Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases

Shan, Y.; Lake, J.; Cham, C. M.; Zhu, M.; Kaur, D.; Ringus, D.; Fei, N.; Weber, C. R.; Spedale, M.; Theriault, B.; Dalal, S.; Rubin, D. T.; Fiebig, A.; Crosson, S.; Lolans, K.; Comstock, L.; Eren, A. M.; Basu, A.; Pott, S.; Sogin, M.; Liu, C.; Chang, E. B.

doi:10.1101/2023.10.29.564605

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bioRxiv · 10.1101/2023.10.29.564605

Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases

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Abstract

Inflammatory bowel diseases (IBD) arise from a convergence of underlying genetic susceptibility, environmental factors, and shifts in gut microbiota function and membership. Although the latter may trigger and contribute to IBD, there is little consensus on a specific causative pathogen. In this study, we demonstrate that commensal Bacteroides fragilis strains from ulcerative colitis (UC) patients before and during the development of ileal pouchitis engraft and promote colitis in specific pathogen free (SPF) IL-10 deficient (IL-10-/-) mice, but not in wild type SPF mice or when mono-associated in germ free mice. The colitis in IL-10-/- mice was also associated with significant alterations in commensal microbiota potentially important for maintaining intestinal and immune homeostasis. UC pouchitis B. fragilis also engrafts in DSS-induced colitis in WT SPF mice, indicating a fitness advantage under conditions of mucosal inflammation over other commensals in the gut microbiota. These findings show that gut inflammation promotes the expansion and fitness of UC-derived Bacteroides species that is associated with changes in the SPF gut microbiota and may be promote colitis in genetically susceptible hosts. ImportanceThis study supports the notion that human inflammatory bowel diseases arise from the emergence of indigenous pathobionts in genetically-prone subjects. Colitis-promoting pathobionts are well-suited to establish themselves in the host inflammatory environment and outcompete endogenous microbiota. Once engrafted, the pathobiont can further aggravate inflammation in a genetically-susceptible host. Such complex interplay among several factors creates a vicious pro-inflammatory cycle and promotes disease development. These findings are consistent with our previous clinical observation that B. fragilis, an otherwise low-abundance commensal species, expands prior to the development of UC pouchitis. We believe these findings are relevant to the pathogenesis of UC pouchitis and possibly human inflammatory bowel diseases in general, underscoring the role of commensal to pathobiont transitions, rather than classical pathogens, in promoting and exacerbating the onset of human IBD.

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Shan, Y., Lake, J., Cham, C. M., Zhu, M., Kaur, D., Ringus, D., Fei, N., Weber, C. R., Spedale, M., Theriault, B., Dalal, S., Rubin, D. T., Fiebig, A., Crosson, S., Lolans, K., Comstock, L., Eren, A. M., Basu, A., Pott, S., Sogin, M., Liu, C., Chang, E. B.. 2023-10-29. Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases. https://doi.org/10.1101/2023.10.29.564605

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