DigestionHealth & WellnessNaturopathNutrition

Dr. Halsey, ND | 5 Ways the Microbiome Contributes to Health…Or Dis-ease

By July 13, 2017March 16th, 2024No Comments

Hello Rogue Valley! I am so excited to be joining the Siskiyou Vital Medicine (SVM) Community. It’s been so wonderful receiving such a warm welcome from patients and co-workers over the past couple of weeks. Please check out my “About” page on the website to learn more about my naturopathic practice!

I’m currently accepting new patients and you can sign up for a FREE 15 MINUTE CONSULTATION by going to the website or calling the office at (541) 210-5687.  I look forward to meeting you and being a part of your wellness journey!

As a sneak peek of SVM’s upcoming 6-week course on nutrition and our relationship to food, this week I would like to talk a little about how the microbiome (the bacteria living in the gastrointestinal tract) effects our health.

5 Ways the Microbiome Contributes to Health.. Or Dis-ease

The digestive tract is home to the vast majority of our microbiome. An estimated 4 to 5 pounds of bacteria live there, with the majority of our gut microbes residing in the large intestine or colon (the last few feet of the digestive tract), and a comparatively much smaller number living further up in the small intestine and stomach.

There is a large and ever-expanding body of research confirming that the complement of bacteria making their home in the colon has EVERYTHING to do with our health. It not only affects our digestion, it dramatically influences many aspects of wellness throughout the body. Dysbiosis is the term used for imbalances in the gut ecosystem, whether from the wrong types of bacteria, overgrowth of yeasts, or the presence of harmful viruses or parasites.

5 Aspects of Health Influenced by the Microbiome:

1.   Mood
Certain bacteria are responsible for stimulating our gut cells to produce proper levels of serotonin (mood regulating neurotransmitter).  In mouse experiments, if these bacteria are absent, serotonin levels fall by 60%! And the research shows that this is likely true for humans as well (1).  Disruption of this process is one of the ways that dysbiosis plays a role in depression.  Another way is that dysbiosis contributes to leaky gut, which leads to body-wide inflammation including the brain.  Brain inflammation can lead to depression, mood disorders, brain fog, memory loss, and other neurodegenerative diseases.

2.   Nutrition
Certain types of bacteria manufacture vitamin K and several B vitamin on-site in the colon, which are absorbed for our use in the body (2).  Also, some types of bacteria ferment cellulose, the fiber found in many plant foods, which does not get broken down by our digestive process.  This fermentation process produces short chain fatty acids, which nourish the cells lining the large intestine and can decrease your risk of colon cancer (3).

3.   Inflammation
Certain less helpful forms of bacterial actually produce inflammation in the colon, contributing to leaky gut and body-wide inflammation.  This can lead to heart disease, asthma, allergies, eczema and autoimmune diseases like rheumatoid arthritis, multiple sclerosis, Hashimoto’s thyroiditis and more (4,5).

4.   Hormone Balance
The liver processes all excess hormones, whether from your own endocrine system, birth control pills, hormone replacement therapy, or xenoestrogens (chemical compounds that act like estrogen in the body).  After these hormones are used, they are attached to carrier proteins to keep them water soluble and dumped into the bile for elimination via the stool.  However, if you have dysbiosis, the ‘bad bugs’ produce excess enzymes that allow the estrogen to be reabsorbed into the body.  Elevated estrogens in the body contribute to menstrual cramps, acne, endometriosis and hormone related cancers.

5.   Immune System Function
Certain bacteria help to educate and stimulate your immune system so that it functions optimally.  Without proper immune system education, conditions such as allergies, asthma and eczema crop up, and autoimmune disease becomes more likely (6).


Unfortunately, keeping your GI ecosystem healthy is not as simple as taking a probiotic pill each day, but there are so many things we can do to cultivate a healthy ecosystem!

Please join Ron Veitel (Lead Nutritionist) and myself for a 6-week course called “My Nutrition Map” to learn more about the microbiome, including tips to cultivate helpful bacteria in the GI and how to keep them thriving! We will also be discussing many other awesome topics about nutrition and our relationship to food.  My Nutrition Map~ starts Thursday, Aug. 17, 2017.

All My Best,
~Dr. Sonja Halsey, ND

  1. Yano JM, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell. 2015;161(2):264-276
  2. Leblanc JG, et al. Bacteria as vitamin suppliers to their host. A gut microbiota perspective. Curr Opin Biotechnol. 2013;24(2):160-168.
  3. Sears CL, et al. Microbes, microbiota, and colon cancer. Cell Host Microbe. 2014;15:317-328.
  4. McLean MH, et al. Does the microbiota play a role in the pathogenesis of autoimmune disease? Gut. 2015;64(2):332-341.
  5. Kelly D, et al. Microbiome and immunological interactions. Nutr Rev. 2012;70.
  6. Purchiaroni F, et al. The role of intestinal microbiota and the immune system. European Review 2013;17:323-333.