":4,"score":0.38839998841285706},{"id":"https://openalex.org/C2780258820","wikidata":"https://www.wikidata.org/wiki/Q5195454","display_name":"Genomic island","level":4,"score":0.3580999970436096},{"id":"https://openalex.org/C3020077223","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomic information","level":4,"score":0.32659998536109924},{"id":"https://openalex.org/C136449434","wikidata":"https://www.wikidata.org/wiki/Q428253","display_name":"Innate immune system","level":3,"score":0.28760001063346863},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.27639999985694885},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2515000104904175}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.04.756616","doi":"https://doi.org/10.64898/2026.10.04.756616","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.04.756616","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/05/2026.10.04.756616.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.04.756616","doi":"https://doi.org/10.64898/2026.10.04.756616","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.04.756616","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/05/2026.10.04.756616.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7220472893.pdf","grobid_xml":"https://content.openalex.org/works/W7220472893.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W4223551334","https://openalex.org/W4391399665","https://openalex.org/W4410019128"],"related_works":["https://openalex.org/W4286680890","https://openalex.org/W4307493886","https://openalex.org/W3107585413","https://openalex.org/W4296381497","https://openalex.org/W2799745506","https://openalex.org/W2784532673","https://openalex.org/W4402755350","https://openalex.org/W7111391101","https://openalex.org/W7152378720","https://openalex.org/W2131730777"],"abstract_inverted_index":{"Abstract":[0],"Bacteria":[1],"encode":[2],"diverse":[3],"antiviral":[4,83,135],"defense":[5,27,37,109],"systems,":[6,28,84],"yet":[7],"the":[8,93,116,143],"evolutionary":[9],"reservoirs":[10,133],"that":[11,112,122],"generate":[12],"this":[13],"immune":[14,147],"innovation":[15,136],"remain":[16,125],"poorly":[17],"defined.":[18],"Although":[19],"genomic":[20,29],"context":[21],"has":[22],"been":[23,46],"instrumental":[24],"in":[25,36],"discovering":[26],"islands":[30],"(GIs),":[31],"variable":[32],"chromosomal":[33],"regions":[34],"enriched":[35],"genes":[38],"and":[39,137],"proteins":[40],"of":[41,51,59,73,100,134,145],"unknown":[42],"function,":[43],"have":[44],"not":[45,105],"systematically":[47],"explored":[48],"as":[49,132],"sources":[50],"new":[52],"bacterial":[53,146],"immunity.":[54],"Here,":[55],"using":[56],"comparative":[57],"genomics":[58],"Streptococcus":[60],"thermophilus,":[61],"we":[62],"identified":[63],"30":[64],"defense-associated":[65],"GIs":[66,78,131],"displaying":[67],"extensive":[68],"accessory":[69],"gene":[70],"diversity.":[71],"Investigation":[72],"candidate":[74],"loci":[75],"from":[76],"three":[77],"uncovered":[79],"15":[80],"previously":[81],"uncharacterized":[82],"including":[85],"10":[86],"with":[87],"novel":[88],"architectures":[89],"or":[90],"features,":[91],"revealing":[92,120],"potential":[94],"within":[95],"even":[96],"a":[97,139],"small":[98],"subset":[99],"GIs.":[101],"Several":[102],"systems":[103,121],"were":[104],"located":[106],"near":[107],"known":[108],"genes,":[110],"highlighting":[111],"GI-based":[113],"discovery":[114],"complements":[115],"traditional":[117],"guilt-by-association":[118],"approach,":[119],"would":[123],"otherwise":[124],"undetected.":[126],"Together,":[127],"our":[128],"findings":[129],"establish":[130],"provide":[138],"framework":[140],"for":[141],"uncovering":[142],"diversity":[144],"systems.":[148]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-06T00:00:00"}
