How Genetics and the Environment Influence Your Gut

A tremendous amount of research is coming out in regards to genetics and personalized wellness. Gastrointestinal health, although largely impacted by environment, is also influenced by genetics. This is why no single diet is universally successful. People have unique biochemical individuality, based on their genes, which governs how well they may tolerate different foods. Indigestion symptoms may vary from upset stomach, abdominal pain, nausea, gas, bloating, heartburn, constipation, and/or diarrhea. This article will discuss how and why environment sets the foundation for proper gut health, and the role of genetics as an influencer.

The Environment

A person’s environment is the external stimuli that surrounds them. A discussion about gut health will always involve food. Food is an important aspect of environment because this is largely manageable. It is an activity that involves choice three to four times a day. For proper gut health, a person should be eating nutrient-dense real food at every meal. Real food is different than the food-like products in the aisles of the grocery store. Food-like products tend to be highly processed and nutrient-devoid. Real food incorporates plants and high-quality unprocessed meat and fish. These foods are rich in minerals that are important for connective tissue health for optimizing gut wall health, amino acids for precursors to neurotransmitters like dopamine and serotonin (important for digestion), vitamins for optimal biochemical enzyme activity, and many other important compounds. Making a shift back towards natural, unprocessed foods is integral for proper gut health.

Food Sensitivities

Food sensitivities and allergies can play a role in one’s environment. Food sensitivities are the product of one’s environment, not their genetics. While food allergy symptoms are remarkable (hives, trouble breathing, itching), food sensitivity reactions are subtle, delayed over the course of 6-48 hours after consumption. Food sensitivity symptoms are vague: headache, fatigue, bloating, or skin irritation. If someone is eating chicken eggs and they have a food sensitivity, this will cause inflammation in the GI tract. Inflammation here can worsen ‘leaky gut’ (or intestinal hyperpermeability), reduce nutrient absorption, and sway the wrong ratio of bacteria in the gut which can cause various subjective symptoms previously mentioned as indigestion.


Antibiotics have a remarkable effect on the digestive tract. Antibiotics trigger large shifts in microbial diversity. Imagine the GI tract as a jungle- a complex biodiversity of plants, trees, animals, and insects all working together to thrive. Now visualize a pesticide coming through and wiping out certain aspects of this ecosystem. After this, it will be a race to see which plants grow back fastest and which animals or insects thrive. Sometimes it will be toxic weeds that grow fastest – depending on the environment’s growing conditions. This is essentially what happens when one uses antibiotics, they kill bad bacteria, but also kill good bacteria, leading to a development of the wrong bacteria afterwards. Antibiotics are useful and life-saving, although public health officials agree they are over-prescribed and frequently misused. The human gut contains about 500 different bacteria species, and most probiotic supplements contain less than 10 species. An antibiotic may destroy a species completely, and that specie may not be replaceable – forever changing one’s gut microbiome. That being said, for the majority of people reading this, probiotics do a great job in reducing indigestion symptoms, especially when associated with post-antibiotic use indigestion.

Viruses & Bugs

Viruses and other stomach bugs can trigger shifts in the microbial diversity. If a toxic bug enters the gut, the body will purge itself in either direction to clear itself of this foreign invader. With this, goes some of the good bacteria populations too. Patients often report a change in overall digestion, such as increased symptom frequency of heartburn, constipation, and diarrhea following one of these acute infections. Their ‘new normal’ can be less comfortable than their original digestive status.


Xenobiotics are foreign substances that are not naturally occurring in a human. This includes antibiotics (previously mentioned), pesticides, cleaning chemicals, air pollutants, and heavy metals. These have all demonstrated a transient change in the gut microbiome diversity. A dominant species of healthy bacteria will be outpaced by another bacteria; and this shift in populations can cause indigestion symptoms. Many of these studies do show that once the aggravating factor, or obstacle to cure, is removed from the system, the body rebalances to the original diversity and symptoms resolve. However in order for this to happen we have to have the proper environment, which consists of whole foods, clean air, clean water, moderate exercise, and proper sleep hygiene.

Lifestyle Factors

Other lifestyle factors, considered a part of one’s environment, is their sleep quality and stress management. Stress will have a deleterious effect on one’s digestive health. Stress stimulates cortisol which stimulates excitatory neurotransmitters which force the body into sympathetic mode also known as ‘fight or flight’. Digestion occurs during parasympathetic mode – ‘rest and digest’. One cannot digest food appropriately when fighting or running from a bear. Today people endure chronic stressors such as unhealthy relationships, family stressors, difficult job conditions, or post-traumatic stress disorder. This leads to high sympathetic tone and one may experience indigestion symptoms. Similarly, sleep is important as it is a time that the body can give digestion a break and repair the gut wall. If one is not getting quality sleep, they will be more likely to experience GI distress.

Exercise has an important role in GI health. Movement activity acts as a physical force to move the bowels. Also, exercise has a beneficial effect on the gut microbiome. Exercise supports a healthy population of good bacteria more than a probiotic over time. The foundations of GI health will be established with proper lifestyle choices, and optimizing the environment.

Genetics & Your Gut

Considering the human genome project was completed in 2003, there has been a tremendous amount of new information coming from genetics research. Coinciding with this is the new research in regards to gut health and the microbiome. Nutrigenomics is the effect of nutrition and lifestyle on genes. Nutrigenomics may detect that someone has a genetic weakness that reduces their ability to create certain enzymes which can predispose them to certain diseases. Nutrigenomics is not used in the setting of genetic diseases.

A fascinating piece of research found that families have similar microbiomes. Part of this is because of the environment (air quality, water source, shared diets, and other lifestyle choices), but independent from this was a genetic influence. Based on shared familial genes put into different environments, gut microbiomes diversity were still related. This is a direct genetic influence on gut health. The apple doesn’t fall far from the tree, or, the apple is digested similarly in the family.

Other direct genetic influences on gut health involve lactase deficiency in patients with Lactose Intolerance. This is a genetic issue where there is not enough lactase made, and the severity exists on a spectrum from mild to severe lactose intolerance. Another inheritable digestive problem is fructose malabsorption. The ALDOB gene that makes an enzyme, aldolase B, which is an enzyme used in the degradation of fructose to useable glucose. The spectrum of symptoms range from low blood sugar, vomiting, stomach pain, to liver disease. There are other possible enzyme deficiencies that impact digestion due to genetic mutations, but these are quite rare.

Indirect Genetic Influence

There are many other examples of indirect genetic influence on gut health. One of these examples involves the HLA genes (human leukocyte antigen, in which there are several), and they make proteins that act as immune system regulators. Patients may have genetic variations in these genes that predispose them to autoimmune diseases such as Crohn’s disease, ulcerative colitis, and Celiac disease.

Genetic variants are not considered genetic mutations or genetic disease. Researchers have discovered the role of single nucleotide polymorphisms (SNP’s, pronounced ‘snips’) in an individual’s health. SNP’s influence the functionality of a gene. Everyone has thousands of SNP’s, but case by case they vary in their influence and importance. Having a SNP does not equal disease, SNP’s can only be used as risk factors. This is why environment is so important, because environment has a positive effect on genetic expression. In fact some ‘normal’ genes in a stressed and nutrient-deplete environment function worse than a gene with several SNP’s.

There are other SNP’s that influence how a person tolerates macromolecules such as fat versus carbohydrates. These can indirectly affect our gut health by affecting overall disease burden. If someone is eating a problematic diet based on their genes there will be higher rates of chronic disease. As previously mentioned, serotonin is important in digestion, playing key roles in intestinal peristalsis and secretion. There are several genes involved with the creation of serotonin, and there may be SNP’s in these genes responsible for objectively low serotonin levels. If this was true for a patient, they may experience improved digestion with optimizing their nutrients for those specific gene’s function.

One cannot separate environment from genetics, they are very closely dependent on one another. Lifestyle medicine leads the way for a healthy environment as well as healthy genetic expression. Despite all the fascinating research coming out about genetics it still comes down to the basics of wellness. Whole foods, regular activity, stress management techniques, and adequate sleep. Beyond this, one can apply nutrigenomics to help better understand a condition and precisely optimize one’s wellness.

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