Improving our Gut Microbiome

Robert Keith Wallace, PhD

This article is adapted from 16 Super Biohacks for Longevity: Shortcuts to a Healthier, Happier, Longer Life.

The microbiome is the totality of all the microorganisms (bacteria, fungi, viruses, etc.) that live in and on you. Our focus is on the 30 trillion microbes in the lower gut. People used to be afraid of bacteria, but it turns out that most of the bacteria in our gut are friendly. What’s even more remarkable is that recent research suggests that the state of our health and longevity depend on the state of these bacteria. This supports the ancient notion expressed by Hippocrates, the father of western medicine, that, “All disease begins in the gut.” Our diet has a huge impact on the composition of the gut bacteria. Switching from a plant-based diet to a meat-based diet or visa-versa can quickly change it. Some bacteria prefer certain food while others prefer entirely different types of food. Whichever bacteria get fed the most, increases in number and changes the ecology of our gut microbiome.

Many of these gut bacteria don’t use oxygen, which, for years, made it hard for researchers to study then, but with the introduction of gene-sequencing techniques, scientists had a new and relatively inexpensive tool to identify and study them. As a result, the microbiome is a very active area of medical research and the subject of hundreds of clinical trials.

Functions of Gut Bacteria

Our gut bacteria help us to digest different types of food. Most nutrients are digested and absorbed in the small intestine, but some foods cannot be digested by these enzymes. Fruits and vegetables, for example, contain fiber that passes right through the small intestine, and goes into the large intestine, where friendly bacteria digest and ferment them. Some of the important products of this fermentation are short-chain fatty acids (SCFAs) like acetic acid, propionic acid, and butyric acid—a primary source of nutrients and energy for cells lining the colon. SCFAs have many other functions, including helping our body absorb essential minerals like calcium, magnesium, and iron.

Second, our gut bacteria makes B vitamins, including thiamine or B1, riboflavin or B2, nicotinic acid (a form of niacin) or B3, pantothenic acid or B5, pyridoxine or B6, biotin or B7, folate (folic acid) or B9, and cobalamin or B12, as well as a certain type of vitamin K, which is necessary to make special blood clotting factors. Vitamin B12 is an interesting example. It’s involved in the metabolism of every cell in our body, and it is especially important to the functioning of our nervous system and the formation of red blood cells. The human body cannot produce vitamin B12, and neither can any animal, plant, or fungi, only bacteria and archaea (microorganisms which are a little more advanced than bacteria). Scientists have suggested that the gut bacteria alone are not capable of fulfilling our B12 needs and that dietary vitamins are required. The production of B12 in the gut, therefore, is probably more important for the health of the cells in the colon rather than for the rest of our body.

Their third important function is in helping to protect us from the invasion of harmful microorganisms. It turns out that 70-80% of our total immune system is located in the lining of the gut. Friendly bacteria occupy critical locations along the gut lining so that bad bacteria are prevented from crossing the gut barrier. The friendly or “good” guys also protect us by secreting antimicrobial chemicals to attack and destroy bad bacteria.

The fourth function is that they play a key role in the development of our gut lining. Without these friendly bacteria, certain gut immune and nerve cells do not mature properly, which jeopardizes the health of the entire gut lining.

The fifth function of gut bacteria is that they produce critical substances that can cross the gut barrier and communicate with our brain and body, influencing digestion, appetite, state of mind—even turning genes on and off throughout your body. These bacteria are part of the gut-brain axis, which consists of the nervous system, endocrine system, immune system, enteric (gut) nervous system, and enteric endocrine system.

Sixth, an abnormal composition of gut bacteria seem to be involved in many different types of diseases, such as: inflammatory bowel disease, irritable bowel syndrome, colon cancer, allergies, asthma, autoimmune diseases, Parkinson’s disease, autism, Alzheimer’s, multiple sclerosis, depression, anxiety, types 1 and 2 diabetes, stroke, high blood pressure, high cholesterol, and heart disease. The list grows longer every day.

Factors Influencing Gut Bacteria

The first factor is the way we are born. Does the child come down the birth canal or from a Caesarian birth. If a Caesarian operation has to be performed then the first bacteria to colonize the infant’s gut are from the hospital environment and are frequently not friendly bacteria. Studies show that children from caesarean births have a higher incidence of asthma, allergies, autoimmune diseases, and a propensity towards obesity in adulthood. In some countries, like China, over 50% of all births are caesarean. In private hospitals in Brazil, the number reaches 80%. Italy has the second highest caesarean birth rate in Europe with 38%, and over 30% of all births in the US are caesarean.

Most of us have taken antibiotics at some point in our lives for a bad infection. The problem is that a single dose can wipe out billions of helpful friendly bacteria. Most medical experts now agree that these drugs have been massively overprescribed. One negative side effect of this is that certain bacteria have eventually become resistant to antibiotics, posing a very real health threat, especially in hospitals. We don’t know how long it takes for a damaged microbiome to recover from an antibiotic. Each person reacts differently; some people can recover completely in a short time while others may lose certain species of bacteria forever. Most doctors now recommend that we take probiotics after a course of antibiotics. But probiotics contain relatively few bacteria, so it is hard to understand how a few friendly bacteria are able to restore the enormous diversity of the hundreds of types of bacteria normally in our gut. Recent studies indicate that probiotics may not work for everyone and might even inhibit the growth of certain good bacteria.

The most important factor to change our gut bacteria is our diet. One excellent study examined gut bacteria in healthy children between ages one and six, living either in Europe (Italy) or in rural Africa (Burkina Faso), and found striking differences between the two ethnic and cultural groups. Scientists concluded that the most important factor causing these differences was the fiber content in the diet, which was almost twice as high in the children from Burkina Faso compared to the Italian children. A number of studies have extended this research and consistently show that diet is the most critical factor in changing our microbial community. Hundreds of clinical studies are trying to discover whether a specific diet, probiotic, or lifestyle can help to cure specific diseases. Other factors, such as medication, infection, environmental toxins, whether we smoke or not, how much we exercise, our age, and even seasonal rhythms, can all affect our microbiome.

There is even a new name, psychobiotics, for a type of probiotics that could treat mental and emotional disorders. An entirely new field of medicine is emerging, which focuses exclusively on creating better health through the repair of our microbiome.

Probiotics and Prebiotics

Probiotics are friendly living bacteria. In 1907, Nobel Prize Laureate Ilya Ilyich Mechnikov promoted probiotics in yogurt as a way to maintain better health and slow the aging process. No one took him seriously at the time, but today well-controlled clinical trials show that probiotics improve a number of intestinal conditions, including irritable bowel syndrome (IBS).

It is impossible to know what the best probiotic is for each person. We all have a different gut microbiome and there are many obstacles on the way. In its natural state our gut contains many hundreds of different strains of bacteria, and one of the main limitations on current products is the lack of diversity of bacteria types. Another problem is the means of delivery. Are the bacteria in the probiotic product able to reach the lower intestine where they are most needed, without being digested or destroyed? Finally, it has been argued that because there are some 30 trillion bacteria in our lower digestive tract and if only a few million are able to make it to this destination, would they be enough to make a change in this very competitive environment. Think of it as sending a small group of well-bred private school children into a gang-ridden inner city and hoping that they will be a positive influence.

Most companies report the number of bacteria contained in their capsules or pills at the date of manufacture. Unfortunately, different storage conditions will reduce this number so that the actual number of bacteria at the time of consumption is difficult to calculate. The European Commission uses stricter labeling requirements and has placed a ban on putting the word “probiotic” on the packaging of products because they do not feel there is enough yet scientific evidence to justify any assumed health benefits. The FDA allows the use of the word but has tried to limit the listing of benefits for specific diseases. Despite these restrictions there has been a increase in the use of these products, as well as foods containing probiotics.

Probiotics are one of the hottest areas of research today, and even though science doesn’t fully understand how or why they work. They are no passing health fad. The National Institutes of Health lists hundreds human clinical trials presently exploring the effectiveness of probiotics to treat a wide range of diseases including: fibromyalgia, obesity, gastrointestinal function, irritable bowel syndrome, anxiety, depression, asthma, type 2 diabetes mellitus, hyperlipidemia, alcoholic liver disease, hypertension, rheumatoid arthritis, bacterial vaginosis, diverticular disease, respiratory infections in children, atopic dermatitis, fatty liver, lactose intolerance, coronary artery disease, bipolar disorder, antibiotic-associated diarrhea, hypertriglyceridemia, HIV, cancer, and necrotizing enterocolitis in preterm infants with very low body weight.

Prebiotics are types of dietary fiber that feed our friendly bacteria. Some of the most potent prebiotics include: asparagus, bananas, barley, oats, cocoa, burdock root, flaxseed, wheat bran, seaweed, Jerusalem artichoke, dandelion greens, garlic, leeks, onions, inulin, gum arabic, and chicory root. Research shows that prebiotics have a number of beneficial effects: improving calcium and other mineral absorption, boosting the immune system, reducing colorectal cancer risk, improving symptoms in inflammatory bowel disease, and improving digestion and elimination. Research is currently being done to determine the potential beneficial effects of prebiotics for a wide number of diseases.

Ayurveda and the Microbiome

Ayurveda treats food as medicine. We know that food change the composition of the microbiome and we know that the microbiome has a huge impact on our health. Like many natural systems of medicine, Ayurveda recommends natural probiotics such as yogurt and a special drink called lassi consisting of yogurt, water, spices, and other ingredients.

In a previous article, we discussed how, according to Ayurveda if your agni (digestive fire) is weak, then ama (undigested food and toxins) accumulates and clogs your system, causing health problems. This is also true of digestion in the colon. If the gut microbiome is imbalanced, digestion won’t be complete and by-products of improper digestion and fermentation can enter the bloodstream and cause problems. One interesting correlation with Ayurveda is that research has shown that Vata, Pitta, and Kapha natures each tend to have different compositions of the gut microbiome.

Ayurveda give excellent advice for improving our microbiome. Eat well, eat fiber, and eat fresh fruit and vegetables that suit each person’s particular mind/body. nature. It is good for us to take opportunities to give our gut a chance to rest, repair itself, and reboot our microbiome.

The microbiome theory of aging attributes the deleterious effects of aging to a disruption of the gut microbiome and a reduction of the diversity of microorganisms. A balanced diet creates a balanced microbiome. This is critical because our microbiome protects the lining of our gut, minimizes inflammation, and helps maintain healthy longevity.



 Gut Crisis: How Diet, Probiotics, and Friendly Bacteria Help You Lose Weight and Heal Your Body and Mind by Robert Keith Wallace, PhD, and Samantha Wallace, Dharma Publications, 2017

 The Rest And Repair Diet: Heal Your Gut, Improve Your Physical and Mental Health, and Lose Weight by Robert Keith Wallace, PhD, Samantha Wallace, Andrew Stenberg, MA, Jim Davis, DO, and Alexis Farley, Dharma Publications, 2019

Wallace, RK. The Microbiome in Health and Disease from the Perspective of Modern Medicine and Ayurveda. Medicina 2020; 56, 462.

Wallace, R.K. Ayurgenomics and Modern Medicine. Medicina 2020, 56, 661.