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Causes and Risks for IBD // The Manitoba IBD Risk Factor Study

In 2002, thanks to funding support from the Crohn’s and Colitis Foundation of Canada, we recruited nearly 500 adults under age 50 with IBD and almost 500 adults who were generally healthy and did not have IBD, to learn about possible factors that might have increased the risk of developing IBD.

We had two main questions in this study:

What are the risk factors associated with developing IBD?

Can we uncover possible causes of IBD?

What did we do?

  • Everyone in the study answered questions about lifestyle and dietary habits, particularly during childhood.

  • Everyone provided blood samples so we could study genetic markers (using DNA) and circulating blood markers (using serum).

  • A smaller group, including those with IBD and those without the disease, had colonoscopies so that we could collect biopsies (tissue samples) directly from the bowel.

What did we find?

1. Risk Factors for IBD

2. Infections as a cause of IBD?

1. Risk Factors for IBD


The survey information suggested several protective factors that may help decrease the risk of developing Crohn’s disease.  These included: growing up on a farm; having unpasteurized milk as the main type of milk as a child; having a pet cat before the age of 5; growing up in a large family.  While these may sound surprising, the findings somewhat support the “hygiene hypothesis”. This refers to the possibility that growing up in a crowded, less clean environment is actually protective against getting a chronic immune disease like Crohn’ disease. 


Why would this be? It is thought that if young children are exposed to infections and gut bugs, even if they do not get sick from these infections or bugs, it ‘exercises’ their immune system and helps it to develop in a healthier way.

The survey information also suggested several factors that may increase the risk of developing IBD.  These included: being Jewish; having a relative with IBD; ever having smoked; living with a smoker. Our findings confirmed those of other studies, which had also found an increased risk of developing IBD among smokers, individuals of Jewish background, and in families where someone already has IBD; our study highlighted that second hand smoke exposure can also increase the risk.

Bernstein CN, Rawsthorne P, Cheang M, Blanchard JF. A population-based case control study of potential risk factors for IBD. American Journal of Gastroenterology 2006; 101: 993-1002.

2. Infections as a cause of IBD?

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.

  • 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.

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.

  • 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.

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.

  • 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.

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.

  • 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.

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.

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.

  • 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.

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.

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.

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.

  • 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.

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.

Other Publications

Herman SM, MD, Zaborniak K, Bernstein CN. Insight into IBD pathogenesis: Is the answer blowing in the wind? Inflammatory Bowel Diseases 2021; in press.


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.

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.

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

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

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.

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

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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