Extended Data Fig. 10: Working hypothesis.

The results of our study may indicate that certain species from the genus Bacteroides, particularly those recently reclassified under the genus Phocaeicola (for example Bacteroides vulgatus & Bacteroides dorei), may be implicated in the transition from remission to active disease in UC. We hypothesize that a stressor in the UC gut such as nutrient deprivation or cell-to-cell competition may increase protease production, and a switch in the utilization of carbohydrates to proteins as a nutrient source. Some of these proteases may be involved in the disruption of the epithelial barrier, allowing an influx of innate immune cells which further exacerbate disease.