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Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the <jats:italic>C. rogercresseyi<\/jats:italic> genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the <jats:italic>C. rogercresseyi<\/jats:italic> microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen <jats:italic>Tenacibacullum ovolyticum<\/jats:italic> (97.87% completeness), followed by <jats:italic>Dokdonia <\/jats:italic>sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the <jats:italic>T. ovolyticum<\/jats:italic> genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between <jats:italic>C. rogercresseyi<\/jats:italic> and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.<\/jats:p>","DOI":"10.1038\/s41598-021-04485-0","type":"journal-article","created":{"date-parts":[[2022,1,17]],"date-time":"2022-01-17T11:03:22Z","timestamp":1642417402000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi"],"prefix":"10.1038","volume":"12","author":[{"given":"Diego","family":"Valenzuela-Miranda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Teresa","family":"Gon\u00e7alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Valenzuela-Mu\u00f1oz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo","family":"Nu\u00f1ez-Acu\u00f1a","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Liachko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bradley","family":"Nelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristian","family":"Gallardo-Escarate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,17]]},"reference":[{"key":"4485_CR1","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1111\/raq.12337","volume":"11","author":"RA Quinones","year":"2019","unstructured":"Quinones, R. 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