How Your Gut Flora Affects Your Health

The gut flora supports your immune system, helps metabolism, and affects brain health.

In medicine, "flora" is the term for microorganisms on or within the human body, such as the gut flora—also called the gut microbiota and gut microbiome. When talking about flora in the context of the human body, the term refers to bacteria, yeast, and other fungi.

The gut flora has many functions and can negatively affect health when it's out of balance. Maintaining a healthy gut is important to your overall health.

3D view of Gut Bacteria
jamesbenet / Getty Images

What Is Gut Flora?

Gut flora refers to the world of microorganisms, predominantly bacteria, that populate our intestines. There are about 100 trillion such organisms in each human gastrointestinal (GI) tract. A variety of names are used to refer to this inner population of bacteria, fungi, viruses, and protozoa:

  • Gut bacteria
  • Intestinal flora
  • Gut microbiota
  • Gut microbiome
  • Gut microflora

Research has been increasingly focused on trying to understand the role that gut flora plays in human health. It has become exceedingly apparent that the gut flora plays an important role in both our health and our vulnerability to disease.

Development

Babies are born with intestines believed to be either completely or mostly sterile. As they go through their mother's birth canal, they are exposed to the microorganisms in the vagina, which is the origin of the population of the microbiome. The microbiome is further populated by environmental exposure and intake of breast milk, formula, and ultimately food.

Infants born via cesarean section, who don't travel through the birth canal, may have fewer microbes in the gut early on—but the differences go away by the time they're 6 months old, thanks to environmental exposure and the nutrients they consume. The makeup of the gut flora then continues to evolve throughout our life span.

Location

The substances secreted through the process of digestion affect where gut bacteria develop. Stomach acid, bile acid, and pancreatic enzymes typically prevent the colonization of bacteria in the stomach or the beginning section of the small intestine.

Therefore, gut bacteria are found to some extent in the last part of your small intestine, but overwhelmingly they're located in your large intestine. It is estimated that there are more than a thousand types of microbes in your body. A 2015 study reported that these microbes make up anywhere from 25% to 54% of your stool.

This world of microorganisms is separated internally from your body through a single layer of cells on your large intestine—known as epithelial cells.

Functions of the Gut Flora

As mentioned, your gut flora is a key player in your health. Its most important roles have to do with immune system protection, metabolism, and brain health. For these important functions, there needs to be an optimal amount of "friendly" bacteria.

Supports the Immune System

There appear to be two ways in which our gut bacteria support our immune system. The first is that helpful bacteria provide direct protection for the lining of our large intestines, keeping out substances that would be harmful to us.

Short-chain fatty acids, the byproducts of helpful gut bacteria, help maintain your gut barrier, keeping the bacteria and bacterial toxins inside the gut from escaping into your bloodstream. When this system is compromised, a state of increased intestinal permeability (leaky gut syndrome) may be present.

The second way is that favorable gut bacteria work with the immune system at the level of the lining of our intestines to fight against disease-causing bacteria or other substances.

Helps Metabolism

Our gut flora plays an important role in providing us with vitamins and other nutrients essential to our health. The microbiome also interacts with carbohydrates that were not digested in the small intestine (such as resistant starch and FODMAPs). This interaction provides further nutrients, encourages epithelial cell growth, and modulates fat storage.

The gut microbiome is involved in the processing of dietary fiber, which leads to the production of helpful acids in the body, such as acetate, propionate, and butyrate. These in turn can help with:

  • Liver diseases
  • Insulin resistance
  • Appetite and weight management

Indolepropionic acid, also associated with gut flora and fiber intake, may reduce the risk of type 2 diabetes.

Gut bacteria help metabolize bile in your intestines. Your liver sends bile to your small intestine to help you digest fats. Bacteria and their enzymes then help break down the bile acids so they can be reabsorbed and recycled by your liver. 

The gut microbiota helps our bodies assimilate vitamins and is involved in the production of vitamins B and K. The B vitamins aid the body in making energy from the food we eat, as well as help form red blood cells. Vitamin K helps make proteins for blood clotting and for your bones and tissues.

Affects Brain Health

Gut flora plays an essential role in maintaining the function of the central nervous system, which includes your brain and spinal cord. For example, the microorganisms help with the generation of serotonin, which in turn affects many aspects of human behavior, including mood and mental health. Changes in gut microbiota have even been shown to increase anxiety in mice.

The gut flora can also regulate the permeability of the blood-brain barrier, which means guarding the brain from harmful blood-borne toxins. In some animal studies, an imbalance in the gut was shown to be an important factor in neurological conditions such as Alzheimer's disease and autism spectrum disorder.

What Affects Gut Flora?

Diet: Good bacteria in your gut need plant fibers to thrive, so they prefer a variety of whole foods, such as fruits, vegetables, beans, fermented foods, and whole grains. On the other hand, a diet high in sugar, saturated fats, and processed foods with additives is low in fiber and tends to increase the growth of less helpful microbes.

Environmental toxins: Substances like antibiotics, heavy metals, organic pollutants, pesticides, and particulate matter can wipe out good microbes and cause an overgrowth of pro-inflammatory microbes. Your gut microbiome can usually recover from temporary chemical exposure, but long-term exposure may make it difficult for certain microbes to grow and thrive.

Medications: Antibiotics can wipe out both good and bad flora when taken long-term. The gut flora can also interact with your medications, both being affected by them and influencing their mechanism of action. Studies have shown that small changes in the gut microbiome can cause large changes in people's responses to chemotherapy and immunotherapy for cancer treatment, as well as biologics for autoimmune disorders.

GI Motility: This refers to the movement of your intestinal tract. Microbes break down undigested compounds into nutrients and then are eliminated with your poop. If the movement of food and waste through your GI tract is too fast (diarrhea), they don’t have time to do their jobs before being removed. If it’s too slow (constipation), they can overeat and overgrow, causing an increase in potentially pathogenic bacteria.

Symptoms of Unhealthy Gut Flora

An unhealthy balance of gut flora, also called dysbiosis, can lead to the following digestive symptoms:

  • Abdominal pain
  • Bloating
  • Gas
  • Diarrhea
  • Constipation

Dysbiosis occurs when there is:

  • A loss of beneficial gut bacteria
  • An overgrowth of pathogenic (bad) bacteria
  • A loss of overall bacterial diversity

Associated Health Conditions

It is now recognized that imbalanced gut flora can contribute to health issues, both digestive and non-digestive. The primary health conditions directly related to dysbiosis include:

  • Small intestinal bacterial overgrowth (SIBO): A condition in which excess bacteria are found in the small intestine, where they don’t belong. Excess bacteria in the small intestine may use up nutrients needed by the body and cause damage to the lining of the small intestine.
  • Inflammatory bowel disease (IBD): A group of autoimmune conditions that cause swelling and damage to the intestines. The two main types are ulcerative colitis and Crohn’s disease. Dysbiosis in these conditions is characterized by depleted diversity of gut bacteria, reduced levels of good bacteria, and elevated amounts of pro-inflammatory bacteria.
  • Infections: Good bacteria in the gut help maintain the intestinal wall. When there is a lack of good bacteria, disease-causing organisms can cause infections, diarrhea, inflammation (colitis), and toxic damage to your gut lining. If the lining gets damaged (leaky gut syndrome) bacteria and bacterial toxins can get through the lining, escaping into your bloodstream.
  • Cardiovascular diseases (CVDs): Dysbiosis contributes to the progression of CVDs by promoting atherosclerosis and hypertension. Harmful gut bacteria can produce trimethylamine N-oxide (TMAO), which contributes to atherosclerosis (hardening of your arteries). These bacteria also cause scarring and changes in blood vessel tone, leading to high blood pressure.

Other conditions that may be indirectly related to dysbiosis include:

Treatment

Some medical treatments for dysbiosis may include:

  • Elimination diet: An elimination diet is a short-term eating plan used to assess whether specific foods are contributing to your gut symptoms. Sometimes there are foods that your gut microbes like to eat. When too many microbes are eating too many of these foods, they produce byproducts that cause intestinal gas, diarrhea, and other symptoms. Removing these foods starves the microbes, which is one way to reduce or eliminate them.
  • Antibiotics: If you have an infection or overgrowth of certain gut bacteria, antibiotics may be used to eliminate them. This in turn allows a healthy gut microbiome to recover. Your healthcare provider might suggest taking prebiotic and probiotic supplements to help restore your microbiome.
  • Fecal microbiota transplantation: This procedure transplants healthy gut bacteria in a donor's stool to another person's colon. It appears to hold some promise in extreme cases for enhancing the health of the gut flora.

How to Improve Gut Flora

Certain lifestyle changes can help optimize your gut flora. These include:

  • Eating a well-rounded nutritious diet: To keep your gut flora balanced, researchers recommend a diet dense with micronutrients and high in fiber. Aim for a variety of whole foods like whole grains, beans, vegetables, and fruits. Vegan and vegetarian diets can also be beneficial because they're rich in fiber.
  • Avoiding high-fat and highly processed foods. Choose foods low in saturated and trans fats, sugar, and high-fructose corn syrup.
  • Including foods that are considered prebiotics. Examples include asparagus, onions, fennel, garlic, legumes, nuts, and more.
  • Staying hydrated: Drinking enough water is key to keeping your gut flora balanced by helping to break down food and prevent constipation.
  • Avoiding cigarette smoking: The more you smoke, the more your gut microbiome may be affected.
  • Avoiding alcohol: Alcohol can affect both the types of microorganisms present in the gut microbiome and their quantities.
  • Managing stress: Stress, anxiety, and depression can negatively affect your gut flora and potentially lead to constipation and diarrhea. Include stress management practices such as yoga, meditation, and deep breathing in your daily routine.
  • Minimizing antibiotic use: Antibiotics can disrupt the composition of gut flora.
  • Exercising: Research has shown that exercise may help regulate the gut microbiota, as well as have other positive effects such as regulating metabolic activity and insulin sensitivity.
  • Taking probiotics: Although the benefits are not fully proven, probiotics may be of help and don't typically make things worse.

Summary

Your gut flora, also known as gut microbiota or gut microbiome, consists of trillions of microorganisms, predominantly bacteria. It plays a crucial role in your metabolism, immune system, and brain health.

An imbalance in gut flora, known as dysbiosis, can contribute to many health conditions, including diabetes, IBD, IBS, and lupus. To keep your gut balanced, consider lifestyle adjustments such as eating a fiber-rich diet, avoiding smoking, exercising, and minimizing antibiotic use.

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Additional Reading
Barbara Bolen, PhD

By Barbara Bolen, PhD
Barbara Bolen, PhD, is a licensed clinical psychologist and health coach. She has written multiple books focused on living with irritable bowel syndrome.