Exploring the Causes and Treatments of Gut Dysbiosis

Gut dysbiosis is the imbalance in the gut microbiome causing intestinal problems, such as gas, bloating, irregular bowel movements, and pain. The imbalance could be due to a reduction in the diversity of the microbiome, typically caused by overgrowth or loss of bacteria strains resident in the gut. Dysbiosis affects the nervous, endocrine, and immune systems through complex pathways causing a wide range of health effects.

What is gut dysbiosis?

Our gut health depends on having a diverse community of microbes residing in it. Dysbiosis can mean too many harmful microbes or the loss of microbes with helpful functions. The loss of diversity is harmful because the microbes also interact with each other, causing broader impacts on the microbiome and our bodies when important members are missing or less abundant than usual.

When the harmonious balance is lost, we feel the effects, such as discomfort due to gas, bloating, pain, and irregular stools. Trillions of bacteria, viruses, and fungi have evolved symbiotically with us and help digest foods that we lack the enzymes to break down.

Difference between the microbiome and the microbiota

The gut microbiome is the entire habitat — the microbes plus the compounds they produce. The microbiota refers to the microbes specifically.

The gut microbiota includes bacteria, viruses, fungi, and archaea. Together, they comprise approximately as many cells as we have in our whole body and weigh about the same as a mango. The microbiota includes helpful bacteria as well as harmful pathogens. What we eat helps shape the relative balance between bacterial families.

A healthy gut microbiome helps us absorb minerals and extract all the nutrients available from the food we eat. The microbiota is also involved in synthesizing enzymes, vitamins, and amino acids and fermenting foods we cannot digest. The byproducts released from fermentation keep the intestinal lining healthy, help regulate the immune response, and provide defense against harmful pathogens.

What causes gut dysbiosis?

An imbalance in the gut microbiota can be caused by dietary changes, infection, and antibiotics. However, the good news is that major changes in the diet can quickly influence the gut microbiota. Changes in the gut microbiota can also be passed from mother to child.

The gut microbiome makeup is influenced by the birthing process (vaginal vs Cesarean section), infant feeding (breastmilk vs formula), household composition (such as having pets or siblings), where we live, our diet, exercise, medications and supplements, and stress. Each of these factors influences the diversity of gut microbes resident in the gut, and this diversity is key to maintaining gut health. As will be discussed next, our diet plays an important role in maintaining a diverse microbiota.

Impact of diet on the gut

The typical Western diet is characterized by highly processed foods. This diet may cause changes in the gut microbiome that promote inflammation. When researchers look for common denominators in eating patterns that are linked to diet-related diseases, whole foods seem to be protective, while ultra-processed foods are harmful.

What are ultra-processed foods?

Ultra-processed foods are those that have gone through industrial processing to extract oils, fats, sugar, starch, and proteins. People who eat a diet high in ultra-processed foods are at a greater risk of obesity. Perhaps not surprisingly, the availability of ultra-processed foods is associated with obesity rates.

Previously, nutrition scientists focused on the sugar and salt content of ultra-processed foods, but the mechanisms are likely more complex. For instance, it appears that interactions between our gut microbiota and the ultra-processed foods can cause inflammation.

Perhaps most fascinating is the fact that the gut microbes respond to the food supply provided to them. In other words, the metabolic activity of the microbes is shaped by the diet as well as by the substances produced by other gut microbes. The response of the microbes then influences the inflammatory and metabolic pathways in the body, setting the stage for inflammation and obesity.

Some examples of ultra-processed ready-to-eat foods include:

Why are ultra-processed foods so unhealthy for the gut microbiome?

The food we eat is contained in cells that must be processed by our bodies during chewing and digestion to release energy. The cells are digested and release nutrients all along our digestive tract.

Animal cells are easily digested because they do not have cell walls like plants do. When we chew vegetables, we break down some of the cell walls, releasing nutrients for digestion, but not all of the vegetable matter is broken down. This undigestible fiber does not go to waste, though, because it can be metabolized by our gut microbiota. In fact, this prebiotics form an important nutrient supply for the probiotics which comprise our microbiota.

When food goes through industrial processing, the nutrients are extracted for us. Our bodies do far less work to digest and release energy. This increased availability of nutrients in pre-processed foods might alter the microbiota and its metabolism. In other words, eating foods that require little additional work to digest affects the microbiota in ways we may not fully appreciate.

For example, having an abundance of nutrients already available without further need for digestion (such as white bread) might signal to some of the microbiota that they can go ahead and multiply — there’s plenty of food available for them — leading to an imbalance in the diversity of the microbiota.

How does sugar affect the microbiome?

In a mouse model, a diet high in sugar caused a loss of microbiome diversity due to an expansion in one type of bacteria that can metabolize sugar. This particular family was not typically present in the colon but multiplied to handle the extra sugar intake. Eating starches and sugary drinks may have the same effect, increasing the absorption of carbohydrates in the small intestine.

The cascade effect of eating ultra-processed foods is easily appreciated: less work needed to metabolize the food leads to an over-abundance of nutrients signaling an opportunity for bacteria overgrowth and less diversity, resulting in increased absorption of calories.

How do antibiotics cause gut dysbiosis?

One major contributor to gut dysbiosis is the use of antibiotics. The use of antibiotics disturbs the relative balance of the bacterial strains colonizing the gut and has long-term effects on inflammation. Decreasing the diversity of the microbiota interrupts human-microbe signaling pathways and as a result, causes the immune system to overreact. In a mouse model, antibiotics caused inflammatory bowel disease (IBD).

This dysregulation of normal signaling caused increased inflammation as well as susceptibility to infection. In mouse models, even short-term, broad-spectrum antibiotic use appeared to cause changes in T-cell function. Broad-spectrum antibiotics are effective against two major classes of bacteria – Gram-positive and Gram-negative.

Importantly for parents, antibiotic use early in life seems to have long-term implications for immune function and risk of IBD.

Is there any treatment for gut inflammation?

Recent research suggests it may be possible to reverse inflammatory processes caused by gut dysbiosis through fecal transplantation. Oral fecal transplant capsules offered 82.1% effectiveness in a recent systemic review.

Long before needing to consider a fecal transplant, you can make immediate changes to your diet and improve your gut health. Fermented foods such as kimchi, kefir, yogurt, kombucha, and sauerkraut are all excellent probiotics. Probiotic supplements may also reduce symptoms derived from gut inflammation. Switch from processed foods to whole foods wherever possible by selecting whole-grain bread, cereals, oats, fruits, and vegetables.

If you need to eat on the run, bananas are a great packaged prebiotic option. Green apples have the highest prebiotic content if you can acclimate to the tart taste or combine it with peanut butter for protein. The changes you make in your diet will improve your gut health and allow your body to extract all the nutrients it needs to stabilize hormones, synthesize antibodies, and produce neurotransmitters.