Inflammatory Bowel, Crohn’s Disease, and Gut Microbes

“Fix your gut!” seems to be the standard advice from most healthy living blogs, but concrete advice on how to actually accomplish this seems to be lacking. While general suggestions abound, specific actions that actually work for an individual are hard to find.

I find the microbiome intriguing: the complexity of the interaction between our human genome, the gut microbiome, and environmental factors is mind-boggling.

While what we eat is important to our microbiome, our genes also play a role in which gut bugs will flourish and which ones will never take up permanent residence.

All of the general advice — fix your gut, eat more fiber, eat fermented foods, avoid sugar, grains, dairy, etc. — may work for some but not for everyone. We need to get personal here and take a good look at some of the genes that affect our microbiome.

Genetic variants:

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NOD2 also referred to as CARD15, is a gene that encodes a protein (nucleotide-binding oligomerization domain-containing protein 2) that recognizes bacteria in order to initiate an immune response.  Specifically, the immune response to lipopolysaccharide (LPS) involves NOD2.  The LPS is an endotoxin and can be found in the outer membrane of Gram-negative bacteria.[ref] The background section of this study will give you more specific information on NOD 1 and 2 if you are wanting to dive deeper.

There are quite a few NOD2 variants that have been studied. Many seem to increase the risk of Crohn’s disease and inflammatory bowel diseases.

rs2066844 -risk allele is T; also known as SNP8 and R702W in studies

  • The T allele is linked to a much higher risk of Crohn’s disease, especially for homozygotes[ref][ref][ref][ref]
  • The T allele has links to a lower risk of tuberculosis.
  • This SNP is not associated with common gastrointestinal diseases such as reflux or irritable bowel syndrom[ref]

Check your genetic data for rs2066844 (23andMe v4, v5):

  • T/T: 17-35x increased risk for Crohn’s disease
  • C/T: 2-3x increased risk for Crohn’s disease
  • C/C: typical

Members: Your genotype for rs2066844 is .

rs2066845 – risk allele is T; also known as SNP 12 and G908R in studies

  • The T allele is linked to a much higher risk of Crohn’s[ref][ref]
  • A 2014 Algerian study found this SNP to be associated with Crohn’s disease (OR = 13.2)[ref]

Check your genetic data for rs2066845 (23andMe v4):

  • C/C: 17-35x increased risk for Crohn’s disease
  • C/G: 2-3x increased risk for Crohn’s disease
  • G/G: typical

Members: Your genotype for rs2066845 is .

rs2066842 – risk allele is T; also known as SNP5 or P268S in studies

  • Several studies have found that this SNP to be associated with an increased risk of ulcerative colitis[ref][ref]
  • A 2005 study found the T allele to decrease the risk of allergic rhinoconjunctivitis by about 20%[ref]
  • A small 2015 study found this SNP to be associated with autoimmune chronic uveitis (OR=4.03)[ref]

Check your genetic data for rs2066842 (23andMe v4, v5):

  • T/T: Increased risk of IBD
  • C/T: Increased risk of IBD
  • C/C: typical

Members: Your genotype for rs2066842 is .

rs2066843 – risk allele is T

  • Associated with an OR = 1.48 for Crohn’s disease, but not with ulcerative colitis.[ref]
  • A large study (2,700 Caucasians) found this SNP to be associated with Crohn’s disease[ref]

Check your genetic data for rs2066843 (23andMe v4):

  • T/T: Increased risk of Crohn’s disease
  • C/T: Increased risk of Crohn’s disease
  • C/C: typical

Members: Your genotype for rs2066843 is .

rs2067085 – risk allele is G

  • A 2010 study showed that in homozygous G/G, the expression of NOD2 was half that of homozygous C/C.

rs17224147 (risk allele is G)

  • 1.9x higher risk of Crohn’s disease[ref]

rs5743289 (risk allele is T)

  • A 2014 study on Danish children found that rs5743289 was associated with an increased risk for CD[ref]


A 2004 study published in Gut found that a TLR4 (toll-like receptor 4) variant and three NOD2 variants were more frequently found in those with Crohn’s disease and ulcerative colitis. The introduction states that “During intestinal inflammation, intestinal epithelial cells (IECs), macrophages, and dendritic cells express TLR4 which represents the first frontline defense receptor against enteric Gram-negative bacteria”. The TLR4 SNP in this study is rs4986790 or Asp299Gly. G is the minor allele associated with a higher risk for CD and UC.

Many other studies have looked at the rs4986790 variant in conjunction with a higher risk for bacterial infections.  Look through PubMed or Google Scholar using either rs4986790 or Asp299Gly as a search term.


rs6596075 (risk allele is C)

  • A 2007 genome-wide association study found this SNP to be associated with Crohn’s disease with an OR = 2 for homozygous (C/C).[ref]
  • A 2011 study confirms the G allele (more common) as having a lower risk of Crohn’s.[ref]


Diet and Lifestyle Actions:

NOD2 can upregulate in the intestines by butyrate.[ref] Butyrate is a short-chain fatty acid produced by certain gut bacteria and also found in small amounts in foods such as butter and other full-fat dairies. Resistant starch (found in cooked and cooled potatoes and rice) feeds the kind of bacteria that produce butyrate.

Vitamin D plays a role in stimulating NOD2.[ref] Get your vitamin D levels checked to see if you have sufficient levels. Sunshine is the natural way to boost your vitamin D levels, but you can supplement vitamin D if you can’t get enough sun to boost your levels. I like the ones that are coconut oil-based. Learn more about vitamin D.

Learn More:

The Health Benefits of Butyrate: Meet the Anti-Inflammatory Fat

Dig deeper by reading this review of NOD2 mutations.

Here is an excellent video overview of how NOD2 plays a role in inflammatory bowel disease:

Related Articles and Genes:

TNF-alpha: Inflammation and Your Genes
Do you feel like you are always dealing with inflammation? Joint pain, food sensitivity, skin issues, gum disease, etc… It could be that your body genetically gears towards a higher inflammatory response due to high TNF-alpha levels.

Emulsifiers in Processed Foods: Your genes and your microbiome
Our genes and our environment both contribute to our gut microbiome, allowing some species to flourish and keeping others away. How does this all come together to cause the diseases that plague our modern society?

Problems with IBS? Personalized solutions based on your genes
There are multiple causes of IBS, and genetics can play a role in IBS symptoms. Pinpointing your cause can help you to figure out your solution.

Author Information:   Debbie Moon
Debbie Moon is the founder of Genetic Lifehacks. She holds a Master of Science in Biological Sciences from Clemson University and an undergraduate degree in engineering from Colorado School of Mines. Debbie is a science communicator who is passionate about explaining evidence-based health information. Her goal with Genetic Lifehacks is to bridge the gap between the research hidden in scientific journals and everyone's ability to use that information. To contact Debbie, visit the contact page.