Intestinal dysbiosis is a term that increasingly pops up, with its role in bothersome gut symptoms and connections to an increasing list of health conditions. But what is dysbiosis, and how can you tell if this is happening to you? Suppose you don’t have a diagnosed health condition connected to dysbiosis (such as inflammatory bowel disease or irritable bowel syndrome). It can be easy to miss the signs of a gut going awry, especially if you’ve had symptoms for a while. Here, we will review a few sneaky symptoms of dysbiosis and ways to address them. You can also check out our overview of dysbiosis symptoms and resources on the human microbiome for more information.

What Is Dysbiosis?

First, a trick question: What organ helps with digestion, metabolism, creation and utilization of specific nutrients, and immune system function? If you answered the large intestine, you would be mostly right, as the majority of our gut microbiota call the large intestine, or colon, home.

The gut microbiome consists of trillions of microbes and might even be considered an organ in itself, with essential roles in metabolic and immune system functions. The intestinal microbiome comprises bacteria, fungi, viruses, archaea (single-celled organisms without a nucleus), and eukarya (cells with a nucleus). The health of a microbiome is generally based on the diversity and density of its microbes, and a disruption to the microbial composition of the microbiome is considered dysbiosis. (Source)

Dysbiosis is now connected with various health conditions, and not all of them are based in the gastrointestinal tract. Neurodegenerative diseases, type 2 diabetes, skin conditions, hypertension, and autoimmune conditions can all be traced back to the microscopic world in our guts and their vital relationships with our immune systems. (Source)

How Can Dysbiosis Happen?

Our gut microbiomes begin to develop in the womb and can be considered hardy and sensitive. Where you live, how you were born, whether you were breast- or formula-fed, food exposures in early life, use of antibiotics, and exposure to physiological stress all play significant roles in the composition of a developing microbiome. In adulthood, diet, medications, physical activity, and stress continue to influence the abundance and functioning of the microbiome. However, early life is considered to be when your baseline is established. (Source)

While your microbiome is as unique as your fingerprints, there are large groupings of microbes widely shared among humans that are considered to be in equilibrium when present in specific proportions. Disruptions to the balance of gut microbiota can occur either short term, as with a stressful experience or high intensity exercise, or long term, such as after using broad-spectrum antibiotics or consuming a highly restricted diet. (Source)

6 Sneaky Signs of Dysbiosis & What You Can Do

You may be surprised at some of the symptoms that can occur when the ecology of your gut microbes is on the move from a balanced state. Bad breath, excessive burping (or belching), chronic constipation, skin conditions, and exacerbated digestive symptoms after eating many fruits and vegetables can be signs of intestinal dysbiosis. Here, we’ll review 6 common symptoms and offer suggestions for recomposing your gut microbiota.

1. Bad Breath

We’re not talking about forgetting to brush your teeth or the pungent aromas after a garlic-laden meal. But if you struggle with chronic bad breath, or halitosis, you may have to take up the issue with your gut and mouth microbiomes. Mouth odors can occur when bacteria residing in films on the teeth and tongue overproduce smelly compounds.

While it is true the mouth has a microbiome all its own, it is part of the gastrointestinal tract and provides an opportunity for bacteria to enter the body and consequently affect the gut microbiome.

Factors influencing breath include meal composition, fasting, alcohol, drugs, smoking, dental health, and decreased salivation. Bad breath can also indicate serious medical conditions such as liver or kidney failure. In the absence of these conditions, attention to oral and tongue hygiene and identifying (and avoiding) foods that promote odor can be helpful. Additionally, unsweetened probiotic foods (those that contain live beneficial bacteria), such as yogurt, and oral probiotics, such as Weissella cibaria, have shown some benefit in reducing this symptom. (Source, Source, Source)

2. Excessive Belching

Drinking carbonated beverages, overeating, swallowing air, and even anxiety can promote belching, or the release of gas from the stomach through your mouth. When you are belching more frequently than normal and don’t know why, it may indicate an underlying imbalance associated with dysbiosis.

While excessive belching may be caused by an imbalance in bacteria (such as with Heliobacter pylori infection), other causes, such as incomplete digestion (known as maldigestion) can also be a sign of dysbiosis. Maldigestion can happen when you’re stressed, don’t chew food thoroughly, or when you have a deficiency of stomach acid (hypochlorhydria).

A decrease in stomach acid occurs with aging and some health conditions, such as hypothyroidism, due to the thyroid’s involvement in the production of gastric acid. With some conditions, such as gastric ulcers, reduction in stomach acid is desirable. Medications called proton pump inhibitors (PPIs) decrease the production of stomach acid and are commonly prescribed for long-term management of conditions such as gastroesophageal reflux disease.

However, this decrease in gastric acid can lead to slowing of gut motility, or the normal movement of food and bacteria through the digestive tract. Stomach acid depletion can reduce absorption of nutrients and weaken defense against harmful bacteria in the intestinal tract. While there are benefits of using PPIs in the short term, risks of long-term use are not always considered in conventional clinical practice. (Source, Source, Source, Source, Source)

If you are experiencing excessive belching, it’s essential to figure out why. Here are some questions to consider:

• Are you speeding through your meals in 5 minutes or less, or eating while distracted?  
• Are you eating gas-promoting foods?
• Are you eating past the point where you feel full?
• Do you often chew gum or drink through straws?
• Are you chronically stressed?
• Are you taking regular medications that suppress stomach acid?
• Do you have a hypothyroid condition?

There is no judgment if you answered yes to any of these questions, but thinking about your responses can help you address potential causes of excessive belching. If you are concerned about medication effects, be sure to check in with your provider before making any changes, and consider consulting with a functional medicine provider to help support optimal digestive function.

3. Fatigue

Fatigue — the kind of tiredness that interferes with daily life and is not relieved by adequate rest — can be a debilitating symptom of several autoimmune diseases. One of the root causes of this kind of fatigue goes back to the gut or, more specifically, increased permeability of the intestinal lining (also known as “leaky gut”) and its connection to the gut–brain axis. (Source)

Dysbiosis is a cause of leaky gut, and the terms are sometimes confused. However, leaky gut refers specifically to the integrity of the intestinal lining and how effectively it holds in bacteria and substances such as lipopolysaccharides (LPS), which may be released from the outer membranes of some kinds of bacteria.

When the intestinal lining has significant gaps, gut bacteria can escape the intestines and enter the bloodstream, activating an immune response and leading to inflammation. Similarly, leaked LPS in the bloodstream can cause a chronically activated immune response and nervous system inflammation, leading to fatigue. (Source)

To make matters worse, some gut bacteria produce neurotoxins, such as D-lactate. It has been hypothesized that in intestinal permeability, neurological symptoms including fatigue can result from D-lactate toxicity that can reach the brain via the gut–brain axis. (Source)

Interventions such as the autoimmune protocol (AIP) diet or a leaky gut diet plan may help remove symptom triggers. Additionally, supplementing nutrients such as zinc, glutamine, and N-acetylcysteine, and symbiotics (combinations of specific probiotics and prebiotics) can help in healing intestinal permeability. Probiotics should be selected carefully after consultation with a trusted provider, because some probiotics are D-lactate producers and may worsen symptoms.

4. Skin Conditions

The skin and the intestinal tract each have immune system-supporting defense barriers,  including distinct populations of beneficial microbes, that provide protection from pathogens and other harmful substances. The gut and the skin microbiomes communicate with each other through the circulation of blood and lymph, in a system known as the gut–skin axis.

Diet affects both the gut and the skin microbiomes. Food allergies may involve an impaired skin barrier when a dermal allergen exposure triggers an immune response in the gut. Through similar immune system pathways, skin conditions such as atopic dermatitis, hidradenitis suppurativa, rosacea, seborrheic dermatitis, and skin cancer are each associated with specific microbes and microbial imbalance in both the skin and the intestinal tract.

The significant connection between the gut and skin microbiomes shows promise that modifying the gut microbiome through diet and maintaining optimal vitamin D through protected skin exposure (or supplementation) can positively affect skin conditions. (Source)

5. Chronic Constipation

There is no consensus on how often you should have bowel movements — anywhere from 3 times a day to 3 times a week can be considered normal. Bowel movement regularity is, however, considered a vital sign of organ function and overall health, and chronic constipation can be a sign of a medical condition that warrants attention. (Source)

Digestion and the process of elimination is a coordinated effort between hormones, nerves, and intestinal tract muscles. Several common health conditions, such as diabetes and hypothyroidism, can affect the secretion of hormones essential to digestion. These hormones signal gastric acid and enzyme production, response to food or hormone signals, and peristalsis, the intestinal contractions that move food through the digestive tract. (Source)

Your microbiome may have an indirect relationship to how frequent your bowel movements are. Changes in the diversity and density of gut bacteria have been linked to changes in stool consistency, or whether the stool is unformed and loose (diarrhea) or formed and hard (constipation). Additionally, intestinal motility disorders and delayed gastric emptying is linked with small intestinal bacterial overgrowth (SIBO), a condition characterized by dysbiosis. (Source, Source)

If adequate fiber, hydration, and physical movement don’t promote regular bowel movements, think about other causes of constipation and consider checking in with your health provider. (Source)

6. When Eating “Healthy” Causes More Digestive Symptoms

If you are one of the many adults who struggle with digestive symptoms that diagnostic tests cannot explain, you may have tried changing your diet, hoping that would help. Fruits and vegetables are unanimously considered to be healthy food choices with a great deal of immune-boosting benefits. But what if you experience more digestive symptoms, such as bloating, gas, pain, or changes in bowel movements after eating more fruits and vegetables?

Digestive symptoms in response to FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) in many foods is a trademark characteristic of irritable bowel syndrome (IBS) and SIBO, two digestive disorders characterized by intestinal dysbiosis. Foods such as garlic, onions, beans, cruciferous vegetables, wheat, dairy products, and many fruits have FODMAPs that may or may not promote symptoms. (Source)  

While a low FODMAP diet can be fantastic for reducing symptoms, it’s not intended to be a long-term eating pattern because it’s so restrictive. WellTheory’s Ultimate Guide to the Low FODMAP Diet will tell you more about how removing high FODMAP foods from your diet may affect your digestive symptoms.

Learn More About Dysbiosis

Supporting the culture of your gut has a host of benefits. In addition to the resources listed in this article, we recommend exploring the gut microbiome:

The Human Microbiome Project

The Poop Cure: Using Fecal Microbiota to Fight Disease in the Gut

Scientific American blog: Which Bacteria Are in My Poop?

The Bottom Line on Dysbiosis Symptoms  

Symptoms of dysbiosis can influence symptoms anywhere along the gut axes, such as in the intestinal tract, the central nervous system, and the epidermis. Dysbiosis can be a multi-cause imbalance that involves early life, diet, medications, hormones, and individual health conditions. Assessing individual root causes of dysbiosis is essential for correcting the imbalance, especially since what is considered “healthy” may provoke worsening symptoms for some.

A WellTheory membership includes access to trained Nutritional Therapy Practitioners ready to help guide you and your microbiome through root-cause approaches to achieving optimal health. We are here to support you on your healing journey.