This one thing or trillions of tiny things can impact your risk for obesity, type 2 diabetes, cardiometabolic disease, gastrointestinal disease, anxiety, depression and certain types of cancer….


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Microbes are microscopic organisms such as bacteria, mold and fungi. It is common for people to view microbes as only “bad” or disease causing however every human hosts billions of these microscopic organisms and most are vital to our life. A microbiome is all the microbes and their collective genes and genomes living together such as those in the gastrointestinal tract of the human body.1

The human intestinal tract is colonized by trillions of microbial cells. In fact, we have more microbial cells than we do human cells. Collectively, these microbial cells have 250 to 800 times more genes than our human cells.2

The microbiome first began being studied more that 300 years ago however, it wasn’t until recently that the evidence became clear that the microbiome has a dramatic influence on whole-body health.

Recent scientific research supports that a balanced, healthy microbiome plays a role in nutrient digestion and absorption, hormone generation, neurotransmitter production, detoxification of environmental chemicals, regulation of metabolism, anti-inflammatory pathways, and regulation of the immune system. In contrast, evidence supports that an unhealthy or disrupted microbiome are associated with type 2 diabetes, obesity, cardiometabolic disease, gastrointestinal upset and disease, anxiety, depression, and some forms of cancer.2,3

Obesity, Type 2 Diabetes and Cardiometabolic Disease

Studies support that there is an “obese microbiome” that extracts more energy from food and leads to metabolic syndrome. Metabolic syndrome is a group of risk factors that increase your risk of disease. These risk factors include a large waistline, low good cholesterol (HDL), and high triglycerides, blood pressure and blood sugar. Most of the bacteria in our intestinal tract is divided into two major families: Firmicutes and Bactroidetes. Research shows that the obese microbiome has a high ratio of firmicutes to bactroidetes.2

Also, we know that disease risk increases when there is poor gut microbial diversity. Lower microbial diversity correlated with higher arterial stiffness, increasing risk for heart attack.4

Gastrointestinal Upset and Disease

When there is dybiosis, or an overgrowth of bad bacteria in the gut, we can develop a “leaky gut”. A leaky gut is one with increased permeability allowing undigested food particles and pathogens to get through and activate the immune system causing inflammation and food sensitivities. We also know that people with inflammatory bowel disease have lower levels of bacteria that protect against inflammation. Certain bacteria are associated with an increased production of the protective short chained fatty acid butyrate. Butyrate has been linked to a decreased risk of inflammatory bowel disease, diabetes, and cardiovascular disease.5

Anxiety and Depression

Gut health has been shown to impact mood, stress, and pain. The gut-brain axis is a bidirectional communication between the central nervous system and the gut (the enteric nervous system). Because of this bi-directional interaction, evidence exists that dysbiosis in the microbiome is associated with increased risk for anxiety and depression.6


There is evidence to support that individuals who develop certain types of cancer have higher levels of disease-causing bacteria. The microbiome plays a major role in detoxification of environmental toxins and neutralization of reactive oxygen species. If the microbiome has too much disease promoting bacteria and not enough anti-inflammatory bacteria, these harmful molecules go unchecked and may promote cancer.

How do you promote a healthy microbiome?

The human microbiome is constantly changing and impacted daily by our environment, what we eat, our stress levels and other influencers. There are however evidence-based strategies you can implement to help feed the good bacteria in your gut and squelch the bad bacteria:

  1. Aim for more plant-based foods in your diet and less animal-based foods. Heavily plant-based diets tend to promote a “leaner” microbiome with higher levels of bactroidetes. Conversely, those who eat a higher animal product diet have higher levels of firmicutes which are associated with increased risk for overweight and obesity.5 Also, higher levels of the anti-inflammatory short-chained fatty acids that promote a healthy microbiome and protect against leaky gut were found in vegans, vegetarians and individuals who follow a Mediterranean diet.5
  2. Minimize exposure to environmental toxins. Chose organic food whenever possible. Avoid or reduce exposure to glyphosate (the chemical in Round-up and other lawn treatments). These chemicals have been shown to disrupt and kill the beneficial bacteria in our gut. Visit the Environmental Working Group at for more information.
  3. Use antibiotics only when absolutely, medically necessary. Antibiotics not only kill bad bacteria, they kill beneficial bacteria in the gut leading to low species diversity in our microbiome.
  4. Exercise daily. Exercise promotes the growth of a diverse and varied microbiota which improves health and decreases your risk for disease.
  5. Avoid simple sugar and refined carbohydrates. These foods fuel the bad bacteria in your gut and are pro-inflammatory which increases your risk for developing a leaky gut.
  6. Eat fermented and other probiotic rich and prebiotic rich foods. Probiotic foods include fermented vegetables, kombucha, sauerkraut, tempeh, yogurt (unsweetened). Prebiotic foods are foods high in fiber that feed the good bugs (probiotics). These include asparagus, bananas, garlic, legumes, and peas. Also, consider adding a medical or professional-grade probiotic supplement.
  7. Limit or avoid foods that you are sensitive or reactive to. Food intolerances or sensitivities promote inflammation in the gut and disrupt the microbiome. If you are unsure of what foods may be causing trouble for you, talk to your dietitian or doctor about doing an elimination diet. Common culprits include gluten, soy, corn, dairy, eggs, fish, peanuts, and tree nuts.
  8. Drink plenty of water. Adequate hydration is critical for maintaining a healthy and balanced microbiome.


  1. “Eating For Your Microbiome”; Institute for Functional Medicine; 2017
  2. Komaroff, A. The microbiome and risk for obesity and diabetes; JAMA. {published online December 22, 2016}/JAMA.2016.20099
  3. Reiman, D. The Human Microbiome and the Future Practice of Medicine; JAMA, September 15, 2015, Volume 314, Number 11
  4. Menni C, Lin C, Cecelja C, et al. Gut microbial diversity is associated with lower arterial stiffness in women [published online May 9, 2018]. Eur Heart J. doi:1093/eurheartj/ehy226.
  5. High Dietary Fiber Intake Linked to Health Promoting Short Chain Fatty Acids; {published online September 29, 2015}; BMJ
  6. Carbotti, M. et al..; The gut-brain axis: Interactions between enteric microbiota, central and enteric nervous systems; Annals of Gastroenterology, 2015 Apr-Jun, 28(2): 203-209



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