top of page

Improve Digestion by Creating a Thriving Microbiome

Purpose: A balanced and thriving microbiome may reduce symptoms of autoimmune diseases, chronic inflammatory diseases, and mood disorders.


The National Institutes of Health established the Human Microbiome Project in 2007 to learn about the bacteria that live on and within the human body. Currently, more than 10,000 different species of bacteria have been identified, with 70% of these living in the large intestine. These bacteria help to digest food and transform it into molecules that are beneficial or harmful to human health. A healthy microbiome can be thought of as a balanced ecosystem, where each species supports the activities of another and grows or shrinks depending on the resources available to it.


Each bacteria in the microbiome consumes and then transforms food that a person eats into byproducts that include; building blocks of hormones such as norepinephrine, serotonin, and GABA that affect mood; vitamins such as B12; enzymes that help absorb vitamins and minerals; fatty acids such as butyrate that improve cognition; and polyamines that are anti-inflammatory and help to repair the intestinal lining. Scientists are able to estimate what a person's diet consists of by analyzing the diversity of the microbiome and their byproducts. These byproducts are shown to communicate with the cells of the human body to influence hormone levels, appetite, mood, sleep, and anxiety levels.


Hunter-gatherer tribes, such as the Hadza tribe in Tanzania consume about 150 grams of fiber per day. Fiber is difficult for the human digestive system to digest, but is easily digested by the bacteria in the microbiome. The diversity and quantity of bacteria is correlated to the amount of fiber that is consumed, with an increased intake of fiber leading to a more diverse and populated microbiome. The best type of fiber for the microbiome is called prebiotic fiber. The Practice section below contains a list of foods that contain prebiotic fiber that are commonly found in grocery stores. 


The diversity of bacteria in the microbiome is also influenced by the variety and quality of food that is eaten. Since each species of bacteria prefers a different type of food, consuming a variety of food prevents one bacteria species from overgrowing. Eating processed and other inflammatory foods that were not historically included in a person’s ancestral diet can harm bacteria that are native to the digestive system while allowing unproductive bacteria to overgrow. Common microbiome disrupters include: antibiotics, pesticides, nonsteroidal anti-inflammatory drugs (NSAIDs), stomach acid blockers, Bisphenol A (BPA), and food that is high in lectins. 


Probiotics may help to rebalance a dysfunctional microbiome by crowding out unproductive bacteria and thereby decreasing the amount of harmful byproducts that are produced. Fascinating research is being conducted on probiotics and the effects that different bacteria species have on human health.

Practice: This practice may help someone to create a thriving microbiome.

Creating a balanced and thriving microbiome involves eating prebiotic fiber, eating a variety of foods that are low in lectins, and avoiding microbiome disruptors. 


To avoid microbiome disruptors, consider the following:

  • Avoid foods that contain a high concentration of lectins. Lectins are a family of proteins that are found in most plants and serve as part of their defense mechanism against predators. Some plants contain a very small amount of lectins while other plants contain a very large amount. Lectins are poorly digested by the human digestive system and can damage the intestinal lining and microbiome. Please refer to the WavyFields topic “Reduce Inflammation by Eliminating Inflammatory Food” for more information about lectins.

  • Choose food that is grown organically because food that is not grown organically may contain biocides. Biocides include herbicides, insecticides, and pesticides. Farmers use biocides to keep pests from eating the food. However, the chemicals within biocides can damage the digestive system and harm the friendly bacteria that live in the intestines. 

  • Choose meat that is pasture-raised or wild-caught. Animals that are pasture-raised are free to roam around the farm and forage for food that they would normally eat in the wild. Animals that are wild-caught live naturally in the wild and have spent their lives eating their native diet. Animals that are farmed or cage-free are often fed diets consisting of foods that contain a high concentration of lectins and antibiotics. The lectins and antibiotics are then contained within the meat. 

  • Avoid drinking milk and eating cheese that are produced by the most common type of cow in North America called the Holstein because its milk contains a genetic mutation (Casein A1) which is difficult for the average human to digest. Milk and cheese that are produced by other milk-producing animals such as goats, sheep, and buffalo do not contain the genetic mutation and can be digested normally. Milk and cheese that are produced by the most common type of cow in Switzerland, France, and Italy contain the normal Casein A2 protein and can be digested normally.

  • Avoid choosing food that is stored in a container made with Bisphenol A (BPA) because BPA can be absorbed into food and may disrupt normal cell signaling. BPA is banned in Europe.

  • Avoid using antibiotics unless absolutely necessary. Antibiotics destroy problematic bacteria as well as the beneficial bacteria that help to transform food into useful molecules. For example, fiber is difficult for the human digestive system to digest, but bacteria routinely transform it into useful molecules such as fatty acids. 

  • Avoid using nonsteroidal anti-inflammatory drugs (NSAIDs) because they can damage the mucus lining of the digestive tract and interfere with the ability of the digestive system to trap and remove toxins.

  • Avoid using stomach acid blockers because they can reduce the amount of acid that is produced by the stomach and thereby interfere with the ability of the digestive system to dissolve toxins. Additionally, a decrease of stomach acid may lead to improper digestion of protein and consequently less amino acid absorption. Stomach acid blockers are often taken to reduce symptoms of gastroesophageal reflux disease (GERD). Well-regarded functional medicine doctors: Steven Gundry, MD, Mark Hyman, MD, and Terry Wahls, MD report that their patients resolve their symptoms of GERD by simply changing their diet.

Foods that are a good source of prebiotic fiber and are commonly found in grocery stores include:

  • Almonds (blanched or Marcona only)

  • Artichokes

  • Arugula

  • Avocados

  • Blackberries

  • Bok choy

  • Broccoli

  • Brussel sprouts

  • Cabbage

  • Cauliflower

  • Cassava

  • Celeriac

  • Chicory

  • Coconuts

  • Collard greens

  • Crispy pears

  • Endives

  • Figs

  • Flaxseeds

  • Garlic

  • Hazelnuts

  • Horseradish

  • Jerusalem artichokes (also known as sunchokes)

  • Jicama

  • Kale

  • Leeks

  • Macadamia nuts

  • Millet

  • Mullberries

  • Mushrooms

  • Okra

  • Onions

  • Parsnips

  • Pistachos

  • Radicchio

  • Radish

  • Raspberries

  • Rutabaga

  • Sweet potatoes

  • Tiger nuts

  • Turnips

  • Walnuts

  • Watercress

  • Yams

To view a list of foods that are high in lectins (avoid) and low in lectins (consume), please view the WavyFields topics "Reduce Inflammation by Eliminating Inflammatory Food" and "Foods to Avoid and Consume."

Donate: Donate to WavyFields and help us achieve our mission to restore, sustain, and enhance human health through an evidence-based integrative health program. WavyFields is a 501(c)(3) public charity. All donations are tax deductible. 

Newsletter: Sign up for the WavyFields Newsletter. The Newsletter contains a short Purpose, Background, and Practice section for an evidence-based health topic about the mind, digestion, movement, breathing, or sleep. The Newsletter will be emailed to you once a month.

bottom of page