{"doi":"10.1101/2023.06.02.543472","title":"The basis of antigenic operon fragmentation in <i>Bacteroidota</i> and commensalism","abstract":"Abstract The causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism within the phylum Bacteroidota remain unclear (1, 2). Using the classical lipopolysaccharide/O-antigen ‘ rfb operon’ in Enterobacteriaceae as a surface antigen model (5-gene-cluster rfbABCDX ), and a recent rfbA- typing strategy for strain classification (3), we characterized the architecture/conservancy of the entire rfb operon in Bacteroidota . Analyzing complete genomes, we discovered that most Bacteroidota have the rfb operon fragmented into non-random gene-singlets and/or doublets/triplets, termed ‘minioperons’. 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 Bacteroides -DNA ( thetaiotaomicron/fragilis ) and likely natural selection in specific micro-niches. Bacteroides -insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota 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 ‘extra-species’ abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohn’s Disease (5), we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal/CavFT Bacteroidota stimulate macrophages with lower potency than Enterobacteriaceae , and do not induce peritonitis in mice. The impact of ‘foreign-DNA’ insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":396536,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9548,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":902766,"name":"Vaidhvi Singh","orcid":"0000-0002-9395-326X","position":1,"is_corresponding":false},{"id":1172353,"name":"Brandon Grubb","orcid":null,"position":2,"is_corresponding":false},{"id":404046,"name":"Blake McCourt","orcid":"0000-0002-1488-2572","position":3,"is_corresponding":false},{"id":232264,"name":"Aaron Burberry","orcid":"0000-0003-1552-8695","position":4,"is_corresponding":false},{"id":1171995,"name":"Kyle Roberts","orcid":"0000-0003-2935-7049","position":5,"is_corresponding":false},{"id":105642,"name":"Alexander Rodriguez‐Palacios","orcid":"0000-0003-0713-5605","position":6,"is_corresponding":false},{"id":1171994,"name":"Norman Bank","orcid":"0000-0001-5295-7662","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-19T01:19:31.472087Z","pmid":"37398285","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}