How Digestive Tract Microbes Can Shape Our Health

The digestive system essentially converts the foods that we eat into the energy needed to support processes critical to the body. The anatomy of our digestive system involves a complex series of organs and glands that work in concert to break down consumed foods into smaller molecules so that they can be utilized by the body.

“The human body turns out to be a vast, highly mutable ecosystem—each of us seems more like a farm than like an individual assembled from a rulebook of genetic instructions. Medicine becomes a matter of cultivation, as if our bacterial cells were crops in a field. When that community is disturbed, either by the presence of an excess of bacteria like S. mutans, which causes cavities, or, more often, through the use of a powerful, broad-spectrum antibiotic, trouble can arise.” – Michael Specter

Where Digestion Begins

Digestion begins in the mouth where food is partially broken down by the process of chewing and by the enzymatic action of the carbohydrate-digesting amylase enzymes present in the saliva. Food is then swallowed and propelled down the esophagus to the stomach.

In the stomach, food is mixed, ground and digested by gastric acid and a protease enzyme called pepsin. Gastric acid consists mainly of hydrochloric acid (HCl), and it efficiently breaks down food material, particularly protein. If production of gastric acid decreases, as is often the case with advancing age, digestion is less efficient. Researchers have found that over 30 percent of men and women past the age of 60 suffer from atrophic gastritis, a condition marked by little or no gastric acid.

Fortunately, natural approaches and nutritional supplements help support optimal digestion in the stomach.

The partially digested food leaves the stomach and enters the small intestine, a tubular structure composed of the duodenum, jejunum and ileum. The duodenum continues the process of breaking down food with the aid of bile from the gallbladder and enzymes released by the pancreas and the duodenal walls.

Bile converts large fat globules into smaller ones. Further digestion of fats, protein and carbohydrates takes place with the help of the pancreatic enzymes lipase, trypsin and amylase, respectively. Certain nutritional enzyme supplements help support the digestive action in the small intestine.

Digestion is basically complete once food passes through the duodenum. In the jejunum and ileum, nutrients are absorbed into the bloodstream. Then the blood is purified by the liver to remove harmful substances. The liver also stores fat-soluble vitamins (A, D, E and K) and excess glucose for future use. Nutritional supplements can help support these valuable liver functions.

The large intestine receives mostly indigestible material and water from the small intestine. Excess water and any residual minerals are absorbed here. Fiber helps move the remaining debris through the large intestine, thus easing the passage of waste. Fiber also helps to support friendly bacteria. About 100 trillion bacteria reside in the digestive system and perform several essential functions.

Friendly Bacteria, or Probiotics

Probiotics, as these bacteria are called, promote efficient digestion, support the immune system, inhibit the growth of pathogenic microorganisms, and produce several vitamins. Many fiber supplements (soluble and/or insoluble) are available from a variety of plant sources. Different bacterial species are available as probiotic (friendly flora) nutritional supplements.

Probiotics have long been known to provide many benefits to human health. I have read with great interest several research reports on some additional actions of probiotics. One experiment found that mice fed broth containing Lactobacillus rhamnosus behaved less anxiously than mice fed broth without these bacteria. The behavioral changes can be partially explained by differences in brain chemical receptors and stress hormone (corticosterone) levels. The overall observation was that a change in the mix of intestinal bacteria provided by L. rhamnosus influenced mouse behavior by way of the vagus nerve. The vagal impulses induced by the microbes resulted in an increase in GABA (gamma amino butyric acid, a brain chemical and neurotransmitter) receptors in the brain and lower levels of stress hormones. The net result was a significant decrease in anxiety observed in the mice receiving the bacteria.

Probiotics Affect More Than The Gut

Just a few years ago, most scientists believed that probiotics only acted locally in the gut. However, this study suggests that gut bacteria could play a role in various brain and psychiatric disorders as well as being involved with individual behavioral differences.

In previous papers, we have addressed the important concept of how the microbial composition of the gastrointestinal tract (microbiome) affects weight loss/gain. The idea that changes in gut microbial populations can occur when an individual loses (or gains) weight was the subject of a recent research publication.


It has been known for quite some time that gastric bypass surgery reduces the quantity of food that can be processed by the stomach, and this usually results in weight loss. The microbial composition of the digestive tract also changes with the loss of body weight. This change in the microbiome that occurs during gastric bypass-induced weight loss gradually approaches the gut flora composition of normal weight people. To determine if this weight loss is caused by microbiome population changes, scientists at Harvard University performed gastric bypass surgery on a group of mice and then, after a certain period of time, implanted the new mouse gut flora into mice bred to have no gut bacteria at all. As it turned out, these mice quickly lost weight, which indicated that an alteration of gut microbe composition might represent a nonsurgical approach to treating the constantly growing worldwide health problem of obesity.

Digestive tract microbes can shape and influence our precious health. Research work on the function and diversity of the microbiome is extremely robust, and valuable therapies will continue to emerge. We will also gain a greater understanding of the relationship between digestive function and health.



1. Krasinski SD, Russell RM, Samloff IM, Jacob RA, Dallal GE, McGandy RB, Hartz SC. Fundic atrophic gastritis in an elderly population. Effect on hemoglobin and several serum nutritional indicators. Journal of the American Geriatrics Society. 1986 Nov;34(11):800-6.


2. Bravo JA, et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proceedings of the National Academy of Sciences of the United States of America. 2011 Sep 20;108(38):16050-5.


3. Liou AP, et al., Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Science Translational Medicine. 2013 Mar 27; 5(178):178ra41.