Many studies have reported changes in gut microbiome composition in patients with inflammatory bowel disease (IBD), including ulcerative colitis (UC), when compared with healthy individuals. While that clearly raises the question about the key role played by gut microbes in IBD pathogenesis, we have yet to pinpoint the causative microbes and their mechanisms. Most studies to date have examined fecal microbiota composition in patients with IBD and controls using prospective or cross-sectional study designs, which include patients with a confirmed diagnosis. In that setting, it is difficult to determine whether changes in gut microbiota composition or function are secondary to the effect of inflammation.

In a recent study published in Gastroenterology, researchers at the Farncombe Institute, McMaster University and Mt Sinai Hospital, University of Toronto used a unique cohort of subjects at risk for IBD ( led by Dr. Ken Croitoru, who had been following the subjects over time since 2008, to help answer those questions.  

The study looked at asymptomatic, healthy individuals who had a first-degree relative with IBD and were therefore at risk for disease development. Participants provided a fecal sample at recruitment (pre-disease) and were then followed over time, or until a diagnosis of UC, at which point they provided another fecal sample (post-disease). Thirteen individuals who developed UC were included in the study. Another 48 subjects, who were matched with the UC patients based on age, sex, geography and time of recruitment and who were also at risk for disease but remained healthy, were included as healthy controls. Using next-generation sequencing, bacterial isolations and functional testing, researchers then compared microbiota composition and proteolytic activity in fecal samples from subjects who remained healthy with those who provided fecal samples before and after UC diagnosis.

Not surprisingly, the authors reported changes in microbiota composition, especially in post-disease samples. They also found in pre-disease samples a lower abundance of anti-inflammatory taxa Adlercreutzia. However, a key finding was the functional differences detected between individuals at pre-disease stage and those who did not develop UC at follow up. Pre-disease fecal samples exhibited increased proteolytic and elastolytic activity, also observed in the feces of individuals who had developed UC.

“Increased proteolytic activity has been reported in IBD patients before, but the source has mainly been attributed to host tissues, and it never has been demonstrated prior to disease development,” said Dr Heather Galipeau, lead author of the study and Research Associate at McMaster University.

Metagenomic analysis identified pathways and gene families related to protein metabolism and proteases that were significantly different between the subjects who remained healthy and those who went on to develop UC, suggesting a bacterial component to the pre-disease proteolytic signature. Moreover, the proteolytic activity that was detected prior to UC onset correlated with the abundance of known proteolytic microbes, such as Bacteroides vulgatus.

Using two different models of colonization, the authors further studied the bacterial contribution and functional relevance of the proteolytic signature discovered. Germ-free mice were colonized either at birth or in adult life using pre-disease, post-disease or control fecal samples. Mice colonized with pre- and post-disease fecal samples had higher proteolytic activity than mice colonized with the control samples and developed a heightened colonic inflammatory immune tone.

“Our study identifies a pre-disease functional microbial signature in patients at risk for IBD who develop UC at follow up,” says Dr Elena Verdu, Professor in the Department of Medicine at McMaster University. “We further demonstrate functional relevance by transferring this proinflammatory phenotype through microbiota colonization of germ-free mice.”

The authors highlight that the results should be confirmed in larger cohorts and investigated in patients with Crohn’s disease. Confirmation of the results could lead to novel non-invasive biomarkers for earlier diagnosis or new treatments directed at patient populations with high proteolytic activity using bacterial anti-proteases.

Graphical abstract created by Heather Galipeau and published in Gastroenterology.


Galipeau HJ, Caminero A, Turpin W, et al. Novel fecal biomarkers that precede clinical diagnosis of ulcerative colitis. Gastroenterology. 2020. doi: 10.1053/j.gastro.2020.12.004.