Written by Dr. Neethu Susan Sunny

Medically reviewed by Dr Anju Lal

Updated on March 08, 2025

Gut Flora Imbalance Treatment: Restore Your Microbiome Naturally

Do you frequently suffer from constipation, loose motions or bloating? 

Then, there is a chance that your gut flora is not in balance. But what is gut flora?

Gut flora, also known as the gut microbiome, comprises trillions of microorganisms essential for digestion, immunity, and overall health. An imbalance in this can occur when the harmful bacteria exceeds the number of beneficial ones, causing symptoms like bloating, irregular bowel movements, fatigue, and even skin and mood issues. However, many natural remedies can help you restore gut health and balance your microbiome. This blog will help you understand gut flora imbalance and natural remedies which can help improve your gut health.

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Signs of Gut Flora Imbalance

Your gut flora constitutes an ecosystem known as your gut microbiome. Usually, gut bacteria live in a commensal manner in your gut.

However, gut bacteria can be potentially harmful when your ecosystem undergoes several changes.

Some of the common signs are:

a) Digestive Issues 

Your gut microbiome is responsible for most of your digestive functions. Imbalance in this can cause digestive issues like gas, bloating, loose motions, abdominal pain, and changes in your stools.

b) Skin Problems 

Your gut health affects your skin to a great extent. One of the most significant ways in which gut health influences skin health is through gut dysbiosis. It can trigger inflammation throughout your body, which may manifest as skin issues. Symptoms that can occur are severe acne, atopic dermatitis, acne, eczema or skin rashes.

c) Poor Immunity 

An incredible 70% of your entire immune system resides in your gut - Pubmed

The foods you eat affect your immune cells. A healthy microbiome creates good immunity, and a poor gut microbiome creates poor immunity. Frequent infections or allergies are seen due to a decrease in immune functions.

d) Urogenital Disorders

Your gut bacteria play an important role in urinary tract infections. Many of the bacteria found in your gut can increase and enter your urinary tract and cause infections. Symptoms seen due to this are pain and burning during urination or itching. 

e) Mood Disorders 

“Your gut produces 95% of your serotonin, the “happiness hormone,” and 50% of your dopamine.”

-PubMed

 

Your gut microbiota communicates with your central nervous system through various routes, thereby controlling brain function. It plays a substantial role in the regulation of your anxiety, mood, cognition, and pain. Mood swings, anxiety, depression, or brain fog due to your gut-brain connection can be seen.

f) Food Intolerances 

If you have a healthy gut microbiome, you can digest and assimilate all kinds of food with ease. However, if there is an imbalance in your gut, you may face various food intolerances. Indigestion of heavy food items.

g) Poor Oral Health 

Both gut and oral microbiomes are interdependent. Symptoms seen due to an imbalance in your gut health are tooth decay, bleeding gums and cavities.

Causes of Gut Flora Imbalance

Your gut flora is essential in keeping your overall health in optimum condition. Any imbalance in this can cause issues in different systems of your body. This is why addressing the causes and limiting them as much as possible in your routine is very important.

a) Diet

 

“Numerous studies suggest that a high-fat diet can lead to gut microbiota dysbiosis”

-Pubmed research

 

If your diet is high in processed foods, sugar, or artificial additives. Also, if your diet lacks fibre, essential nutrients and whole foods.

b) Antibiotic Use 

Antibiotics target specific microorganisms in your body, and in this process, they can disrupt he balance of harmful and beneficial bacteria in your gut.

c) Stress 

Stress can increase your gut barrier permeability. This can cause a condition known as ‘leaky gut,’ which allows bacteria to seep into your circulation, producing an inflammatory response.

It can affect your immunity, gut motility, and microbiome consumption. 

d) Infections 

Any infection, be it bacterial, viral, or parasitic, may affect your gut health, disrupting gut flora.

e) Lack of Fiber 

Fiber is essential to create a microbiome with diverse bacteria. A lack of this can reduce the diversity of beneficial bacteria in your gut.

f) Alcohol consumption 

Alcohol, due to its high sugar content, disturbs your gut flora. Drinking two or more alcoholic beverages per day can contribute to this.

g) Poor oral hygiene 

There are many possible pathways for oral microbes to act on your intestinal tract, causing imbalances in your intestinal microbiome and affecting organs of your digestive system. These may be a cause of infection, especially when you have poor oral hygiene. Poor dental hygiene can allow bacteria to grow out of balance in your mouth.

Natural Remedies to Restore Gut Flora Balance

Natural remedies can be very useful to balance your gut flora. You can include it in your daily routine to restore your gut flora.

A. Probiotics

What They Do: Probiotics are living microorganisms that, when ingested, provide health benefits. They introduce beneficial bacteria into your gut. Different probiotics have been found to address different health conditions.
Sources: Yogurt, kefir, sauerkraut, kanji, buttermilk, kimchi, miso, and probiotic supplements.
Best Strains: Lactobacillus acidophilus, Bifidobacterium bifidum, and Saccharomyces boulardii.

B. Prebiotics

What They Do: Unlike probiotics, they act as a food source for the beneficial bacteria, hence promoting their growth.
Sources: Garlic, onions, bananas, asparagus, chicory root, almonds, flax, whole grain, soy, cabbage and dandelion greens.
How to Use: Add prebiotic-rich foods to your daily meals for support

C. High-Fiber Diet

Why It Helps: A high-fibre diet is crucial for a healthy gut. It promotes the formation and smooth passage of stools. It also encourages diverse bacterial growth in your gut and improves digestion.
Sources: Whole grains, legumes, fruits, vegetables, nuts, oats, brussels sprouts, artichoke, quinoa, chocolates, chia seeds and seeds.

D. Fermented Foods

Why They Help: Fermentation is a very common method across various cultures worldwide and increases the beneficial bacteria in the food. Fermented foods contain live microorganisms that boost your gut biodiversity and your microbiome.
Examples: Tempeh, kombucha, pickles (naturally fermented), cultured milk, yoghurt, wine, beer, miso, kimchi, sauerkraut and natto.

Detox and Cleanse Your Gut

You may have heard the word detox a lot on social media recently. But how can you do a detox on your own? Let’s see some simple and easy methods to detox 

A. Hydration

Water plays an essential role in your digestive health. It helps to produce and release certain digestive juices. Drink at least 2–3 litres of water daily to flush toxins and support your digestion.

B. Herbal Teas

Herbal teas are easy to make and very helpful in managing your digestion.

i. Chamomile or Peppermint 

Chamomile possesses anti-inflammatory properties and helps to reduce your stomach discomfort and promote better digestion. Peppermint is known for its calming properties and is commonly used to reduce digestive issues. Peppermint tea reduces symptoms of indigestion, gas, and bloating.

ii. Ginger Tea 

Ginger tea aids your digestion by stimulating the release of digestive juices like saliva, bile and gastric enzymes. It also promotes smooth digestion and eases an upset stomach. It also improves gut motility and reduces bloating.

C. Lemon Water or Apple Cider Vinegar

Citric acid in lemon juice helps boost your gastric acid secretion. This is a digestive fluid produced in your stomach that helps your body break down and digest food. Apple cider vinegar is used for many gastrointestinal disorders to calm your digestive issues.
How to Use: Drink a glass of warm water with the juice of half a lemon or 1 tablespoon of apple cider vinegar in the morning. However, if you are a person who suffers from acid reflux, then refrain from this practice.

Lifestyle Changes to Support Gut Health

Modifying your lifestyle can also help improve your gut and overall health. Some lifestyle changes which you can add to our routine are:   

A. Stress Management

Do you know that your brain is connected to your gut? This is known as the gut-brain axis, and you may have felt its presence in instances like a hollow or weirdness in your stomach when you are stressed or scared. This happens due to this axis. Chronic stress disrupts this gut-brain axis and microbiome balance.

i) Meditation: 

Meditation is one of the most effective ways to manage stress. Sit in a quiet place whenever possible, close your eyes and meditate. If you have trouble meditating this way, you can also do guided meditations with audio available online.

ii) Yoga:

Yoga is one of the most ancient practices for your overall well-being. Simple exercises like vajrasana after meals and pawanmuktasana (wind-relieving pose)are very practical to boost your gut health.  

iii) Deep breathing exercises: 

Deep breathing exercises like anulom vilom (alternate nose breathing) and kapalbhai (rapid exhalations) are best for boosting your immune system and simulating your digestive fire, improving your gut health.

iv) Journaling:

Journaling is an effective way to remove trapped emotions which can cause chronic stress.

B. Regular Exercise

Moderate physical activity improves gut motility and microbial diversity. It also helps to relieve issues like constipation and irregular bowel movements. Engage in at least 30 minutes of any kind of physical exercise.
Examples: Walking, cycling, swimming, or strength training.

C. Quality Sleep

Poor sleep can have adverse effects on your health. This, in turn, can also affect your gut health.
Tips: Maintain a consistent sleep schedule and aim for 7–9 hours of sleep daily.

Foods to Avoid for Gut Health

Certain foods can trigger inflammation in your body and disrupt your gut microbiome. This creates an imbalance in your gut and causes digestion, absorption, and difficulty in elimination. Identifying these foods can be difficult, so here’s a list of foods which can trigger gut imbalance and that you should avoid as much as possible:

A. Processed Foods 

They are high in sugar and unhealthy fats that fuel harmful bacteria in your gut. They also cause sugar spikes in your body, which can weaken your body in the long run.

B. Artificial Sweeteners 

They contain chemicals which can be toxic to your body. They also contain materials that disrupt your microbiome and may cause bloating.

C. Alcohol 

Alcohol overconsumption damages your gut lining. It can cause various gastrointestinal issues and reduce microbial diversity in your gut. It also increases the risk of GERD (gastroesophageal reflux Disorder).

D. Red and Processed Meats 

Processed and red meats, if consumed excessively, can harm your gut. These can promote the growth of harmful bacteria if consumed in excess. Also, many animals are injected with antibiotics to prevent infections. This can further destroy your gut health.

Supplements for Gut Restoration

Vitamins and supplements are very beneficial to improve your overall health. They can also boost your gut health. Here is a list of natural supplements that help improve your overall gut health. However, before taking any supplement, consult your doctor to determine the recommended dose that suits your body.

A. Digestive Enzymes

Digestive enzymes help break down your food. Your pancreas, stomach, and small intestine produce them. Sometimes, your body may not produce the required digestive enzymes, which can cause bloating, gas, and indigestion. Supplements can help do this and reduce the strain on your gut.

B. L-Glutamine

Glutamine has several benefits for your gut. It supports your gut microbiome and promotes the integrity of your gut mucosal wall. It can significantly help you if you suffer from irritable bowel syndrome (IBS), constipation, abdominal pain and bloating.

C. Omega-3 Fatty Acids

Omega-3 fatty acids are a group of essential acids that your body needs for various activities. It reduces gut inflammation and supports the growth of beneficial bacteria.

D. Collagen or Bone Broth

Collagen is rich in amino acids, a protein component that helps heal and repair your gut lining and promotes a healthy microbiome.

E. Magnesium

It improves the regularity of your bowel movements and supports your gut motility. It promotes the growth of beneficial bacteria and helps to relieve constipation.

It is necessary to consult a healthcare provider if you face the following symptoms:

  • Your symptoms persist even after natural remedies.
  • Severe abdominal pain, blood in stool, or sudden weight loss.
  • Infections or conditions like IBS or leaky gut.

I joined Nirva recently. After 2 weeks, I  feel a lot of improvement in my gut health issues, and my mood swings are reduced with yoga, which helps a lot. The coaches are absolutely good, and they are guiding nicely - Shabeen Fatima (Nirva client)

Wrapping Up

A balanced gut microbiome is essential for your overall health and well-being. Your overall health is compromised and can present in various systems if your gut health is not in balance. Probiotics, prebiotics, a fibre-rich diet, and healthy lifestyle habits can help naturally support your gut microbiome and reduce any symptoms or issues of gut imbalance. Consult a healthcare provider if you face severe symptoms that are hampering your daily life. Contact our Nirva team of healthcare experts for a personalised treatment plan according to your needs. For more information on gut health, refer to this blog.

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Dr. Neethu Susan Sunny

Dr Neethu Susan Sunny is an Ayurvedic physician and educator with expertise in Ayurvedic pharmaceutics and wellness management. She integrates her clinical knowledge and well-researched content to provide informed guidance on lifestyle corrections and holistic wellness through Ayurveda. With a focus on evidence-based practices, Dr. Neethu empowers individuals to embrace natural living as a sustainable path to long-term health and well-being.