Foods for the Microbiome

March 7th, 2022 | Posted in Info

Foods for the Microbiome

Microbiomes are communities of micro-organisms living in and on the bodies of all living things. The mouth, gut and skin all have their own microbiomes which consist of a mix of beneficial and potentially harmful bacteria that change constantly in response to local conditions. They can affect their host’s health in many ways. A diverse microbiome is generally agreed to be a good thing for health.

The balance of bacteria in the gut microbiome plays a key role in immune regulation and has been linked to many aspects of health including weight and. mental health. If you’ve read the blog post Microbiome and COVID-19 you’ll have some understanding of the impact the microbiome can have on the severity of Covid-19. The blog post Microbiome, Stress and Anxiety highlights the interaction between the gut microbiome and the brain.

It is what we eat that feeds the microbial ecosystem in our guts. Evidence suggests there is a high level of individual variability in the human microbiome and the same diet won’t have the same effect on each person. There are also many ways to achieve a good diet. Here is a round up of what some of the research tells us about the effect of food on the gut microbiome:

Plant Foods –  healthy dietary patterns that emphasise plant foods support favourable microbiome profiles. This is likely to be partly due to the phytochemicals in plant-based foods that may have prebiotic effects (1).

Animal products – may increase the abundance and activity of certain bacteria that may be capable of triggering inflammatory bowel disease (2).

Nitrogen – researchers found that the availability of intestinal nitrogen to microbes in the gut plays a key role in regulating interactions between gut microbes and their host. Nitrogen is gained from dietary protein. They found that while high-carbohydrate diets support positive interactions in the microbiome, such benefits are relative to the protein intake of the host (3). In other words, a combination of carbohydrates and protein is likely to have a beneficial effect on gut health.

Tryptophan – recent research has found that a combination of Lactobacillus reuteri in the gut and a tryptophan-rich diet promotes a more tolerant, less inflammatory gut immune system. This could shift the gut immune system away from inflammation and may help soothe an inflamed gut as found in those with Inflammatory Bowel Diseases. Tryptophan is found in poultry, nuts, eggs, seeds, beans, yogurt, cheese and chocolate (4)

Very Low Carbohydrate Diets – scientists have shown that Very Low Carbohydrate Diets reduce the numbers of certain types of bacteria (5). These important gut bacteria ferment carbohydrates to produce a short chain fatty acid called butyrate. Butyrate is used by the bacteria and the cells of the gut lining as a source of energy. Studies have shown that butyrate can prevent cancer cells in the gut from growing and so reduces the risk of colorectal cancer. It may be that following Very Low Carbohydrate Diets in the long term increases the risk of colon cancer.

Fermented Foods – microbial fermentation converts food into more nutritionally and functionally rich products with probiotic effects. Fermented foods may increase microbial diversity and decrease inflammatory markers, as well as converting phenolic compounds from foods to biologically active compounds and reducing anti-nutrients (6,7,8,9,10). Fermented foods include kefir, yoghurt, kombucha, sauerkraut, tempeh, natto, miso, kimchi and sourdough bread.

Prebiotics, Probiotics, and Postbiotics – The use of prebiotics, probiotics, and postbiotics to alter the gut microbiome is growing in popularity. Postbiotics include any substance released by a microorganism, which exerts a beneficial effect on the host. As postbiotics do not contain live microorganisms, the risks associated with their intake are minimized. Postbiotics may have immunomodulatory, anti-inflammatory, antioxidant, and anti-cancer properties (11).

Leafy greens – a sugar found in leafy green vegetables is used as an energy source by beneficial gut bacteria. It’s suggested that leafy greens are essential for feeding good gut bacteria thus limiting the ability of bad bacteria to colonise the gut by reducing the space available for them (12).

Walnuts – eating 50-60g of walnuts daily as part of a healthy diet is associated with increases in certain bacteria that promote health and improve some risk factors for heart disease (13).


1. Prog Mol Biol Transl Sci. 2020;171:237-263. Diet, nutrients and the microbiome. Dahl WJ et al.

2. 2014 Jan 23;505(7484):559-63. Diet rapidly and reproducibly alters the human gut microbiome. David LA et al.

3. Holmes AJ et al. Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints. Cell Metabolism, 2016;

4. Cervantes-Barragan L, et al. Lactobacillus reuteri induces gut intraepithelial CD4 CD8 alpha alpha T cells. Science, Aug. 3, 2017

5. Rowett Research Institute. “Very Low Carbohydrate Diets May Disrupt Long-term Gut Health.” Applied and Environmental Microbiology, 73:1073-8.

6. 2019 Aug 5;11(8):1806. Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Dimidi E et al.

7. FEMS Microbiol Rev. 2020 Jul 1;44(4):454-489. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. De Filippis F et al.

8. Biotechnol Adv. Jan-Feb 2019;37(1):223-238. Bioactivity of soy-based fermented foods: A review. Zhen-Hui Cao et al.

9. Nutr Neurosci. 2020 Sep;23(9):659-671. Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety. Aslam H et al.

10. 2021 Aug 5;184(16):4137-4153.e14. Gut-microbiota-targeted diets modulate human immune status. Wastyk HC et al.

11. 2020 Jul 23;12(8):2189. Postbiotics-A Step Beyond Pre- and Probiotics. Zolkiewicz J et al.

12. Speciale G et al. YihQ is a sulfoquinovosidase that cleaves sulfoquinovosyl diacylglyceride sulfolipids. Nature Chemical Biology, 2016;

13. Tindall AM et al. Walnuts and Vegetable Oils Containing Oleic Acid Differentially Affect the Gut Microbiota and Associations with Cardiovascular Risk Factors: Follow-up of a Randomized, Controlled, Feeding Trial in Adults at Risk for Cardiovascular Disease. The Journal of Nutrition, 2019;