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Isolates from anatomically specialized sites such as the ocular surface are underrepresented in comparative genomic datasets.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We performed integrated phenotypic and genome-resolved characterization of\n                      <jats:italic>Chryseobacterium<\/jats:italic>\n                      sp. NG-CE01, isolated from a bovine corneal infection. A high-quality hybrid assembly was analyzed using phylogenomics, curated comparative gene-content profiling across a 14-genome\n                      <jats:italic>Chryseobacterium<\/jats:italic>\n                      panel, CAZyme annotation, synteny-guided locus interrogation, mobilome profiling, and systematic screening of antimicrobial resistance, virulence, and genome-defense determinants, supported by functional curation of isolate-specific genes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Genome-based taxonomy placed NG-CE01 as a genomically distinct lineage most closely related to\n                      <jats:italic>Chryseobacterium cheonjiense<\/jats:italic>\n                      , falling below established species delineation thresholds and thus consistent with a putative novel genomospecies within the genus. Comparative gene-content profiling across the multi-species panel yielded an open interspecies repertoire (Heaps\u2019 law \u03b1\u2009=\u20090.6897), with NG-CE01 contributing a focused isolate-specific set enriched in defense- and recombination-associated functions. Across analyses, the dominant axis of differentiation was synteny-guided, locus-scale remodeling of discrete carbohydrate-foraging modules (CBM48\u2013GH13, CBM6\u2013GH5, and a GH43-rich super-block), supported by conserved neighborhood architecture, Jaccard similarity gradients, and locus-centric enrichment patterns. Three genomic islands were identified; GI_3 represented the principal reservoir of isolate-specific functional novelty, enriched in envelope biogenesis and regulatory functions and consistent with a restrained mobilome. Comprehensive screening detected no acquired antimicrobial-resistance or virulence genes; instead, NG-CE01 encoded chromosomal intrinsic resistance and fitness-associated loci, while disk-diffusion results are reported as zone diameters given limited validated breakpoints for\n                      <jats:italic>Chryseobacterium<\/jats:italic>\n                      . Collectively, these results support a hypothesis that ocular-associated persistence may be shaped primarily by genome architecture and synteny-defined locus innovation rather than CAZyme burden or virulence acquisition.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      NG-CE01 exhibits pronounced synteny-defined remodeling of carbohydrate-foraging and intrinsic resistance loci, providing a genome-informed, hypothesis-generating framework for how\n                      <jats:italic>Chryseobacterium<\/jats:italic>\n                      may persist in specialized host environments and illustrating the value of synteny-aware comparative genomics for resolving functional remodeling beyond gene abundance alone.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-026-04950-8","type":"journal-article","created":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T07:16:34Z","timestamp":1774941394000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomics reveals synteny-guided remodeling of carbohydrate-foraging and intrinsic resistance in an ocular Chryseobacterium isolate, NG-CE01"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6588-3866","authenticated-orcid":false,"given":"Farouk","family":"Hassan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1363-4534","authenticated-orcid":false,"given":"S\u00fcheyla","family":"T\u00fcrky\u0131lmaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2315-6801","authenticated-orcid":false,"given":"Taghrid S.","family":"El-Mahdy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,31]]},"reference":[{"issue":"4","key":"4950_CR1","first-page":"421","volume":"42","author":"JF Bernardet","year":"2018","unstructured":"Bernardet JF, Bowman JP. 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No experimental animals were used and no additional sampling was performed for research. In accordance with Article 8(o) of the ADU-HADYEK Directive, diagnostic\/therapeutic clinical procedures are not subject to ethical approval; therefore, ADU-HADYEK confirmed that ethics approval was not required for this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"326"}}