Digestive Health

The Care & Feeding of a Healthy Human Microbiome

By Kim Crawford, M.D. Last updated: September 6, 2018
good for microbiome

Introduction to the Microbiome

The human microbiome is made up of 10–100 trillion symbiotic microbial cells with unique genes; primarily from bacteria in the gut. Our gut bacteria, of which we have up to 10 times more than human cells, thrive on the very things that create inflammation in our body including sugar, refined carbs, unhealthy fats, and processed foods (to name the biggest offenders.) These 100 trillion “bugs” send out chemical messages to the brain to influence not just our gut health but our overall health and mood as well. If you have symptoms and need to restore gut health, please read this leaky gut article. If you are symptom-free and want to stay that way, you need to follow a proper microbiome diet plan for life.

Here’s what I’ll be covering in this article.

  • Microbiome Diet
  • Prebiotics
  • Probiotics
  • Pharmaceuticals
  • Environmental gut toxins
  • Stress
  • Hormones
  • Dysbiosis
  • GI Motility

A Microbiome Diet

Let’s discuss the foods that do not support, and in fact, hurt our microbiome:

  • Added sugars
  • Pasteurized dairy products
  • Grains and other refined carbohydrates
  • Trans fat and vegetable oils
  • Most processed and fast food
  • Non-organic and/or GMO fruits/vegetables (Due to high levels of glycophosphates.)
  • Non-grass-fed meats (If animals eat “bad grains,” then you do too.)
  • Farmed fish
  • Specific additives: carrageenan, guar gum, food dyes, and artificial preservatives

good for microbiomeYour diet should consist primarily of grass-fed meats, pastured eggs, and vegetables.

Fruits (not juices) in small quantities are also nutritionally sound and anti-inflammatory.

For full details, please refer to the anti-inflammatory diet.

Prebiotic Fiber is Necessary for Optimal Gut Health

Prebiotics are nondigestible carbohydrate compounds found in fibrous foods which assist in the growth of healthy bacteria in the gut. One mechanism of action: good prebiotics often create short-chain fatty acids such as the very healthy-bacteria-friendly SCFA butyrate. Good sources of prebiotics include less-than-ripe bananas, raw or cooked onions, raw leeks, raw dandelion greens, Jerusalem artichokes, asparagus, raw garlic, chicory, and lectin-treated beans.

If it’s hard to track your intake of adequate prebiotic fiber, I suggest you add a multi-fiber supplement to your morning smoothie or vitamin drink. Look for things such as inulin, psyllium husk, and modified citrus pectin.

Maintain or Restore Gut Health with Probiotics

Probiotics are live bacteria which are ingested, take hold in the gut, and have beneficial effects. Sources of probiotics are dairy or coconut kefir or yogurt and fermented foods such as sauerkraut and kimchi. A more complete list is below.

  • Yogurt (sugar-free), including non-dairy coconut yogurt (Homemade from starter cultures is best.)
  • Cheese made from raw (unpasteurized) milk with the latest research showing that A2 dairy is the healthiest choice
  • Lassi (Indian yogurt drink)
  • Kefir (fermented milk or coconut drink)
  • Pickles (refrigerated, nonpasteurized)
  • Sauerkraut and other fermented vegetables (refrigerated, nonpasteurized)
  • Olives (organic, no additives)
  • Tempeh and Miso as well as fermented soy (natto)
  • Kimchi (spicy Korean condiment)
  • Kombucha (sugar-free, effervescent cultured drink)

Since you have to make a daily effort to eat sufficient quantities of probiotics as store-bought yogurt, for example, “doesn’t cut it,” many people use probiotic supplements. If you have a disease-free, symptom-free gut, you want 30-50 B CFU’s per day with mostly the Lactobacillus and Bifidobacterium species. If you have leaky gut, autoimmune disease or even IBS, you might want to add some healthy yeast (Saccharomyces) and some soil-based bacillus organisms; and use a minimum of 100 B CFUs per day.

Avoid Particular Pharmaceuticals

Non-steroidal anti-inflammatory painkillers are the most commonly used gut irritants. Your gut lining can easily be compromised by just a couple of over-the-counter products such as Aleve or Motrin. Indeed, I’d be willing to bet that the majority of people who take OTC pain relievers on a regular basis have some degree of leaky gut.

Non-bioidentical hormones such as steroids (Medrol or Prednisone) or birth control pills can feed the growth of excess candida (yeast), which can also damage the gut lining.

Another very problematic category of pharmaceuticals is antibiotics. Antibiotics quickly upset the ratio of good:bad bacteria in the GI microbiome. Due to this reason, I always recommend gut protection when my patients need antibiotics. Another category where we always see disruption is chemotherapy. Lastly, the seemingly harmless proton pump inhibitors (PPI’s) which were never designed for more than short-term use will disrupt the integrity of the GI tract lining. Many people use these drugs (Prevacid, Protonix, Nexium) for chronic heartburn and cause themselves major problems in the long-run.

Avoid Environmental Contaminants

Direct GI toxins we absorb via bathing or consume such as the fluoride/chlorine in water, methylmercury in fish, polluted air or even dust mites and mold toxins can damage our gut. Likewise, there is a cumulative dose of toxins from food additives, un-filtered showers, and preservatives in products we apply to our skin. Antibacterial soap and hand sanitizer are also harmful; as they kill off both good and bad bacteria.

Stress Management

We all seem to know that stress is bad for our health, but do you know why? Stress causes a sustained high cortisol level, and that’s what’s harmful. Cortisol can be the cause of leaky gut which leads to many other diseases. It can also kill brain cells. Further, it nukes your energy level and quality of sleep; to name but a few of the deleterious effects of high cortisol.

Adrenal adaptogens and glandulars (A.K.A. adrenal fatigue supplements), as well as the right aromatherapy, will lower cortisol levels. “Vagal breathing,” yoga, and meditation have all been shown to lower cortisol levels, too.

Hormonal Balance

Hormonal deficiencies such as hypothyroidism and low progesterone levels (as just two examples) can slow down GI motility and cause constipation. Chronic constipation can cause many issues including SIBO (small intestinal bacterial overgrowth), which then causes problems such as dysbiosis, often causing gas, bloating and eventually, leaky gut. Now let’s touchback on the concept of dysbiosis.


An imbalance in our microbiome is a condition we refer to as dysbiosis. Dysbiosis is associated with many aspects of modern day life; from stress to the use of hand sanitizers and overuse of antibiotics. When we cart around more pathogenic bacteria than we should, and additionally lack the proper range of protective bacteria we need, the microbiome is unbalanced and essentially unhealthy.

We require a higher ratio of gut-friendly microbes to outnumber the harmful ones in order to stay symptom-free and healthy. Unfortunately, due to the factors we’ve discussed, most people’s microbiomes are filled with billions of potentially dangerous bacteria, viruses, and other pathogens.

Gut Motility Issues

Most people are aware that they need to eat adequate amounts of dietary fiber for optimal gut health. Fiber is a non-digestible carbohydrate which you can find mainly in plant foods such as fruits, vegetables, legumes and whole grains. Furthermore, fiber helps maintain a healthy microbiome and supports healthy bowel movements (via bulk and motility) to decrease the risk of diverticulosis and even colon cancer. The recommended amount of fiber is a minimum of 25 grams per day if you are a woman and 38 grams per day if you are a man. This doesn’t include prebiotic fiber which is in the prebiotic vegetables or in powder-fiber supplement mixes which contain things such as inulin, prune powder, citrus pectin and psyllium husk.

In cases of leaky gut, with or without SIBO, as the gut lining becomes destroyed, some segments of the small and large intestine can get “out of sync” causing cramping and, often, constipation. In this case, we usually recommend products to either bulk up the stool (modified citrus pectin), and/or a fiber blend as noted above. We can also improve GI transit at the smooth muscle level with 5-HTP supplementation.

Final words

All “healthy life” programs include adequate sleep and proper exercise. This also holds true for cultivating a healthy microbiome. Finally, let me mention that, right now, microbiome sequencing kits don’t give us useful, actionable information.

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