Written by Dr. Sudarshan Cheral

Medically reviewed by Dr. Bhavya

Updated on February 12, 2025

Signs of an Imbalanced Gut Microbiome & How to Fix It?

Your body is home to countless microbes, and the microbes in your digestive tract play a role in protecting your health. Your gastrointestinal tract contains trillions of microorganisms, known as the gut microbiome. Gut health depends on the microbiome's composition, adequate digestion and absorption of food, the absence of gut illnesses, and an effective immune system. 

When your gut health gets imbalanced, that condition is called dysbiosis. Dysbiosis indicates a lack of diversity and balance. This is stomach-related and causes other health conditions. When your gut microbiome is imbalanced, you are more likely to develop gut diseases. Changes to your gut microbiome can occur because the different microbes in your intestines are out of balance.

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Different types of microbes are inside your body, but bacteria are the most studied microbes. Some bacteria present in your microbiome are associated with disease, and others are significant for your immune system, heart health, weight, and other aspects of health. There are up to 1000 species of bacteria in the human gut microbiome, each with different bodily functions. Most are significant for your health, whereas others can cause diseases.

Sign 1: Digestive Disturbances

A well-balanced gut plays a significant role in protecting your GI health. To maintain a healthy microbiome, you should have both protective and harmful bacteria. 

  • An imbalance in the gut microbiome may cause stomach problems, which could lead to other health conditions, including digestive disturbances. 
  • When your gut microbiome is in dysbiosis, your health may decline. This may lead to mild symptoms like cramps, diarrhoea, and constipation to more serious chronic conditions. Other digestive symptoms include acid reflux or heartburn, food intolerance, gas, and bloating. Microbes produce a lot of gas and other chemicals, contributing to digestive disturbances.
  • Studies have shown that dysbiosis is connected with IBD. IBD is an intestinal condition that causes inflammation in your GI tract. Studies show that when your gut microbiome is out of balance, you may be more likely to have stomach problems. When your gut microbiome is affected by IBD or other gastrointestinal conditions, it can be hard to regain the right balance in your GI tract. 

If you are having stomach problems or experiencing the symptoms above, you should talk to your doctor.

Read more about Gut Microbiome and Chronic Inflammation: A Complete Guide

Sign 2: Unexplained Weight Changes

Let's explore how gut bacteria affect body weight. The gut microbiome plays a critical role in maintaining metabolic health and body weight. Unexplained weight changes are usually linked to an imbalance in the gut microbiome.

  • Gut bacteria play a role in controlling your appetite, which means they control when and how much you eat. According to a study, gut microbes produce the hormones needed for appetite regulation.
  • A diet high in fat and carbohydrates decreases beneficial bacteria and increases pathogenic bacteria in your gut. Inadequate gut barrier function, inflammation, dyslipidemia, and hormonal imbalances induced by these alterations in the composition of the microbes eventually lead to changes in your body weight.
  • The gut microbiota is involved in the control of nutrient availability, appetite, and body weight. 

Both obesity and cachexia (extreme weight loss) are associated with altered gut microbiota. Specific dietary approaches positively impact body weight and gut microbiota. However, changes in gut microbiota alone are not enough to change your body weight.

Sign 3: Fatigue and Low Energy

Diets that can increase feelings of energy or reduce feelings of fatigue may also be connected with changes in the concentration of the gut microbiome. Gut microbes may correlate with four distinct aspects of mental and physical well-being:

  •  Mental energy
  • Mental fatigue
  • Physical energy,
  • Physical fatigue. 

The gut-brain axis and fatigue are always interconnected.

The gut is so powerful that it can affect our moods and thinking. People who experience less energy and fatigue on a daily basis may be experiencing changes according to the population of their gut-healthy microbiome. Evidence suggests that you may be more tired or exhausted from alterations in your gut microbes. 

Low energy levels can also be associated with a viral infection or any other illness due to reducing healthy gut microbes.

  • The microorganisms that reside in your gut can influence how you digest food and how your intestines absorb the nutritional content of the diet you consume. This disturbance can induce irritations and inflammation in the gastrointestinal tract and affect your sleep cycles. 

All of these factors affect how energetic you feel during the day. Long-standing inflammation of the gut causes an unusual experience of tiredness that can also be caused by bad gut health.

Sign 4: Skin Issues

Skin problems and gut health are Interlinked. 

  • Your gut microbiome can influence skin conditions through their metabolic activity and immunological impact. Certain gut microbes induce white blood cells, which contribute to anti-inflammatory responses, causing skin issues. 
  • Changes in gut flora may increase the porosity or permeability of the membrane of the intestine with leakage of the gut microbiome into the blood circulation and skin, resulting in cutaneous inflammation or, in simple words, skin inflammation.
  • Gut microbes change the levels of chemicals (neurotransmitters) which may influence the skin. 
  • Gut microbes also help our body heal wounds, reduce acne, and maintain normal skin health. 

Compositional gut microbiota changes have been linked to increased inflammatory skin diseases such as eczema, psoriasis, and more. 

Sign 5: Mental Health Symptoms

It is true that Guts Imbalance Imbalances the Brain. Mental health and gut connection are strongly intertwined. Gut microbiomes good for gut health are crucial in regulating emotions, cognition, and overall mental health. There is always a directly proportional relationship between the gut and the brain. 

  • The gut-brain axis is a bidirectional communication network connecting the gut and brain through neural signal pathways, non-nutrient chemicals like hormones, and immune signals. This constant exchange shapes emotions, mood, and cognitive function.
  • Hormones like serotonin and cortisol, many of which are produced in the gut, influence the mental well-being of your body. An imbalance in the gut microbiome can bring anxiety, depression, and emotions like high stress or low mood. Gut-brain axis and fatigue

Sign 6: Immune System Weakness

 

Interactions between the immune system and gut balance play key roles in maintaining intestinal homeostasis and inhibiting inflammation. According to research, nearly 70 per cent of the immune system is located in the stomach and intestine. 

  • The beneficial bacteria and microorganisms that live there protect your gut from infection or any sort of antigens and support the immune system. Low amounts of these helpful gut bacteria are prone to various pathogens like viruses, chronic inflammation, and even autoimmune disorders. 
  • An impaired interaction between your gut microbiome and the immune system can increase the pathogenic gram-negative bacteria and their associated metabolic changes. This disrupts the epithelial barrier and increases susceptibility to various infections by weakening the immune system.

Read more about Gut Microbiome and Autoimmune Disorders: All You Need to Know 

How to Fix Imbalanced Gut Microbiome?

How to fix gut health? You can improve your gut microbiome by changing your lifestyle. Lifestyle changes, mainly healthy eating habits, can improve your digestive health. Consider these tips to improve your digestive health naturally:

  • Chronic high-stress levels can affect your gut health. So, reduce your stress level and live a stress-free life to build a healthy gut microbiome. Practise regular meditation, yoga, breathing exercises, spend time with friends or family, limit alcohol intake, and get a massage to help reduce stress. 
  • If you don't get sufficient quality sleep, it may seriously affect your gut health. Therefore, maintain a regular bedtime and wake-up time. Consult your doctor if you have trouble sleeping.
  • Eating slowly and chewing well will reduce digestive discomfort and maintain a healthy gut. Eat fermented food and always avoid food which is refrigerated.
  • Drinking sufficient water improves the diversity of bacteria in the gut. According to a study, bacteria that can cause gastrointestinal infections are less likely to be present in the gut if you are well hydrated. 
  • Prebiotic or probiotic supplements may help improve your gut health. Prebiotics promote the growth of beneficial bacteria in the gut, while probiotics themselves are live, good bacteria that can maintain gut health. Note that you are not supposed to take probiotics if you have a severe illness or a weak immune system. And all probiotic supplements are not beneficial for your health. Seek help from a healthcare professional while choosing a probiotic or prebiotic supplement.

Read more about Tips to Boost Your Gut Microbiome.

Wrapping Up!

After reading this blog, you will understand the signs of an imbalanced gut microbiome. You now understand the concept of gut microbiome well; maintaining your gut health may not be difficult.

Gut health affects physical and mental health. Similarly, mood, stress level, and mental health also depend on gut health. Therefore, a healthy gut microbiome is essential for maintaining overall health, good digestion, immunity and mental health. You can regain or re-establish the balance of your gut microbiome through a healthy diet, lifestyle, stress management and sound sleep.

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Dr. Sudarshan Cheral

Dr Sudarshan Cheral is an Ayurveda practitioner with over 9 years of rich clinical experience. Also, as an experienced Ayurveda medical writer with more than 4 years in the field, he has skillfully contributed to Ayurveda literature, assisting in writing 4 books and translating 2 essential texts. Dr. Sudarshan is deeply committed to the art of teaching and has guided numerous international students on their journey to mastering Ayurveda.