{"id":"https://openalex.org/W7224997484","doi":"https://doi.org/10.64898/2026.10.26.761872","title":"SYMBIO-SCAN, a full-length 16S rRNA gene-based workflow optimized for bacterial symbiont detection and discovery from long read sequencing","display_name":"SYMBIO-SCAN, a full-length 16S rRNA gene-based workflow optimized for bacterial symbiont detection and discovery from long read sequencing","publication_year":2026,"publication_date":"2026-10-30","ids":{"openalex":"https://openalex.org/W7224997484","doi":"https://doi.org/10.64898/2026.10.26.761872"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.26.761872","doi":"https://doi.org/10.64898/2026.10.26.761872","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.26.761872","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.26.761872.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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.26.761872.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044320790","display_name":"Carlo Croci","orcid":"https://orcid.org/0009-0006-7411-335X","observed_orcids":["https://orcid.org/0009-0006-7411-335X"]},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Carlo Croci","raw_affiliation_strings":["Department of Biology and Biotechnology, University of Pavia, Pavia, Italy"],"raw_orcid":"https://orcid.org/0009-0006-7411-335X","affiliations":[{"raw_affiliation_string":"Department of Biology and Biotechnology, University of Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160265508","display_name":"Giulia Iamundo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giulia Iamundo","raw_affiliation_strings":["Department of Biology and Biotechnology, University of Pavia, Pavia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology and Biotechnology, University of Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160242253","display_name":"Azita Baharibabadi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1516879","display_name":"Tarbiat Modares University","ror":"https://ror.org/03mwgfy56","country_code":"IR","type":"education","lineage":["https://openalex.org/I1516879"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Azita Baharibabadi","raw_affiliation_strings":["Department of Entomology, Tarbiat Modares University, Tehran, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Entomology, Tarbiat Modares University, Tehran, Iran","institution_ids":["https://openalex.org/I1516879"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073176148","display_name":"Simone Sabatelli","orcid":"https://orcid.org/0000-0002-8282-7882","observed_orcids":["https://orcid.org/0000-0002-8282-7882"]},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Sabatelli","raw_affiliation_strings":["Department of Biology and Biotechnologies \u201cCharles Darwin\u201d, Sapienza University of Rome, Roma, Italy"],"raw_orcid":"https://orcid.org/0000-0002-8282-7882","affiliations":[{"raw_affiliation_string":"Department of Biology and Biotechnologies \u201cCharles Darwin\u201d, Sapienza University of Rome, Roma, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039280459","display_name":"Davide Sassera","orcid":"https://orcid.org/0000-0003-0442-5252","observed_orcids":["https://orcid.org/0000-0003-0442-5252"]},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]},{"id":"https://openalex.org/I4210151645","display_name":"Policlinico San Matteo Fondazione","ror":"https://ror.org/05w1q1c88","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210151645","https://openalex.org/I4210153126"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide Sassera","raw_affiliation_strings":["Department of Biology and Biotechnology, University of Pavia, Pavia, Italy","Fondazione IRCCS Policlinico San Matteo, Pavia, Italy"],"raw_orcid":"https://orcid.org/0000-0003-0442-5252","affiliations":[{"raw_affiliation_string":"Department of Biology and Biotechnology, University of Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]},{"raw_affiliation_string":"Fondazione IRCCS Policlinico San Matteo, Pavia, Italy","institution_ids":["https://openalex.org/I4210151645"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062566362","display_name":"Michele Castelli","orcid":"https://orcid.org/0000-0003-2177-5772","observed_orcids":["https://orcid.org/0000-0003-2177-5772"]},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]},{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michele Castelli","raw_affiliation_strings":["Department of Biology and Biotechnology, University of Pavia, Pavia, Italy","Department of Biology, University of Pisa, Pisa, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2177-5772","affiliations":[{"raw_affiliation_string":"Department of Biology and Biotechnology, University of Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]},{"raw_affiliation_string":"Department of Biology, University of Pisa, Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5062566362"],"corresponding_institution_ids":["https://openalex.org/I108290504","https://openalex.org/I25217355"],"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/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00019999999494757503,"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/T11750","display_name":"Phytoplasmas and Hemiptera pathogens","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bacterial-endosymbionts","display_name":"endosymbiotic bacteria","score":0.9620000123977661},{"id":"https://openalex.org/keywords/16s-rrna-gene","display_name":"16S rRNA gene","score":0.8299999833106995},{"id":"https://openalex.org/keywords/long-read-sequencing","display_name":"long-read sequencing","score":0.7609999775886536},{"id":"https://openalex.org/keywords/wolbachia","display_name":"Wolbachia","score":0.7559999823570251},{"id":"https://openalex.org/keywords/rickettsia","display_name":"Rickettsia","score":0.9599999785423279},{"id":"https://openalex.org/keywords/arsenophonus","display_name":"Arsenophonus","score":0.9160000085830688},{"id":"https://openalex.org/keywords/spiroplasma","display_name":"Spiroplasma","score":0.9679999947547913},{"id":"https://openalex.org/keywords/novel-bacterial-lineages","display_name":"novel bacterial lineages","score":0.746999979019165},{"id":"https://openalex.org/keywords/enterobacterales","display_name":"Enterobacterales","score":0.8100000023841858},{"id":"https://openalex.org/keywords/rickettsiales","display_name":"Rickettsiales","score":0.777999997138977},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.6869999766349792}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8422999978065491},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6528000235557556},{"id":"https://openalex.org/C42062724","wikidata":"https://www.wikidata.org/wiki/Q1209205","display_name":"16S ribosomal RNA","level":3,"score":0.6518999934196472},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5281999707221985},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5020999908447266},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4740999937057495},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.4657000005245209},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4618000090122223},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.4410000145435333},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.42260000109672546},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.38659998774528503},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3862999975681305},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.373199999332428},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.37040001153945923},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.3546999990940094},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.3379000127315521},{"id":"https://openalex.org/C2776989901","wikidata":"https://www.wikidata.org/wiki/Q134668","display_name":"Gammaproteobacteria","level":4,"score":0.3240000009536743},{"id":"https://openalex.org/C124104306","wikidata":"https://www.wikidata.org/wiki/Q4840005","display_name":"Bacterial taxonomy","level":4,"score":0.32010000944137573},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3066999912261963},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3019999861717224},{"id":"https://openalex.org/C2993206177","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon sequencing","level":4,"score":0.3019999861717224},{"id":"https://openalex.org/C180223184","wikidata":"https://www.wikidata.org/wiki/Q4839986","display_name":"Bacterial genetics","level":4,"score":0.2825999855995178},{"id":"https://openalex.org/C174160445","wikidata":"https://www.wikidata.org/wiki/Q27980903","display_name":"Phylotype","level":4,"score":0.27390000224113464}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.26.761872","doi":"https://doi.org/10.64898/2026.10.26.761872","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.26.761872","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.26.761872.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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.26.761872","doi":"https://doi.org/10.64898/2026.10.26.761872","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.26.761872","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.26.761872.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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7224997484.pdf","grobid_xml":"https://content.openalex.org/works/W7224997484.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4293546600","https://openalex.org/W1922423415","https://openalex.org/W6892151282","https://openalex.org/W1794849966","https://openalex.org/W4318472730","https://openalex.org/W1499999823","https://openalex.org/W2904975029","https://openalex.org/W4400090954","https://openalex.org/W2565659426","https://openalex.org/W6958734424"],"abstract_inverted_index":{"Abstract":[0],"Bacterial":[1],"endosymbionts":[2],"are":[3],"often":[4],"unculturable,":[5],"making":[6],"sequencing-based":[7],"approaches":[8],"essential":[9],"for":[10,22,42,45,192],"their":[11,90],"discovery":[12,203],"and":[13,44,87,118,141,149,189],"characterization.":[14],"Here":[15],"we":[16,55,106],"developed":[17],"SYMBIO-SCAN,":[18],"a":[19,52,73,158,186],"dedicated":[20],"workflow":[21,58],"recovering":[23],"high-quality":[24,109],"nearly":[25],"full-length":[26,174],"16S":[27,175],"rRNA":[28,176],"gene":[29,177],"sequences":[30,110],"of":[31,76,93,163,196,204],"symbionts":[32,95],"from":[33,64],"long":[34],"reads,":[35],"which":[36],"provided":[37],"an":[38],"adequate":[39],"discriminatory":[40],"power":[41],"identification":[43],"accurate":[46],"phylogenetic":[47],"analyses.":[48],"After":[49],"validation":[50],"on":[51],"mock":[53],"community,":[54],"applied":[56],"this":[57],"to":[59,80,112],"30":[60],"beetle":[61],"(Coleoptera)":[62],"specimens":[63],"10":[65],"species.":[66],"Beetles":[67],"were":[68,124,155],"selected":[69],"since":[70],"they":[71],"host":[72,82],"wide":[74],"variety":[75],"bacterial":[77,114,198],"symbionts,":[78,130,199],"able":[79],"influence":[81],"physiology,":[83],"ecology,":[84],"population":[85],"dynamics,":[86],"evolution.":[88],"Despite":[89],"importance,":[91],"most":[92,127],"these":[94],"remain":[96],"completely":[97],"unknown":[98],"or":[99],"poorly":[100],"characterized.":[101],"By":[102],"the":[103,126,164,194,202],"novel":[104,147,153,206],"approach,":[105],"obtained":[107],"80":[108],"belonging":[111],"diverse":[113],"lineages,":[115],"mostly":[116],"Rickettsiales":[117],"Enterobacterales":[119,160],".":[120,143,168],"Putative":[121],"reproductive":[122],"manipulators":[123],"among":[125],"frequently":[128],"detected":[129],"including":[131,157],"Wolbachia":[132],",":[133,135,140],"Rickettsia":[134],"\u201c":[136],"Candidatus":[137],"Lariskella\u201d,":[138],"Arsenophonus":[139],"Spiroplasma":[142],"Moreover,":[144],"three":[145],"putative":[146,152],"genera":[148],"one":[150],"additional":[151],"species":[154],"identified,":[156],"possible":[159],"nutritional":[161],"symbiont":[162],"weevil":[165],"Holotrichapion":[166],"pisi":[167],"Overall,":[169],"our":[170],"results":[171],"support":[172],"that":[173],"amplicon":[178],"sequencing":[179],"combined":[180],"with":[181],"tailored":[182],"bioinformatic":[183],"analyses":[184],"provide":[185],"quick,":[187],"cost-effective,":[188],"robust":[190],"approach":[191],"investigating":[193],"diversity":[195],"host-associated":[197],"also":[200],"allowing":[201],"entirely":[205],"lineages.":[207]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-11-01T00:00:00"}
