{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:46:04Z","timestamp":1768506364639,"version":"3.49.0"},"posted":{"date-parts":[[2023,6,2]]},"group-title":"Microbiology","reference-count":52,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The causes for variability of pro-inflammatory surface antigens that affect gut commensal\/opportunistic dualism within the phylum\n                  <jats:italic>Bacteroidota<\/jats:italic>\n                  remain unclear (1, 2). Using the classical lipopolysaccharide\/O-antigen \u2018\n                  <jats:italic>rfb<\/jats:italic>\n                  operon\u2019 in\n                  <jats:italic>Enterobacteriaceae<\/jats:italic>\n                  as a surface antigen model (5-gene-cluster\n                  <jats:italic>rfbABCDX<\/jats:italic>\n                  ), and a recent\n                  <jats:italic>rfbA-<\/jats:italic>\n                  typing strategy for strain classification (3), we characterized the architecture\/conservancy of the entire\n                  <jats:italic>rfb<\/jats:italic>\n                  operon in\n                  <jats:italic>Bacteroidota<\/jats:italic>\n                  . Analyzing complete genomes, we discovered that most\n                  <jats:italic>Bacteroidota<\/jats:italic>\n                  have the\n                  <jats:italic>rfb<\/jats:italic>\n                  operon fragmented into non-random gene-singlets and\/or doublets\/triplets, termed \u2018minioperons\u2019. To reflect global operon integrity, duplication, and fragmentation principles, we propose a five-category (infra\/supernumerary) cataloguing system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly\n                  <jats:italic>Bacteroides<\/jats:italic>\n                  -DNA (\n                  <jats:italic>thetaiotaomicron\/fragilis<\/jats:italic>\n                  ) and likely natural selection in specific micro-niches.\n                  <jats:italic>Bacteroides<\/jats:italic>\n                  -insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why\n                  <jats:italic>Bacteroidota<\/jats:italic>\n                  have fewer KEGG-pathways despite large genomes (4). DNA insertions overrepresenting DNA-exchange-avid species, impact functional metagenomics by inflating gene-based pathway inference and overestimating \u2018extra-species\u2019 abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohn\u2019s Disease (5), we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal\/CavFT\n                  <jats:italic>Bacteroidota<\/jats:italic>\n                  stimulate macrophages with lower potency than\n                  <jats:italic>Enterobacteriaceae<\/jats:italic>\n                  , and do not induce peritonitis in mice. The impact of \u2018foreign-DNA\u2019 insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.\n                <\/jats:p>","DOI":"10.1101\/2023.06.02.543472","type":"posted-content","created":{"date-parts":[[2023,6,3]],"date-time":"2023-06-03T00:35:12Z","timestamp":1685752512000},"source":"Crossref","is-referenced-by-count":2,"title":["The basis of antigenic operon fragmentation in\n                  <i>Bacteroidota<\/i>\n                  and commensalism"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5295-7662","authenticated-orcid":false,"given":"Nicholas C.","family":"Bank","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vaidhvi","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brandon","family":"Grubb","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Blake","family":"McCourt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron","family":"Burberry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle D.","family":"Roberts","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Rodriguez-Palacios","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023060608200597000_2023.06.02.543472v1.1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.00906"},{"key":"2023060608200597000_2023.06.02.543472v1.2","doi-asserted-by":"crossref","unstructured":"Ezeji J , Sarikonda D , Hopperton A , Erkkila H , Cohen D , Martinez S , et al. 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