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15 Hidden Causes of IBD (Ulcerative Colitis and Crohn’s)

Written by Nattha Wannissorn, PhD | Last updated:

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Ulcerative colitis and Crohn’s are two major types of Inflammatory Bowel Diseases (IBD), which are chronic inflammatory digestive problems of unknown causes. Read this post to learn more about genetics, lifestyle factors, immune system activation, and infections that contribute to IBD.

What is Ulcerative Colitis and Crohn’s?

Crohn’s and Ulcerative Colitis are two of the most frequently diagnosed subtypes of inflammatory bowel diseases (IBD).

IBDs are chronic inflammatory diseases characterized by inflammation and sores in the gut lining, which can result in diarrhea, abdominal pain, fatigue, fever, rectal bleeding, nutritional deficiencies, and weight loss [1].

Both innate and acquired immunity are activated in IBD, although Crohn’s and colitis follow different patterns of T-cell activation.

Characteristics of Crohn’s Disease

Crohn’s may affect any portion of the gastrointestinal tract, but mostly in the ileum (lower portion of the small intestine) [1].

Crohn’s disease mainly involves Th1 and Th17 overactivation [2].

Crohn’s disease involves ulcerations of all cell layers of the gut lining [1].

Characteristics of Ulcerative Colitis

Ulcerative colitis typically affects the colon and rectum [1].

It is mainly a Th2 dominant condition, although in some cases it is not clear [2].

Ulcerative colitis involves the inflammation of the mucosal layer (innermost cell layer) of the gut [1].

Causes and Risks Factors of Crohn’s and Colitis


If someone has Crohn’s, their identical twin with the exact same genetics has a 50% chance of developing Crohn’s [3].

If someone has ulcerative colitis, their identical twin has a 10% chance of developing colitis [3].

Genetics, therefore, contributes to the development of IBD but is not the sole cause.

Genes that have been associated with Crohn’s and colitis include:

1) CARD15 is Associated with Crohn’s Disease

CARD15 binds to the bacterial cell wall and activates NF-kB, which then stimulates the production of proinflammatory signals [4].

CARD15 mutation results in a defective innate immune response to gut bacteria, which can cause dysbiosis in IBD [5].

2) OCTN1 and OCTN2 are Associated with Crohn’s Disease

Two genetic mutations that in OCTN1 and OCTN2, SLC22A4 and SLC22A5, respectively, have been associated with Crohn’s disease [6].

These mutated genes are mostly expressed in the gut lining, macrophages, and T cells, and cause decreased carnitine transport [6].

However, there is still no direct evidence other than genetic data that demonstrate that these two genes are directly involved in the development of IBD.

3) DLG5 is Associated with Crohn’s Disease and Ulcerative Colitis

DLG5 helps maintain gut lining integrity.

A mutation (G113A) of DLG5 is associated with a CARD15 mutation in Crohn’s disease [7].

4) MDR1 (Multi-Drug Resistant 1) is associated with Crohn’s and Colitis

MDR1 transports drugs and foreign substances outside of cells [8].

MDR1 has been associated with Crohn’s and colitis [8, 9].

MDR1 is associated with treatment-resistant IBD (10).

Mice without MDR1 spontaneously develop colitis [11].

5) PPAR-gamma is Associated with Crohn’s and Colitis

PPARγ gene has been linked to susceptible to a mouse model of Crohn’s [12].

A rare PPARγ mutation was found to be associated with human Crohn’s disease [12].

PPARγ helps to reduce inflammation by inhibiting NF-kB activity.

Ulcerative colitis patients have decreased PPARγ levels (13).

Treatment with a drug that targets PPARγ is effective against ulcerative colitis in a clinical trial (14).

To learn more about PPARγ and how you can improve PPARγ function, read this post.

Environmental Causes of Leaky Gut

5) NSAIDs can Cause Leaky Gut and IBD

NSAID painkillers can temporarily create inflammation and leaky gut, leading to activation of the gut immune system by components of normal gut bacteria (that wouldn’t otherwise cause a problem).

Leaky gut caused by NSAIDs can stimulate T-cell-mediated intestinal inflammation and cause IBD in genetically susceptible humans [15].

Mice lacking IL-10 taking an NSAID to develop colitis within 2 weeks [16].

6) Diet can Contribute to IBD

Lectins and gluten can contribute to the development of IBD [17].

Food additives that can stimulate the immune system and bacterial virulence such as aluminum and iron may also contribute to the development of IBD [18].

Avoiding common inflammatory food substances such as lectins, gluten, and food additive may help manage IBD. If you suffer from IBD, you may want to consider trying the SelfHacked Lectin Avoidance Diet to see if it might help.

7) Smoking and IBD

Active smoking is a risk factor for Crohn’s disease but does not affect the outcome or needs for treatment [19].

Interestingly, smoking is associated with better outcomes for ulcerative colitis, as indicated by reduced needs for treatments and surgery. In addition, quitting smoking is associated with worsened outcome for ulcerative colitis [19].

Interactions between Gut Bacteria and the Gut Immune System

In IBD, gut bacteria interact with receptors on the surface of the gut lining and gut immune cells (TLR and NOD2 receptors) thus activating NF-kB signaling and causing inflammation [2].

8) Normal Gut Bacteria Causes Inflammation Only in Crohn’s and Colitis

In mice lacking IL-10, native (commensal) bacterial species like Enterococcus faecalis and E. coli increases gut inflammation. These two bacterial strains don’t cause increased inflammation in mice that have normal IL-10 [20].

Good bacteria metabolites, such as butyrate, may contribute to IBD.

Butyrate may prevent stem cells in the gut from growing and repairing the gut after an injury or autoimmune diseases like inflammatory bowel disease (IBD) [21]. Butyrate inhibits the growth of these cells by increasing the Foxo3 gene, which is associated with IBD [22].

Gut crypt and butyrate
Gut crypt and butyrate [23]
The gut crypts are structured such that the stem cells at the top are protected from butyrate in the gut. However, in conditions where the villi are sufficiently damaged, the stem cell in the gut may not be protected [23]. Therefore, if you have IBD, butyrate supplementation should be avoided.

9) Introducing Beneficial Strains Alleviates IBD

Supplementation of probiotic VSL#3 is more effective than placebo at reducing inflammatory bowel disease score in ulcerative colitis patients [24].

In rats, Lactobacillus rhamnosus GG does not prevent colitis but is superior to Lactobacillus plantarum 299v in preventing recurrent colitis [25].

In another study, L. plantarum 299V helps with immune-mediated colitis in mice [26].

Protective species include (27):

  • Lactobacillus
  • Bifidobacteria
  • specific beneficial E. coli strains
  • Streptobacillus salivaris
  • Saccharomyces boulardii
  • Clostridium butyricum

10) Some Strains of E. coli Infection May Contribute to UC

E. coli is a normal part of the gut flora. However, certain strains of E. coli grow rapidly in inflammatory environments produce alpha-hemolysin (a toxin) that causes leaky gut, inflammation, and bleeding characteristic of ulcerative colitis [28].

However, it’s possible that E. coli are the consequence of increased inflammation rather than the cause [29].

In fact, the presence and action of E. coli bacteria may actually lower free radical formation by preventing the Fenton reaction and thereby induce remission [30].

A strain of E. coli, called Nissle 1917, is actually considered the equivalent of mesalazine, generally the drug of choice for treating Ulcerative Colitis [31].

E. coli Nissle 1917 (EcN) is the active ingredient of the microbial drug (pharmaceutical-grade probiotic), Mutaflor® [32].

Pathogenic bacteria and viruses

11) Mycobacterium avium paratuberculosis (MAP) is Associated with IBD

One of the most studied infections associated with both Crohn’s Disease and Ulcerative Colitis (UC) is called Mycobacterium avium paratuberculosis (MAP) [33].

It is thought that besides genetic predisposition, other factors that determine whether MAP manifests as Crohn’s Disease or Ulcerative Colitis is the sex of the individual, his or her age, the route of infection, and the dose [33].

Higher exposure to MAP is associated with Crohn’s while a lower exposure is associated with UC [33].

This infection is passed from ruminant animals (those that chew their cud) to humans via consumption of MAP-contaminated meat or secretions (milk) [34].

It may also be passed to humans (or between animals) through MAP-contaminated water [33].

Ruminant animals include cattle, bison, sheep, goats, deer, elk, and the like. Therefore, consumption of beef, lamb, dairy (cow, sheep, and goat), venison and another ruminant wild game carries the risk of MAP infection.

One of the arguments for the MAP – IBD connection is a number of instances where not only did a number of family members receive a diagnosis of IBD, but couples or groups of friends living together had co-diagnoses of IBD –indicating an environmental factor in addition to genetic predisposition. In some families, couples, or housemates, some individuals were diagnosed with Crohn’s Disease and others with Ulcerative Colitis [33].

However, a more recent (2016) study found that while MAP was significantly higher in patients with Crohn’s (29%) than controls (0%), no significant difference was found in the prevalence of MAP in patients with UC compared to controls [35].

Another earlier study found no correlation between MAP infection and either Crohn’s or Ulcerative Colitis [36].

It’s also been suggested that while MAP is a fairly common infection, it tends to colonize intestines that are inflamed due to an already active disease process [37].

And so the jury is still out on MAP and IBD.

12) Salmonella or Campylobacter Infections May Contribute to UC.

Salmonella or Campylobacter infection resulted in 8 to 10 times increased risk for that person developing UC within 1 year following the infection [38].

While the risk for developing UC decreased over time, there was still a heightened risk 10 years post infection [38].

One surprisingly high-risk food for both Salmonella and Campylobacter infections is poultry.

In 2011, tests conducted by the National Antimicrobial Resistance Monitoring System (NARMS) found Campylobacter in nearly half (47%) of all the raw chicken they tested at grocery stores [39].

A Salmonella infection may also be derived from raw poultry during food preparation [40]. The risk of Salmonella infection is also increased by the presence of live chickens. So, raising your own chickens for meat or eggs does carry a risk of infection [41, 42].

13) Clostridium difficile Worsens Outcomes for Those with UC

IBD patients with C. Difficile infection have twice the risk of having a colectomy and 4-6 times the risk of dying [43].

14) Infections of Serpulina, Fusobacterium, Enterobacteriaceae, and/or Gardnerella May Leading to UC

Bacteria that infect the gut, including Serpulina, Fusobacterium, and Enterobacteriaceae can create biofilms on the surface of the gut wall, making it easier for normal gut bacteria to get into the mucosa, where they don’t belong [44].

Fusobacterium varium is significantly higher in the mucosa of patients with ulcerative colitis (84%) than in those with Crohn’s Disease (16%) or other controls (3-13%) [45].

A follow-up study found that a combination of antibiotic therapy against Fusobacterium was effective for patients with Ulcerative Colitis [46].

Aggressive/detrimental strains include (27):

  • Enterococcus faecalis
  • invasive and toxic E. coli strains
  • Eubacterium
  • Peptostreptococcus species
  • Fusobacterium varium
  • Helicobacter species (such as H. pylori) 

Viral Infections

15) Cytomegalovirus Infection May Contribute to UC

Inflammatory cytokines from an inflamed colon, in particular, TNF-alpha, can activate dormant cytomegalovirus and cause it to replicate quickly [47].

Additionally, when the immune system is compromised, such as in the case of immune therapy for UC (steroids), Cytomegalovirus can become activated and make the inflammation worse, causing a vicious cycle [48].


Cytokines Associated with Inflammatory Bowel Disease

(source: http://www.nature.com/nrgastro/journal/v3/n7/fig_tab/ncpgasthep0528_T2.html)

CytokineCrohn’s diseaseUlcerative colitis

aRepresentative of a large number of chemokines. Abbreviations: the arrow indicates increase; IL, interleukin; N, normal.

Innate immune response
IL-1betaup arrowup arrow
TNFup arrowup arrow
IL-6up arrowup arrow
IL-8aup arrowup arrow
IL-12up arrowN
IL-18up arrowup arrow
IL-23up arrowN
IL-27up arrowN
T-cell response
IFN-gammaup arrowN
IL-5Nup arrow
IL-13Nup arrow
IL-17up arrowN
IL-21up arrowN
How IBD susceptibility gene products modulate host cells function response to microbial flora. source: doi:10.1038/nature06005
Receptor activation in IBD http://www.nature.com/nrgastro/journal/v3/n7/full/ncpgasthep0528.html

Probiotic Products that Contain Beneficial Strains

Culturelle contains L. rhamnosus GG

Avoiding lectins in the diet can help ease unwanted inflammation and may calm symptoms, try out our Lectin Avoidance Diet Cookbook.

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About the Author

Nattha Wannissorn

Nattha Wannissorn

Nattha received her Ph.D. in Molecular Genetics from the University of Toronto and her undergraduate degree in Molecular and Computational Biology from the University of Pennsylvania.
Aside from having spent 15 years in biomedical research and health sciences, Nattha is also a registered holistic nutritionist, a certified personal trainer, has a precision nutrition level 1 certification, and is a certified functional diagnostic nutrition practitioner. As a holistic practitioner with a strong science background, Nattha is an advocate of science literacy in health topics and self-experimentation.

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