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bioRxiv · 10.1101/2023.06.02.543472

The basis of antigenic operon fragmentation in Bacteroidota and commensalism

Bank, N. C.·Singh, V.·Grubb, B.·McCourt, B.·Burberry, A.·Roberts, K. D.·Rodriguez-Palacios, A.
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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 Crohns 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.

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Bank, N. C., Singh, V., Grubb, B., McCourt, B., Burberry, A., Roberts, K. D., Rodriguez-Palacios, A.. 2023-06-02. The basis of antigenic operon fragmentation in Bacteroidota and commensalism. https://doi.org/10.1101/2023.06.02.543472

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