2. Infections as a cause of IBD?

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We partnered with other researchers and completed several studies examining the bowel tissue and blood gathered from the IBD and healthy participants, to try and figure out if certain kinds of infections might cause IBD.

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• Together with researchers at Stanford University in California, we were the first to report on the normal human gut microbiome. The human gut microbiome refers to the bacteria or ‘gut bugs’ that normally reside within the bowel. All humans have millions of bugs of different varieties in their bowels that help keep the bowels working properly.

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Eckburg P, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson K, Relman DA.  Diversity of the human intestinal microbial flora. Science 2005; 308:1635-1638.

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• Together with researchers from McMaster University in Hamilton, Ontario, we searched for the presence of Helicobacter pylori, the bug that is known to cause stomach ulcers. We found that some people with ulcerative colitis had DNA for this bug in their bowel, and that none of the non-IBD participants had this bug, so we initially thought it might provide a clue to a cause of IBD. Since this study, however, others have not found Helicobacter pylori to be important for people with ulcerative colitis, even in a subset.

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Streutker C, Bernstein CN, Chan VL, Riddell RH, Croitoru K. PCR analysis for species-specific Ribosomal DNA detects Helicobacter species DNA in intestinal tissues from patients with inflammatory bowel disease. Journal of Clinical Microbiology 2004; 42: 660-664.

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• Together with researchers at Agriculture Manitoba, we looked for the presence of a gut bug called Mycobacterium avium paratuberculosis. This bug causes a disease in cattle called Johne’s disease that is very much like human Crohn’s disease. We did not find that any tissues from persons with Crohn’s disease or from the study’s healthy participants contained any DNA for this bug.

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Bernstein CN, Nayar G, Hamel A, Blanchard JF. A pursuit of animal borne infections in the mucosa of subjects with inflammatory bowel disease and population-based controls. Journal of Clinical Microbiology 2003; 41:4986-90.

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• In related studies, together with researchers at the University of Wisconsin, we tested the blood of the IBD and healthy (non-IBD) participants to determine if the blood contained antibodies to Mycobacterium avium paratuberculosis. We did not find that persons with Crohn’s disease were any more likely to have developed antibodies to fight this infection than healthy individuals, so we concluded that it was unlikely that this gut bug is important in IBD.

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Bernstein CN, Wang MH, Sargent M, Brant SR, Collins MT. Testing the interaction between NOD-2 status and serological response to Mycobacterium paratuberculosis in IBD. Journal of Clinical Microbiology 2007; 45: 968-71.

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Bernstein CN, Blanchard JF, Rawsthorne P, Collins MT. A population-based case control study of seroprevalence of Mycobacterium paratuberculosis in patients with Crohn's disease and ulcerative colitis. Journal of Clinical Microbiology 2004; 42:1129-1135.

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• Together with researchers in the Faculty of Agriculture, University of Manitoba, we explored whether there were any gut bugs unique to IBD. We found a special type of Escherichia coli (E coli) that was especially common in Crohn’s disease. The E coli had properties of an adherent invasive E coli; this technical description refers to how the E coli interacts within its environment in the gut. What was exciting about this finding is that other labs in other countries were also discovering a similar E coli associated with Crohn’s disease, which confirmed we were on to something important. In a related study we analyzed tissue from a tissue bank of newly diagnosed patients established by the Crohn’s and Colitis Foundation of Canada, and we found an increased presence of this E coli in those tissues, suggesting that this bug is present early on in the disease process. Hence, it remains a possibility that this bug is a trigger for Crohn’s disease.

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Sepehri S, Khafipour E, Bernstein CN, Coombes BK, Pilar AV, Karmali M,  Ziebell K, Krause DO. Characterization of Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease. Inflammatory Bowel Diseases 2011: 17: 1451-63.

 

Krause DO, Dowd SE, Little AC, Bernstein CN. Complete genome sequence of adherent invasive Escherichia coli UM146 isolated from ileal Crohn’s disease biopsy tissue. Journal of Bacteriology 2010; 193(2):583.

 

Sepehri S, Kotlowski R, Bernstein CN, Krause DO. Phylogenetic analysis of inflammatory bowel disease associated Escherichia coli and the fimH virulence determinant. Inflammatory Bowel Diseases 2009; 15:1737-45.

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Kotlowski R, Bernstein CN, Sepehri S, Krause DO. High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut 2007; 56: 669-75.

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Sepehri S, Kotlowski R, Bernstein CN, Krause DO. Microbial diversity of inflamed and non-inflamed gut biopsy tissues in inflammatory bowel disease. Inflammatory Bowel Diseases 2007:13: 675-683.

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• We examined whether rubella (German measles) might contribute to the development of IBD. This question was triggered by two observations: (1) rising rates of Crohn’s disease among boys and young men compared to girls and young women; and (2) that until the 1980s, only girls were vaccinated against rubella and boys were not. We measured antibody responses to three viruses, measles, mumps and rubella, in persons with IBD compared to healthy individuals without IBD. We found that the healthy individuals were more likely to have antibodies to rubella (meaning they were exposed to rubella) than individuals with IBD,  suggesting that the presence of the rubella may have been protective against developing IBD.

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Bernstein CN, Rawsthorne P, Blanchard JF. A population-based case control study of measles, mumps and rubella and inflammatory bowel disease. Inflammatory Bowel Diseases 2007;13:759-762.

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Other Publications

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Kuenzig ME, Bernstein CN, Coward S, Dummer TJB, Elten M, Jones JL, Kaplan GG, Lavigne E, Murthy SK, Pena-Sanchez JN, Targownik LE, Li Z, Guan J, Tang F, Benchimol EI and the Canadian Gastro-Intestinal Epidemiology Consortium (CanGIEC). The association between artificial light at night and inflammatory bowel disease incidence, surgery, and health services utilization: population-based observational studies. Inflammatory Bowel Diseases 2026; in press.

 

Introduction: The urban environment increases the risk of inflammatory bowel disease (IBD). Specific environmental exposures involved in IBD etiology remain unknown. We examined the association between outdoor artificial light at night (ALAN) and IBD incidence, surgery, and health services utilization (HSU).

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Methods: Using population-based deterministically linked health administrative data from Ontario, Canada we conducted a birth cohort study (incidence), matched case-control study (incidence), and cohort study (surgery, HSU). Individuals with IBD were identified using previously validated algorithms. ALAN, the average digital number of lights consistently present, was a 3-level variable: <35 (reference), 35-60, > 60. We used Cox proportional hazards models (birth cohort, surgery), conditional logistic regression (matched case-control study), and Poisson regression (HSU).

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Results: Among 3 929 374 individuals in the birth cohort, 5539 (0.1%) developed IBD; no association between ALAN at birth and IBD was observed (35-60: hazard ratio [HR] 1.03, 95% confidence interval [CI] 0.87-1.22; >60: HR 0.93, 95% CI 0.78-1.11). Among 32 176 IBD cases matched to 160 709 controls, high ALAN was associated with a lower IBD risk (>60: odds ratio [OR] 0.84, 95% CI 0.78-0.92); there was no association between IBD and the middle ALAN level. High ALAN was associated with fewer IBD-specific outpatient visits (rate ratio [RaR] 0.93, 95% CI 0.86-0.99) and hospitalizations (RaR 0.83, 95% CI 0.72-0.95) 1 year after diagnosis. ALAN was not associated with surgery or emergency department visits.

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Discussion: The association between ALAN and IBD is heterogeneous. Additional research is needed to understand how ALAN impacts IBD and identify other environmental exposures contributing to IBD etiology.

 

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Xue M, McSHane C, Kim J, Khorasaniha R, Leibovitzh H, Shao J, Chen R, Jeong S, Li Q,. Madsen KL, Griffiths AM, Walters TD, Steinhart AH, Dieleman LA, Huynh HQ, Panaccione R, Aumais GL, Bitton A, Mack D, Jacobson K, Bressler B, Marshall JK, Plotkin L, Focht G, Bernstein CN, El-Matary W, Hyams JS, Otley A, Lee SH, Turner D, Armstrong H, Croitoru K, CCC-GEM consortium, Turpin W. β-Glucan and Inulin Estimated Intake are Associated with Reduced Risk of Crohn’s Disease, Improved Gut Barrier and Systemic Inflammation Markers, and Multi-Omic Signatures in a High-Risk Cohort.  Gastroenterology 2026; Oct;171(4):641-655.    

 

Background & aims: The cause of Crohn's disease (CD) remains unclear; however, evidence suggests fiber intake may play a role. We aimed to investigate the association between intake of total fiber and select fermentable fiber subtypes and future risk of CD in an at-risk population.

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Methods: The Genetic, Environmental, Microbial Project prospectively followed asymptomatic first-degree relatives of individuals with CD. Habitual intake of total fiber and select fiber subtypes was estimated from baseline food frequency questionnaires and biologic samples were collected. Incident CD was confirmed during follow-up. Cox proportional hazards models estimated hazard ratios (HRs) for CD. Associations between fiber subtype intake and urinary fractional excretion of lactulose-mannitol ratio, C-reactive protein, gut microbiota (16S ribosomal RNA sequencing), and serum proteomics (Olink) were evaluated using multivariable regression models.

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Results: During a median follow-up of 8.5 years of 3314 first-degree relatives, 94 developed CD. Higher β-glucan (HR, 0.70; 95% confidence interval, 0.54-0.92) and inulin (HR, 0.68; 95% confidence interval, 0.49-0.96) intake were associated with lower CD risk. Associations were strongest in those with higher baseline relative abundance of Erysipelotrichaceae UCG-003, but weaker with higher Colidextribacter. Higher β-glucan and inulin intake were associated with lower lactulose-mannitol ratio, lower abundance of pathobionts (Ruminococcus torques and Lachnoclostridium), and lower concentrations of inflammation- and barrier-related proteins, including C-reactive protein, triggering receptor expressed on myeloid cells-1, oncostatin M, and matrix metalloproteinase 9.

Conclusions: Higher estimated β-glucan and inulin intake was associated with preserved gut barrier function, lower systemic inflammatory markers, and lower CD risk, which was modified by the microbial context. These findings support microbiome-informed dietary strategies and intervention trials for CD prevention.

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Leibovitzh H, Neustaeter A, Lee SH, Xue M, Espin-Garcia O, Olivera PA,. Huynh HQ, Griffiths AM, Turner D, Madsen KL, Silverberg MS, Steinhart AH, Mack DR, Jacobson K, Moayyedi P, Aumais G, Bernstein CN, Marshall JK, Panaccione R, Xu W, the CCC GEM Project Research Consortium, Turpin W, Croitoru K.  Association of IL-23 receptor genetic variants with risk of Crohn’s disease and gut microbiome and intestinal permeability in a cohort of healthy first-degree relatives of subjects with Crohn’s disease. Clinical Gastroenterology and Hepatology 2026; in press.

 

Background & aims: Single nucleotide polymorphisms in the interleukin23 receptor gene are associated with Crohn's disease, suggesting a role in pathogenesis, and several biologic agents targeting this pathway are now established therapies. Interleukin23 has been suggested to be involved in regulation of intestinal barrier function and may impact gut microbial composition. We investigated whether interleukin23 receptor genetic variants predict Crohn's disease risk and influence gut barrier function and microbiome composition in healthy first-degree relatives.

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Methods: A total of 3055 healthy first-degree relatives with genotypic data from the Crohn's and Colitis Canada Genetic, Environmental, Microbial (CCC-GEM) cohort were included. A weighted interleukin23 receptor genetic risk score was generated from 7 Crohn's disease-associated interleukin23 receptor single nucleotide polymorphisms and dichotomized as high (top quintile) vs low interleukin23 receptor genetic risk score. A subset of this cohort was assessed for intestinal permeability (n = 1698) and microbiome profiling (n = 2523). Cox proportional hazards models evaluated Crohn's disease onset risk.

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Results: High interleukin23 receptor genetic risk score was associated with increased Crohn's disease risk (hazard ratio, 1.67; 95% confidence interval, 1.01-2.75; P = .044). This association remained significant after adjusting for fecal calprotectin, indicating genetic risk independent of subclinical inflammation. High interleukin23 receptor genetic risk score was not associated with intestinal permeability (P = .84) but was associated with differences in 15 genera, including decreased Faecalibacterium and increased Akkermansia (q < 0.1).

Conclusions: High interleukin23 receptor genetic risk score was associated with increased Crohn's disease risk in healthy first-degree relatives and was associated with microbial differences, but not with intestinal permeability. These findings suggest potential clinical applications for interleukin23 receptor genetic risk score in identifying high-risk individuals who may benefit from closer monitoring or future interleukin23 pathway-targeted preventive interventions.

 

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Narvey S, Ghia JE, Marrie RA, Armstrong H, Bernstein CN. Heavy Metals and Inflammatory Bowel Disease. Gastroenterology 2025; in press.

 

Given the global impact of inflammatory bowel disease (IBD), its uncertain etiology merits further attention. IBD pathogenesis is multifactorial: Humans are exposed to many environmental factors throughout their life-spans, composing the “exposome,” that directly and indirectly affect the gut microbiota, intestinal mucosa, epithelial cells, and gut immune cells. Potentially, the most consequential components of our exposome include dietary factors, air and water pollution, drugs, microbes, stress, and lifestyle factors.

Heavy metals are environmental factors that warrant greater examination in the context of IBD. The increasing prevalence of IBD, in parallel with drastically increased exposure to toxic heavy metals as a consequence of global industrialization, has prompted investigations into the effects of heavy metals on the gut. Various heavy metals cause toxicity through reactive oxygen species and carcinogenicity through altered gene expression. However, less is known about the impact of heavy metals on intestinal immune activity, the gut microbiota, or on IBD pathogenesis. This commentary reviews key concepts and synthesizes findings from diverse investigations implicating heavy metals in the pathogenesis of IBD. We identify gaps in our understanding of the association between heavy metals and IBD and discuss potential avenues for addressing these gaps.

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Xue M, Lee SH, Shao J, Leibovitzh H, Huynh HQ, Griffiths AM, Turner D, Madsen KL, Moayyedi P, Steinhart AH, Silverberg MS, Deslandres C, Bitton A, Mack DR, Jacobson K, Ropeleski MJ, Cino M, Aumais G, Bernstein CN, Panaccione R, Bressler B, Espin-Garcia O, Xu W, Turpin W, Croitoru K; Crohn’s and Colitis Canada Genetics Environment Microbial Project Research Consortium. Metabolomics reveal distinct molecular pathways associated with future risk of Crohn's Disease. Gut Microbes 2025 Dec;17(1):2546998.

 

Host - microbiome interactions are central to Crohn's disease pathogenesis; yet the early metabolic alterations that precede disease onset remain poorly defined. To explore preclinical metabolic signatures of Crohn's disease, we analyzed baseline serum metabolomic profiles in a nested case-control study within the Crohn's and Colitis Canada - Genetics, Environment, Microbiome (CCC-GEM) Project, a prospective cohort of 5,122 healthy first-degree relatives of Crohn's disease patients. We included 78 individuals who later developed Crohn's disease and 311 matched first-degree relatives who remained disease-free. In an untargeted assessment of metabolomic data, we identified 63 metabolites significantly associated with future Crohn's disease risk. Integrative analyses further identified multiple associations between Crohn's disease-related metabolites and proteomic markers, gut microbiome composition, antimicrobial antibody, fecal calprotectin and C-reactive protein. Quinolinate, a tryptophan catabolite, was elevated in individuals who later developed Crohn's disease and showed strong positive correlations with C-reactive protein, fecal calprotectin, and C-X-C motif chemokine ligand 9 (CXCL9).In contrast, higher levels of ascorbate and isocitrate were associated with reduced Crohn's disease risk and were negatively correlated with C-reactive protein and Crohn's disease -associated proteins. These findings identify several distinct molecular pathways that contribute to Crohn's disease pathogenesis.

 

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Lee SH, Turpin W, Espin-Garcia O, Xu W, Croitoru K; Crohn's and Colitis Canada-Genetic, Environmental, Microbial (CCC-GEM) Project Research Consortium. Development and Validation of an Integrative Risk Score for Future Risk of Crohn's Disease in Healthy First-Degree Relatives: A Multicenter Prospective Cohort Study. Gastroenterology 2025 Jan;168(1):150-153.

 

Despite advances in medical therapy, approximately one-half of patients with Crohn’s disease develop complications ultimately requiring surgery. Currently, no treatment offers a chance of cure. The increasing incidence and prevalence of Crohn’s disease globally pose a substantial burden at the population and individual levels. Thus, a better understanding of the early triggers of Crohn’s disease is desperately needed to enhance early detection, improve medical therapy, and offer a possibility of interventions that prevent development of Crohn’s disease. Previous studies have reported candidate predisease biomarkers associated with future development of Crohn’s disease, supporting the concept of a preclinical phase. However, these studies lack integration of individual predisease signatures and the multidimensional mechanisms of disease pathogenesis. To date, no risk-stratification model has combined multiple predictive biomarkers to predict future risk of developing Crohn’s disease in healthy at-risk individuals.

In this study, we leveraged a large prospective multicenter cohort of healthy first-degree relatives of people with Crohn’s disease —the Crohn’s and Colitis Canada-Genetic, Environmental, Microbial (GEM) study. Using available demographic characteristics, physiologic biomarkers, and fecal microbiome data, we developed an integrative multidimensional risk model—the GEM integrative risk score (IRS)—that predicts an first-degree relatives future risk of developing Crohn’s disease. We subsequently validated the performance of GEM-IRS in 2 testing cohorts.

We included participants with a minimum 3 months of follow-up duration as of February 28, 2021; participants recruited from countries with sufficient median follow-up duration of at least 5 years (ie, Canada, United States, and Israel). Fecal microbial profiling was performed by 16S ribosomal RNA sequencing; microbial function was imputed using PICRUSt2. Fecal calprotectin (FCP) was measured as a biomarker of gut inflammation and intestinal barrier function was assessed by the ratio of the urinary fractional excretion of lactulose over that of mannitol (LMR).

After quality control of microbiome data and removal of missing data, there were 2619 participants (1170 North American training set, 1141 North American test set, and 308 from Israel), which we used for subsequent analyses. During a median follow-up duration of 6.8 years (interquartile range 4.2–9.6 years), 61 of 2619 participants (2.3%) developed Crohn’s disease.

The GEM-IRS, built with random survival forest, resulted in a predictive performance measured by a Harrell’s concordance index of 0.951 (95% CI, 0.925–0.976) in the North American training cohort. On validation, the GEM-IRS had a concordance index of 0.789 (95% CI, 0.713–0.865) in the pooled testing cohort. Of note, the performance was higher compared with the other models tested (ie, 0.777 for gradient boosting survival and 0.717 for penalized Cox proportional hazards model).

The cumulative incidence of CD in the 2 testing cohorts was assessed using the quartiles of the GEM-IRS from the training cohort. The fourth quartile compared with the lower 3 quartiles showed a significantly increased risk of Crohn’s disease onset (hazard ratio, 6.42; 95% CI, 3.10–13.30) in the pooled testing cohort.

 

 

Herman SM, MD, Zaborniak K, Bernstein CN. Insight into IBD pathogenesis: Is the answer blowing in the wind? Inflammatory Bowel Diseases 2022; Mar 2;28(3):486-491.

 

Inflammatory bowel diseases (IBD) including Crohn's disease and ulcerative colitis are conditions characterized by immune dysregulation to a trigger in those with a genetic predisposition. Environmental factors are thought to contribute to IBD, but no definite trigger has been identified. Aeroallergens have not been thoroughly investigated in their potential contribution to the pathogenesis to IBD. The geographic distribution of aeroallergens and IBD, the association of atopic disease with IBD, seasonality and IBD, and cross-reactive food allergens require further study with implications for targeted dietary and immunomodulatory therapies.

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Siegel C, Bernstein CN. Risk Stratifying Patients with IBD – Identifying Patients at High- vs. Low-risk of Complications. Clinical Gastroenterology and Hepatology 2020 18(6):1261-1267.

 

This editorial reviewed the available evidence to classify patients with IBD at either high risk or low risk for progressing to more aggressive disease or complicated outcomes.

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Bernstein CN. Is antibiotic use a cause of IBD worldwide? Inflammatory Bowel Diseases 2020; 26: 448-449.

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This editorial reviewed the evidence for antibiotics as a possible culprit in triggering IBD onset.

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Bernstein CN, Burchill C, Targownik LE, Singh H, Roos LL. Events within the first year of life, but not the neonatal period, affect risk for later development of inflammatory bowel diseases. Gastroenterology 2019; 156(8):2190-2197.

 

We performed a population-based study to determine whether there was an increased risk of inflammatory bowel diseases (IBD) in persons with critical events at birth and within 1 year of age. We collected data from the University of Manitoba IBD Epidemiology Database, which contains records on all Manitobans diagnosed with IBD from 1984 through 2010 and matched controls. From 1970 individuals' records can be linked with those of their mothers, so we were able to identify siblings. All health care visits or hospitalizations during the neonatal and postnatal periods were available from 1970 through 2010. In previous studies using this data source we showed that development of IBD was not associated with being born by caesarean section (versus vaginal delivery) and was not associated with mothers’ having antenatal or perinatal infections. In this study we collected data on infections, gastrointestinal illnesses, failure to thrive, and hospital readmission in the first year of life and sociodemographic factors at birth. From 1979, data were available on gestational age, Apgar score, neonatal admission to the intensive care unit, and birth weight. We compared incident rate of infections, gastrointestinal illnesses, and failure to thrive between IBD cases and matched controls as well as between IBD cases and siblings. Data on 825 IBD cases and 5999 matched controls were available from 1979. Maternal diagnosis of IBD was the greatest risk factor for IBD in offspring (increased the risk for IBD development in offspring 4.5x). When we assessed neonatal events, only being in the highest vs lowest socioeconomic quintile increased risk for later development of IBD. For events within the first year of life, being in the highest socioeconomic quintile at birth and infections increased risk for developing IBD at any age. Infection in the first year of life was associated with diagnosis of IBD before age 10 years (by 3x)  and before age 20 years (by 1.5x) Risk for IBD was not affected by gastrointestinal infections, gastrointestinal disease, or abdominal pain in the first year of life. In a population-based study, we concluded that infection within the first year of life was associated with a diagnosis of IBD. This might be due to use of antibiotics or a physiologic defect at a critical age for gut microbiome development.

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Samarani S, Mack DR, Bernstein CN, Iannello A, Debbeche O, Jantchou P, Faure C, Deslandres C, Amre DA, Ahmad A. Activating Killer-cell Immunoglobulin-like Receptor genes confer risk for Crohn’s disease in children and adults of the Western European descent: Findings based on case-control studies. PLOS One 2019;14(6):e0217767. Published 2019 Jun 13

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Killer-cell Immunoglobulin-like Receptor genes encode receptors, which are mainly expressed on, and control functional activities of, Natural Killer (NK) cells. These cells are important in the inflammatory response. Activated NK cells can potentially cause tissue destruction, which might be important in development Crohn disease. In this study we performed case control studies on three independent Canadian Crohn’s disease patient cohorts (all of Western European descent): two comprising children [one from Montreal (438 children) and one from Ottawa (213 children)] and one comprising predominantly adults (from Winnipeg having 364 adults)]. We assess the gene types for for activating Killer-cell Immunoglobulin-like Receptor. We observed strong associations between all the six Killer-cell Immunoglobulin-like Receptor genes and Crohn’s disease in Ottawa children. The results were mostly replicated in the Montreal cohort of children nd the Winnipeg cohort of adults. Similarly, associations between five genes were observed in the adult Winnipeg cohort. An overall analysis for all cohorts showed strong associations with four of the genes, with the strongest association evident for a gene called KIR2DS5. In the combined analysis for four Killer-cell Immunoglobulin-like Receptor genes, individuals carrying one or more of the Killer-cell Immunoglobulin-like Receptor genes were at significantly higher risks for acquiring Crohn’s disease.

We concluded that activating Killer-cell Immunoglobulin-like Receptor genes are associated with risk for developing CD in both children and adults.

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