top of page
  • Writer's pictureDoug Joachim

Gut Feeling: The Microbiome Connection

Updated: Jul 11, 2023

Trillions of microorganisms live in cozy complex ecosystems inside our bodies. Most of these bacteria mill around our digestive systems. Recently scientists have expanded our knowledge of the roles - both beneficial and deleterious - bacteria play in our overall health. Even so, the majority are a mystery and have yet to be classified. This microbial cloud is thought to shape our behavior, disease rates, degrees of inflammation, enzyme composition, digestion, fat storage, and obesity. Some researchers hypothesize that many of our brain processes are influenced by the microbiome. Few people know that approximately 90% of our serotonin (a neurotransmitter that affects mood) is actually located in our gut. Certain bacteria are linked to increases in serotonin, which in turn potentiate the neurotransmitter's anti-depressive effects. Other bacteria in our microbial community seem to promote healthy immune systems, while others yet are linked to disease and obesity. Some preliminary research published in 2014 suggests that the microbiome affects performance, and inversely, exercise positively affects our microbiome by promoting the production of greater bacterial diversity. The entire system can be seen, to some degree, as a symbiotic process.

Physiologically speaking, the main functions of the microbiome are digestion, vitamin synthesis, and metabolism. There is evidence that certain gut microbiota increases energy production from food, provide low-grade inflammation, and impact fatty acid tissue composition. These mechanisms may link the gut microbiota with obesity.

Myth: The human body does not contain 10X more bacterial cells than human cells; the ratio is about 1 to 1.

Big pharma is pouring lots of money into developing drugs that would decrease bacteria strains that have been seen to increase inflammation and obesity. According to Dr. John DiBaise at the Mayo Clinic:

"Accumulating evidence suggests that the gut microbiota plays an important role in the harvest, storage, and expenditure of energy obtained from the diet. The composition of the gut microbiota has been shown to differ between lean and obese humans".

Many obesity researchers are looking into the possibility of manipulating digestive bacteria to decrease body weight and obesity-associated diseases. Interestingly, it's been common knowledge since the 1950s in the farming industry that antibiotics contribute to increases in animal size. Scientists think that antibiotic medication changes the digestive flora and makes it easier for animals to store fat and increase biomass. When it comes to autoimmune diseases, some doctors recently started performing successful fecal transplants, which may completely revitalize one's bacterial community to fight certain afflictions like Crohn's disease and IBS. Want to increase the beneficial bacteria in your gut? Diet, exercise and dirt just might do the trick.

Probiotic Supplementation

The problem with probiotic supplementation is at most it only has 6-7 differing species of helpful bacteria. Our bodies carry thousands of different species. The human gut presents conditions that are unfavorable for bacteria, including probiotics. It remains to be seen if probiotics from supplements can tolerate acids and bile salts that may undermine their efficacy. Disrupting the balance of bacteria living in our bodies may be just as deleterious as killing them off. Yet probiotics have a long record of safety relating primarily to lactobacilli and bifidobacteria. Knowledge of other forms of probiotics is more limited. Unfortunately, there is a scarcity of good research on the efficacy of probiotic supplementation. Frontiers in Microbiology states that probiotic supplements:

...often carry antibiotic-resistant determinants that can be transferred to and accumulate in resident bacteria of the gastrointestinal tract and risk their acquisitions by opportunistic pathogens. While the health benefits of probiotics have been widely publicized, this health risk, however, is underrepresented in both scientific studies and public awareness.

There is little evidence to support any consistent effect of probiotics on the gut microbiota of healthy individuals, according to a systematic review published in the journal Genome Medicine.

Many supplements have dubious ingredients and low efficacy rates for healthy individuals. Most vitamins are a waste of money. Talk to your doctor before starting a regimen.

Colonics and Colon Cleansing Pills

There is no scientific evidence that colon cleaning through colonics and laxatives has any known medical value. However, the risks are well documented, including infections, electrolyte imbalances and the removal of many good types of bacteria (and bad ones too). The body has evolved a natural way of removing waste and colon cleaning. California Health Department's Infectious Disease Branch states: "The practice of colonic irrigation by chiropractors, physical therapists, or physicians should cease. Colonic irrigation can do no good, only harm." The National Council Against Health Fraud agrees. Want a clean colon? Eat more vegetables and fiber.

Overuse of Antibiotic Medication

The CDC estimates that about 30 percent of human antibiotic prescriptions are unnecessary. Antibiotics kill the weakest bacterial specimens in a population and sometimes permanently eradicate beneficial bacteria. Those that are resistant to the drug survive and resume breeding. Over time, the resistant strains outnumber the susceptible ones – and the antibiotic becomes useless. This subsequent resistance hurts the patient and introduces dangerous new antibiotic-resistant superbugs into the population. Our obsession with cleanliness and antibacterial soaps and cleansers increase pressure for newer and stronger bacteria to evolve. Ubiquitous prescriptions for antibiotics may ultimately put society at risk. There may be a point in the near future when a robust strain develops full resistance to all antibiotics...and opens us up to another pandemic. There are also potential downstream effects: new research shows links between early antibiotic use and increased obesity rates, asthma, eczema and ADHD. When we overuse antibiotics, the consequences may be truly dire. Antibiotic medication is primarily for bacterial infections and should be used sparingly.

FACT: All meat, poultry and dairy foods sold in the U.S. are free of antibiotic residues, as required by federal law — whether or not the food is labeled "antibiotic-free."

Many Foods Contains Natural Bacteria and Probiotics

Eating fermented foods is one of the best methods to increase your beneficial bacteria and restore balance to your digestive flora and fauna. Here is a list of some foods that may help:







Fermented cheese


Apple cider vinegar


Red wine

Cottage cheese

Special Mention: Asparagus, garlic, potato starch, onions, apples, flax and leeks are considered prebiotic foods. These foods have vital life-sustaining nutrients (inulin) for the healthy bacteria in your intestines.

Fermented foods have been around for thousands of years and are thought to help better digest and absorb the nutrients in food. Have you ever eaten at a Jewish Delicatessen? It is typical at these restaurants to be served pickles before your meal. Try eating some fermented foods before your next feast - it may just help you digest better.

Many kinds of fermented foods carry higher levels of vitamins and nutrients, and several are low-calorie and high fiber foods. Current data show that increasing one's daily fiber intake will also nourish the microbiome. For most people, it's a good idea to eat more fiber-rich vegetables and fruits. I try to incorporate at least 6-10 servings of fruits and vegetables and at least one fermented food into my daily diet. Diet, environment and medications play an important role in controlling and affecting the microbiome, do your part and help out your gut.


1- Eisen, Jonathan.  TED talks: Meet your Microbes.  TEDMED, April 2012.

2- Alvarez, WC (1919). “Origin of the so-called auto-intoxication symptom”. JAMA 72 (1): 8–13.

3-Krajmalnik-Brown R, Ilhan ZE, Kang DW, DiBaise JK.NutritionClinical Practice. “Effects of gut microbes on nutrient absorption and energy regulation”. 2012 Apr.

4- Shanahan F. Gastroenterol Clin North Am.  “A commentary on the safety of probiotics”.  2012 Dec;41(4):869-76. doi: 10.1016/j.gtc.2012.08.006.

5-Jarvis WT. Colonic Irrigation. National Council Against Health Fraud, 1995.

6- Boyd W. Making meat: science, technology, and American poultry production. Technol Cult. 2001;42:631-64.


Recent Posts

See All


bottom of page