Microbiome Diet: Maintaining Healthy Gut Flora to Improve Digestion

By: Michael Lam, MD, MPH; Justin Lam, ABAAHP, FMNM

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Promoting Healthy Gut Flora: Strategies

It's not only you that is nourished by what you eat, but gut flora as well. Use healthy foods to promote a microbiome dietIn those with psychiatric or neurological conditions, it is difficult to determine which came first, the disorder or the unhealthy gut. Dysbiosis of the gut could account for both, but so could stress. It is also important to consider the environmental risk factors—such as an unhealthy diet and lifestyle—that may upset the health of both the gut, gut flora, and brain. Promote healthy flora in your gut with a microbiome diet.

It is clear that neurological/neurodegenerative and psychiatric disorders share similar causes and symptomatology, as well as a common underlying pathophysiology of an unhealthy gut that influences numerous intersecting pathways on the microbiome-gut-brain axis. However, it is difficult to determine the function of these individual systems separately. The entire microbiome-gut-brain axis is therefore still poorly understood.. For brain conditions, the gut could prove to be the missing piece of the puzzle, providing new understanding of the etiology in ways that might support the introduction of new public health and clinical interventions.

The composition of the gut microbiome is quite resilient and adaptable. The key factors that are essential to its stability and diversity are all components of lifestyle. Several strategies for improved gut health, and in turn brain health, are given below.

Microbiome Diet

Diet plays an important part in determining the amount of each type of bacteria and the phylogenetic diversity of gut flora. A healthy diet of vegetables, fruits, and a variety of whole grains, will help the population of Bacteroidetes. Bacteroidetes are particularly useful in the production of short chain fatty acids (SCFAs), which assist in the regulation of gut inflammation. Large amounts of SCFAs tend to decrease intestinal pH and prevent growth of some pathogenic bacteria such as E.coli and Enterobacteriaceae. SCFAs also help curb appetite; they attach to the receptors in the gut and regulate the hormones for appetite control. Thus, the microbiome and its production of SCFAs may play important roles in dietary intake, rate of fat deposition, utilization of fat, insulin resistance, and diabetic inflammation. Vegan and vegetarian diets also increase phylogenetic diversity of the gut flora compared to diets that include meat.

Body weight in mice can be affected by the transplantation of microbes in the cecum (the beginning of the large intestine). In one study, genetically obese mice had significantly less Bacteroidetes and more Firmicutes relative to their lean counterparts; but in another, when the gut microbes of a lean mouse that had undergone gastric bypass surgery were transferred to germ-free mice, those mice experienced weight and fat loss. These studies showed that dietary patterns that favorably alter the gut microbiome—specifically those that emphasize plant-based foods—might have significant benefits to human health and confer greater resilience and adaptability to change.

There are three food components that are largely thought to promote gut health:

  • Probiotics, living microorganisms that can be found in consumer goods such as yogurt and kimchi,
  • Non-digestible carbohydrates, such as fiber commonly found in vegetables, whole grains, and fruits,
  • Secondary plant metabolites, especially flavonoids found in red wine and brightly colored fruits.

Individuals who adopt what’s known as the Standard American Diet (SAD) experience fewer benefits of plant foods, while simultaneously provoking disruptions of other metabolic functions by eating large quantities of processed sugar and fat. These two aspects of the SAD both contribute to the development of gut inflammation and dysbiosis.

Prebiotics, Probiotics, and Fermented Foods

The gut flora boosting power of prebiotics, probiotics and fermented foods can be good microbiome diet optionsPrebiotics fibers that are not digestible by your gut enzymes. They are usually fermented in the GI tract by bacteria and selectively stimulate certain intestinal flora and metabolic activities. Probiotics are foods that contain helpful microbes that are able to survive stomach acid and bile; they enter the intestines and adhere to the lining, growing and establishing temporary residence in the intestines.

There is evidence to suggest that prebiotic and probiotic supplements and fermented foods are beneficial for the gut. The digestion of fermented fibers has natural anti-inflammatory effects. Fermentation of food makes it more digestible, turning polyphenols into an active state. It also produces more vitamins, enzymes, and amino acids while breaking down phytates, tannins, and oxalic acid. An additional benefit of fermented food is, of course, the lengthened shelf life.

Probiotics and Behavior/Central Neurotransmitters

Since 90% of neurotransmitters are made in the gut, it makes sense that gastrointestinal conditions can influence mood and behavior. Irritable Bowel Syndrome (IBS) is found in 10-20% of adults in the US, and they have much higher rates of anxiety and depression than the background population. Studies have shown that probiotics are beneficial in the treatment of both the GI symptoms and anxiety and depression, in those affected. There is mounting clinical evidence for probiotics reducing stress and anxiety responses, as well as for improving the general mood of IBS patients who suffer from chronic fatigue. Studies have assessed the effect of a mixture of Bifidobacterium longum and Lactobacillus helveticus on human subjects and rats showing that anxiety was reduced . Although the mechanism of action is still to be determined, some probiotics seem to lower inflammation, decrease stress from oxidation, and improve general nutrition.
Specific probiotic strains can assist in the modulation of various facets of the microbiome-gut-brain axis. However, it is important to note that these effects vary from organism to organism and individual to individual. Nevertheless, the data strongly suggests that probiotic strains have great potential to bolster the gut flora and thus regulate behavior and the brain.


Exercise may diversify the gut flora. Athletes had increased bacterial diversity in the gut and fewer indications of inflammation compared to non-athletes. Researchers found that individuals who participated in moderate exercise more than 30 times a month presented with escalated levels of brain-derived neurotrophic factor (BDNF), compared to individuals who either didn’t exercise at all or exercised at an extreme level. BDNF promotes anti-inflammatory pathways and leads to the promotion of both brain and gut health.

When Strategies Do Not Work

The above strategies will work well for most healthy people. You should be more cautious, however, if you suffer from certain conditions such as:
If you have certain bacterial infections such as Lyme disease or Candida, a microbiome diet may help

  • If you have Small Intestine Bacterial Overgrowth (SIBO) or a systemic infection, such as Lyme Disease and Candida, fermented foods or supplements may actually makes the overgrowth worse, leading to bloating, flatulence, and pain.
  • If you have Inflammatory Bowel Disease (IBD), enzymes supplements may trigger inflammation in certain people.
  • If you have Irritable Bowel Syndrome (IBS), excessive exercise can trigger constipation and fatigue.
  • Excessive enzyme supplementation may lead to diarrhea. The proper blend of digestive pancreatic enzymes should be considered for the clinical setting.
  • Excessive probiotics may lead to constipation. The largest number of beneficial bacteria is not always the best. In fact, it can often lead to brain fog, bloating, fatigue, and anxiety. The primary focus should be finding the proper amount to match the body’s ability to assimilate the metabolites.
  • Excessive fermented food in a body that is already congested can lead to brain fog, anxiety, and depression.

The weaker your health is, the more careful planning you will need to use with these rebalancing strategies due to other conditions that are often preexisting, such as liver congestion, extracellular matrix pollution, receptor site damages, and hypersensitivities. This includes most Adrenal Fatigue, chronic fatigue, and those struggling with advancing cancer. Always consult a knowledgeable and experienced healthcare professional, because the wrong approach can worsen your condition quickly.

Microbiome Diet Summary

Since the microbiome plays a major role in the gut-brain connection, gut flora can be used to alter the neuroaffective and inflammatory circuits of the NEM stress response system. The connections are so complex and numerous that much more research needs to be done to explore these mechanisms and individual variations. In the meantime, however, consider using prebiotics or probiotics in your recovery plan to promote optimal gut and mental health.

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© Copyright 2016 Michael Lam, M.D. All Rights Reserved.

Microbiome diet