Best Foods For Gut Health (2024)

Best Foods For Gut Health

Best Foods For Gut Health

You may like to read my blog How To Improve Your Gut Microbiome which discusses non-food ways to improve it.

Prebiotic Foods

Prebiotic dietary fibers act as substrate (food) for fermentation pathways in the gut, and support digestive health in many ways. Fructooligosaccharides (FOS), inulin, and galactooligosaccharides (GOS) are universally agreed-upon prebiotics. One paper summarised the 8 most prominent health benefits of prebiotic dietary fibers as (source):

1. Increases in Bifidobacteria and Lactobacilli
2. Production of beneficial metabolites
3. Increases in calcium absorption
4. Decreases in protein fermentation
5. Decreases in pathogenic bacteria populations
6. Decreases in allergy risk
7. Effects on gut barrier permeability
8. Improved immune system defence.

The best foods for gut health from this category include: leeks, onion, garlic, wheat, Jerusalem artichoke, asparagus, bananas among others.

Fermented Foods

For thousands of years, humans have been eating fermented foods. Scientists have been studying these foods closely because they believe they can be really good for our health. They’ve found special compounds and tiny organisms in fermented foods that might help keep us healthy. Each type of fermented food has its own set of these tiny organisms. When we eat fermented foods, these organisms and special compounds travel into our gut. Now, with advanced technology, scientists can see exactly which types of organisms are in our gut.

They’re figuring out if the organisms from fermented foods stick around in our gut for a little while or if they have a longer-term effect. They’re also seeing how fermented foods might change the other tiny organisms already in our gut.. (source)

It is difficult to definitively establish the number of fermented foods produced globally; most estimates suggest that there are in excess of 5000 different kinds. However, when local and regional variations are considered, this figure is likely to expand significantly.

Groupings of fermented foods are:

  1. Cereals
  2. Vegetables
  3. Legumes,
  4. Roots/tubers
  5. Milk
  6. Meat
  7. Fish
  8. Alcoholic beverages,
  9. Miscellaneous

Studies include investigations that revealed strong associations between weight management and consumption of fermented dairy products, reduced risk of cardiovascular disease, type 2 diabetes, and mortality associated with consumption of yoghurt, and enhanced glucose metabolism and reduced muscle soreness following acute resistance exercise as a consequence of consuming fermented milk. Consumption of kimchi was linked to anti-diabetic and anti-obesity effects, while consumption of different fermented foods was associated with alterations in mood and brain activity and in the gut microbiome. (source)

Recommended Products (U.S.A): Kefir,

Best foods for gut health from this category therefore include kefir, sauerkraut, kimchi, kombucha and others.

Foods High In Polyphenols

Polyphenols, described as plants’ secondary metabolites, are probably the most abundant antioxidants in our daily life. The main dietary sources of these compounds include fruits, vegetables, grains, green tea, coffee, etc. Total dietary polyphenol intake is as high as 1 g per day for each adult, which is about 10-times higher than the intake of Vitamin C, and even 100-times higher than that of Vitamin E and carotenoids (source)

They have attracted tremendous attention due to their health-promoting effects, including their antioxidant, anti-inflammatory, antibacterial, anti-adipogenic, and neuro-protective activities, as well as health properties. (source)

There is mutualistic relationship between the gut microbiome and polyphenols. Dietary polyphenols can modulate the composition of gut bacteria, and, bacteria metabolise polyphenols to release more bioactive molecules.

Polyphenols can also inhibit the growth of pathogenic bacteria. Examples include:

  • Flavonoids in red wine showed a slight inhibition of the Clostridium.
  • Ellagic acid and anthocyanins in raspberry juice may inhibit the growth of Ruminococcus.
  • Grape polyphenols can inhibit the growth of Clostridium histolyticum.

But it doesn’t sop there. Polyphenols can promote the growth of beneficial bacteria as well! For example:

  • Tannin in pomegranate, gingerol in ginger, grape polyphenols, and sorghum polyphenols can promote the growth of Bifidobacterium.
  • Tannin can also promote the growth of Lactobacillus.
  • Gingerol and grape polyphenols can promote the growth of Enterococci. (source)
  • Sorghum polyphenols can cooperate with fructooligosaccharides to enhance the abundance of lactic acid bacteria, Roseburia, and Prevotella. (source)

A great product for those in the U.K to boost polyphenol intake is Bio.Me Essential.

Best foods for gut health from this category therefore include green tea, olive oil and olives, coffee, green peppers, tomatoes, and so on. Just think colour!

Omega 3 Rich Foods

There is a link between the level of omega-3 in our diet and blood, and microbiome composition  which has been shown to be independent of dietary fibre intake. This is especially true for the bacteria of the Lachnospiraceae family.

Evidence clearly suggests we can use omega-3 supplementation to improve the composition of the gut microbiome. (source).

Omega 3 could affect the gut microbial composition in three different ways:

  1. Modulating the gut microbial community.
  2. Altering the pro-inflammatory mediators, viz. endotoxins (lipopolysaccharides) and IL17.
  3. Regulating the levels of SCFAs.

Dietary intake of omega 3’s may have a direct effect on the diversity and abundance of the gut microbiome. Interestingly, studies showed that fish oil consumption had the greatest impact on the diversity of the gut microbiome (compared to sunflower oil).

It has been theorised that the omega 3 content in fish oil might be responsible for the changes in the gut microbiome pattern due to its inhibitory effect on some of the bacterial strains, which might explicate its health benefits. Omega 3 fats are beneficial for gut microbiome as they reduce the growth of Enterobacteria, support the growth of Bifidobacteria, and subsequently inhibit the inflammation cascade linked with metabolic endotoxemia (source).

Learn more about metabolic endotoxemia (leaky gut) in my interview with Kiran Krishnan from Microbiome Labs:

Best foods for gut health from this category therefore include salmon, mackerel, sardines, herring, anchovies.

Herbs And Spices

Culinary herbs and spices may exert a prebiotic effect.

They may also be promotors of positive microbial modulation by stimulating beneficial gut bacteria during fermentation, increasing the production of short chain fatty acids and thereby exhibiting a prebiotic effect. (source)

These aspects may result in potential health benefits such as a reduction in inflammation, reduced risk and or progression of non-communicable diseases such as obesity, cardiovascular disease (CVD) and dementia.

Best foods for gut health from this category therefore include ginger, rosemary, oregano, turmeric, cinnamon among many others.


To conclude there are several groups of food that can be included in the list of best foods for gut health. In my clinical work I see a simple correlation – a more diverse diet correlates with a more diverse microbiome. It’s important to note that diet is just one of many ‘inputs’ that will influence gut health. And I have frequently seen people with dysbiosis and low microbiome diversity who eat a diverse ‘healthy’ diet. These individuals always have something going on which is limiting the effectiveness of the diet – stress, environmental toxins, sedentary lifestyles, or a poorly managed systemic health issue (an autoimmune disease for example).  A holistic approach is always needed when wanting to improve gut health.

It’s also important to appreciate that research clearly shows we have a unique response to food – so we have to take the research with a pinch of salt. The best foods for gut health depend on your gut, your health status, your genetics (perhaps), and your overall lifestyle. One reason I love polyphenols so much is that they aren’t fermented and so people with fermentation issues (IBS/SIBO issues) can still focus on these to support their gut.

Nevertheless, the focus should still be on eating a diverse diet full of the above foods.

Share this post