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What can you do to feed your most helpful gut bacteria?

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Our gut bacteria have a strong preference for plants and fibers as they pass through digestion relatively undigested and are able to fuel our gut bacteria instead.

Protein can also be a fuel source for gut bacteria. Plant protein also contains fibers and plant pigments which seem to help balance things. The omega 3’s in fatty fish seem to also have a net positive effect when it comes to our gut bacteria.

Best Fuel for our Gut Bacteria:

  • Fruits
  • Vegetables
  • Nuts & Seeds
  • Legumes
  • Omega 3 fatty acids (especially wild-caught fatty fish, walnuts)

Looking at the picture below, plant proteins seem to increase bifidobacterium and lactobacillus which help with inflammation reduction through the production of short-chain fatty acids (SCFA’s). Plant proteins are also associated with decreasing more harmful bacteria like Bacteroides. Another downstream effect is the increase of T-immune helper cells which help to regulate and reduce inflammation.

These “Fiber Loving” Bacteria Produce SCFA’s which help to:

  • Nourish our gut lining
  • Repair damage to our digestive tract
  • Supports our immune system
  • Reduces inflammation in the digestive tract
  • Prevents inflammation
  • Reduces risk of cancer
  • Decreases more harmful bacteria correlated with IBD flares

Most animal protein tends to lower Bifidobacterium, which increases the chance of more harmful bacteria which can link with a higher chance of inflammation. In addition, animal protein also increases levels of something called TMAO and decreases short-chain fatty acids which is associated with inflammatory bowel disease.

It’s all about Balance

If this is a huge dietary shift for you, try to let go of the “all or nothing” mindset. Small changes can still allow us to have big changes! Although we do know that our gut bacteria prefer a mostly plant-based diet to grow in populations, if you do choose to have animal protein occasionally, opt for pasture-raised organic options. Pasture-raised organic meats and those from smaller local farmers tend to have higher levels of omega-3 fatty acids and better farming methods which decrease the likelihood of salmonella and E. coli growth.

Why is this? Other thoughts

Why is it that some animal proteins can create such an impactful downstream effect? Some researchers in this area think that it could be the overall effect of fibers in plants and the type of fats that tend to accompany proteins. 

For example, we do know that milk fat causes a type of concentrated bile to be produced which a bacteria called Biophyla wadsworthia prefers. This gut bacteria is sulfur-producing and can cause disruption to the gut lining and the leaky barrier common with IBD.

On the other hand, omega-3 fatty acids tend to increase a friendly gut bacteria called Akkermansia muciniphilia. Higher levels of this gut bacteria seem to correlate with a healthier gut barrier and omega-3 fats from things like wild fatty fish and walnuts help to increase this gut bug.

At this point you might be thinking- Are we eating for us… or out gut bacteria?


Russell WR1, Hoyles L, Flint HJ, Dumas ME. (2013). Colonic bacterial metabolites and human health. Current Opinion in Microbiology 16(3):246-54.

Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P. C., & Mazmanian, S. K. (2014). Specialized metabolites from the microbiome in health and disease. Cell Metabolism, 20(5), 719–730.

Singh, R. K., Chang, H.-W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., … Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15, 73.

Yadav M, Verma MK, Chauhan NS. (2018). A review of metabolic potential of human gut microbiome in human nutrition. Archives of Microbiology 200(2):203-217.