Improving Microbiome with Diet
Written By Ana Aleksic, MSc Pharm

Improving Microbiome with Diet

Microbiome and Diet: How are the two linked?

Our microbiome is home to trillions of diverse microbes (a property called microbial diversity) that regulate almost every function of our body. In addition to several environmental factors, dietary patterns have the largest impact on our microbiome. Unfortunately, the current Western diet is gradually clearing away the healthy bacteria from our body while boosting the bad ones. This is leading to higher rates of obesity, cardiac, and metabolic diseases like diabetes mellitus and increased blood cholesterol levels. This interaction between diet and the health of microbiome has become a subject of great interest for the Science experts. [1]

Food functions to shape the microbiome right after we are born. A majority of infants are fed with the formula milk supplemented with prebiotics. These prebiotics account for the high levels of beneficial bugs found in these infants. [2] Similarly, millions of healthy bugs are present in the colostrum and breast milk. Because of the higher levels of these bugs and antibodies present in breast milk, these infants are considered to have a stronger immune system; not to mention, they are less prone to develop allergic diseases. [3]

The good news is that by modifying our diet, we can not only optimize our digestion but also improve our overall physical and emotional wellbeing.

So, what is the ideal diet to optimize our microbiome’s health?

1. Heap on more fiber into the diet

People who consume more fiber in their diet have a healthy microbiome. Dietary fiber acts as a fuel for the friendly bacteria residing in our gut. The colonic bacteria break down the dietary fiber into short-chain fatty acids (SCFAs). These SCFAs enable us to harvest otherwise unattainable nutrients and serve as a source of energy for the cells lining the colon as well as for the healthy bacteria. Moreover, the SCFAs also tend to fight gut inflammation and consequently colorectal cancer. [4] Conversely, a diet that is low in fiber-rich fruits and vegetables called as the “fiber gap” [5] by the experts, fails to provide these health benefits. In fact, this fiber gap depletes our gut of the beneficial nutrients and supports the growth of harmful bacteria. These harmful bacteria can predispose us to metabolic and obesity-related diseases, inflammatory bowel disease, and colorectal cancer. [5]

2. Cut back on foods that Promote Inflammation

A high intake of pro-inflammatory foods (or foods that promote inflammation) alters the balance of the microbiome such that the levels of good microbes drop whereas the bad guys prevail. Cutting back on these foods will help restore the balance of the gut microbiome and prevent a variety of illnesses. [4] [6]

These foods include:

  • Added sugars (present in condiments, processed snacks, white bread, canned food products)
  • Refined vegetable oils (like canola and soybean oils, which are high in pro-inflammatory omega-6 fatty acids) [7]
  • Meat (high in omega-6 fatty acids, which have a negative impact on microbiome)
  • Pasteurized dairy products
  • Trans fats/hydrogenated fats (such as those found in processed food items and fried foods)

3. Consider adding Probiotic-rich Foods in your Diet

As is obvious by their major component, i.e. a probiotic, these foods help restore the stability of the microbiome by supplying your body with an abundance of beneficial bacteria. Some of the common examples of probiotic-rich foods include:

  • Yogurt
  • Kimchi
  • Kefir
  • Kombucha

4. Increase Omega-3 Fatty acid Consumption

As stated above, substituting your diet with omega-3 fatty acids such as that present in seafood positively affects your microbiome. These foods maximize the production of SCFA-producing bacteria, [8] which can improve your microbiome and general health.


  1. Sheflin AM, Melby CL, Carbonero F, Weir TL. Linking dietary patterns with gut microbial composition and function. Gut Microbes. 2017 8(2):113-129. doi: 10.1080/19490976.2016.1270809.
  2. Voreades N, Kozil A, Weir TL. Diet and the development of the human intestinal microbiome. Frontiers in Microbiology. 2014;5:494. doi:10.3389/fmicb.2014.00494.
  3. Stuebe A. The Risks of Not Breastfeeding for Mothers and Infants. Reviews in Obstetrics and Gynecology. 2009;2(4):222-231.
  4. Conlon MA, Bird AR. The Impact of Diet and Lifestyle on Gut Microbiota and Human Health. Nutrients. 2015;7(1):17-44. doi:10.3390/nu7010017.
  5. Han M, Wang C, Liu P, Li D, Li Y, Ma X. Dietary Fiber Gap and Host Gut Microbiota. Protein Pept Lett. 2017;24(5):388-396. doi: 10.2174/0929866524666170220113312.
  6. Manzel A, Muller DN, Hafler DA, Erdman SE, Linker RA, Kleinewietfeld M. Role of “Western Diet” in Inflammatory Autoimmune Diseases. Current allergy and asthma reports. 2014;14(1):404. doi:10.1007/s11882-013-0404-6.
  7. Kaliannan K, Wang B, Li X-Y, Kim K-J, Kang JX. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Scientific Reports. 2015;5:11276. doi:10.1038/srep11276.
  8. Noriega BS, Sanchez-Gonzalez MA, Salyakina D, Coffman J. Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota. Case Reports in Medicine. 2016;2016:3089303. doi:10.1155/2016/3089303.
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