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Gut Microbiome

The Best Foods for a Healthy Gut Microbiome

Eating certain foods can help diversify the gut microbiome


Published on 05/22/2017
Mind and BodyMicrobiomeGut MicrobiomeHealthy Living is Healthy SkinWesternNaturopathy
 stack of pancakes with raspberries and blueberries on blue plate on blue carpet

The trillions of microbes that make up our gut microbiome are highly active and constantly changing. It turns out they are sensitive to the foods and drinks we consume. In fact, research has uncovered how the types of species of bacteria in our gut can change in as little as two days after switching from a plant-based diet to an animal-based diet and vice-versa.[1] Perturbations in the gut microbiome have been associated with health concerns, including irritable bowel disease, insulin resistance, and obesity.[2] In an emerging area of research, the gut microbiome has been associated with various skin diseases including rosacea, psoriasis, and acne in a complex communication network called the skin-gut axis. As scientific research reveals more connections between diet, the gut microbiome, and skin health, it becomes apparent how the foods we eat are very important in living healthy lives.[3]

There is well-established research showing the harmful effects of certain foods, such as meat and sugar, on disrupting gut microbiome homeostasis.[4,5] However, there are foods we can consume that may help bolster a diverse and healthy gut microbiome and possibly even improve or prevent skin conditions. 

Fermented Foods

Fermented foods contain probiotics, which are living microorganisms that can bestow health benefits in the correct doses.[6] Consuming probiotics may potentially help to diversify our gut microbiome and promote a healthier gut. In fact, several studies have demonstrated that probiotics improve skin conditions, including eczema, acne, and psoriasis.[7-9] There are many delicious fermented foods to incorporate into a regular diet.

Table 1. Fermented Foods
Fermented FoodOrigin


Mexico, Tibet, and North Caucasus Mountains













Yogurt (look for non-dairy alternatives if lactose intolerant)


Low FODMAP Foods

The low FODMAP diet emphasizes the limitation of foods that contain certain low fermentable carbohydrates, including short chain oligosaccharides, disaccharides, monosaccharides, and polyols. The FODMAP diet originated to improve symptoms of irritable bowel syndrome and recent studies have demonstrated the ability of the FODMAP diet to significantly alter the gut microbiome and improve gastrointestinal distress.[10]

  • Examples of Low FODMAP foods (food to include): vegetables (alfalfa, collard greens, cucumber, kale, lettuce, pumpkin, potato, spinach, yam, zucchini), fruits (bananas, berries, grapes, oranges), meat, fish, gluten-free bread and flour, brazil nuts, oats, rice, seeds, walnuts, lactose free dairy, eggs.[11]
  • Examples of High FODMAP foods (foods to avoid): include garlic, onions, asparagus, beans, high fructose fruits (apples, blackberries, cherries, mangoes, peaches, watermelon), processed meat, wheat products, cashews, pastries, pasta, agave, artificial sweeteners, fruit juice, whey protein.[11]

High Fiber Foods

Soluble and insoluble fiber is found in foods such as vegetables, berries, seeds, and whole grains. In a study comparing the gut microbiome of European children consuming a Western diet versus African children consuming a rural diet rich in vegetables, there were significant differences between their gut microbiomes. Those following a high fiber diet had a microbiome rich in Bacteroidetes (considered “good” bacteria), depleted of Firmicutes (considered unhealthy bacteria), and also had lower inflammation and irritable bowel disease than the European children following a Western diet.[12]

Resistant Starches

Resistant starches are a type of fiber in high carbohydrate foods and in starch degradation products that cannot be digested and absorbed by the small intestine. Examples of resistant starches include beans, unripe (slightly green) bananas, yams, barley, and cooked potatoes and rice after cooling. When potatoes are cooled after being cooked, the carbohydrates undergo a process called retrogradation and form chemical structures that are less easily digested.[13,14] Ingestion of resistant starches may improve insulin resistance,[15] although more studies are needed to assess this connection. Furthermore, resistant starches are metabolized by our gut microbiota to release molecules called short-chain fatty acids. It is believed these short chain fatty acids (such as butyrate and propionate), along with other gut microbiota metabolites, offer health-promoting hormonal, physiological, and immunologic effects.[16] Dietary fiber that is metabolized by gut microbial organisms is termed “prebiotics” and is important for the production of health-promoting metabolites, including molecules such as short chain fatty acids, serotonin, gamma-aminobutyric acid (GABA), and deoxycholic acid.[17,18] 

Our lifestyle factors may influence the diversity of our gut microbiome. Diet appears to have a prominent and important effect on the species diversity and richness of the microorganisms that reside in our gut, which in turn can influence many factors in our health including intestinal health, body composition, and even skin health. The connections between the gut microbiome and the skin are only now being uncovered. There is some evidence that the health of the gut may associate with the health of the skin,[19-21] which is a new and exciting research arena.


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