Written by Dr. Neethu Susan Sunny

Medically reviewed by Dr Godmi Tresa

Updated on March 21, 2025

How to Improve Gut Flora: Treatments to Restore a Healthy Microbiome

Many of us focus on our external health. Whether it’s eating right, exercising, and staying hydrated. But have you thought about the trillions of microbes surviving inside your gut?

Your gut flora, or microbiome, is like an invisible army that works around the clock to digest food, fight infections and keep you healthy. When the microbiome is thriving, you feel energised and balanced. But when stress, poor diet or antibiotics disturb this delicate ecosystem, you may experience bloating, fatigue and even skin issues.

Want to know how antibiotics affect your gut flora and what steps you can take to heal?

Check out this blog: How Antibiotics Impact Gut Microbiota: What You Need to Know

So, how do you support your gut flora and keep it happy?

Here’s how to restore healthy gut bacteria and improve your gut flora naturally and effectively.

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Why Is Gut Flora Important?

‘All disease begins in the gut’- Hippocrates, The Father of Medicine

Centuries ago, it was recognised, and modern science now confirms that gut health is the foundation of overall well-being.

Are you aware that your gut flora is like a well-orchestrated symphony?

But like any ecosystem, it needs the right conditions to flourish. Even the tiniest chaos can alter the harmony, throwing your entire system off balance.

A. Functions of Gut Flora:

Let’s take a closer look at the key functions that make your gut flora important:

  • Digestion: Every bite you eat is only as good as what your gut absorbs! Your gut bacteria play a crucial role in breaking down food and absorbing nutrients, ensuring your body gets the fuel it requires. In Ayurveda, your gut is the seat of Agni or digestive fire, which keeps your digestion strong and efficient.
  • Immune System Regulation: Your gut acts as your body’s first line of defence! It serves as a protective barrier, helping your body fight off harmful pathogens and boosting your immunity.
  • Neurotransmitter Production: Did you know that your gut is sometimes called your “second brain”? This is because gut bacteria produce serotonin, a key neurotransmitter that influences your mood and mental health.
  • Inflammation Control: A balanced microbiome keeps inflammation in check, preventing chronic health problems. 

B. Signs of Imbalanced Gut Flora:

When your gut flora is out of sync, the effects can show up in various ways.

  • Digestive issues (bloating, gas, diarrhoea, or constipation)
  • Frequent infections or poor immunity
  • Fatigue and brain fog
  • Food intolerances or sensitivities
  • Skin conditions like acne or eczema

How to Improve Gut Flora

Improving your gut flora is key to better digestion, a stronger immune system and even a happier mood. In short, a healthy gut means a more energised you!

The following are some tips to improve gut flora that you can adapt to enhance your overall health:

A. Dietary Adjustments

The first step to focus on optimal gut health begins with mindful dietary changes that encourage the growth of good bacteria and eliminate harmful disruptors.

  • Incorporate Probiotic Foods: Do you want to strengthen your gut’s defence squad? The secret weapon lies in probiotics.
    What they do: The probiotic foods introduce beneficial bacteria that help maintain microbial balance.
    Sources of probiotic foods for microbiome health: Yogurt, kefir, sauerkraut, kimchi, miso, and kombucha.

“Multiple studies suggest that probiotics protect the function of the barrier by promoting mucus secretion. For example, Lactobacillus(lactic acid bacteria) secretes extracellular proteins that weaken pathogen adhesion and protect the intestinal barrier.”

-Effects of Probiotics on Gut Microbiota: An Overview, PubMed

 

  • Add Prebiotic Foods: Probiotics need food, too! The gut microbiota obtains its survival energy from prebiotics.
    What They Do: Prebiotics are non-digestible carbohydrates or a group of nutrients degraded and fermented by the beneficial gut bacteria for their growth.
    Sources: Garlic, onions, asparagus, bananas, oats, and dandelion greens.
     
  • Eat a Fibre-Rich Diet: Fibre is your gut’s best friend!
    Why It Helps: Fibre is the secret ingredient that helps your microbiome multiply, keeps them diverse and makes your digestion smooth.
    Sources: Whole grains, fruits, vegetables, legumes, and nuts..
     
  • Reduce Processed Foods and Sugar: Are you someone who just can’t resist sweets? An occasional treat is fine, but too much sugar lets the bad bacteria take over your gut health.
    Why it helps: Processed foods and high sugar can fuel harmful bacteria and can throw your microbiome off balance. 
    Time to swap processed sweets for natural, gut-friendly alternatives.

Are you curious how quitting sugar benefits not just your gut health but your skin, too? Take a look through this blog - How Will Your Skin Change After You Quit Sugar?

  1. Stay Hydrated: Think of water as your gut’s personal detox agent!
    Why it helps: Water helps transport nutrients, flush out toxins, and keep digestion effortless, promoting a healthy microbiome.

B. Probiotic Supplements

If you would like to give your gut an extra boost, then probiotic supplements act like reinforcements. These help to fill in the gaps and strengthen your microbiome when diet alone isn’t enough!

  • Choose Multi-Strain Products: Different probiotic strains offer unique benefits. Lactobacillus promotes digestion, Bifidobacterium enhances immunity, and Saccharomyces boulardii keeps harmful bacteria in check. A diverse probiotic blend ensures all-around gut support.
  • Dosage: Opt for supplements with at least 10–50 billion CFUs (colony-forming units) for maximum impact. 
  • When to Take: Take on an empty stomach or as directed by the product for better absorption. Let your gut soak up all the goodness!

C. Lifestyle Changes

A happy gut is the reflection of a balanced lifestyle!

Here is how to fine-tune your routine to keep your digestive system running smoothly.

  • Manage Stress: Your gut listens to your mind! Feeling overwhelmed? Your gut feels it, too! How Stress Affects Gut Flora? The brain and the gut have a lively ongoing relationship through the gut-brain axis. Chronic stress disrupts gut-brain communication, harming beneficial bacteria.

 

“Studies show that the gut microbiota plays a role in stress response. Reduce stress with Yoga, meditation, and mindfulness practices like deep breathing.”

-Dr Aswathy Krishna, Senior Ayurveda Consultant, Nirva Health

 

To get more insights on natural ways for stress management, check out this blog: Finding Balance Within: Ayurveda and Yoga for Mental Health is the Key

  • Get Regular Exercise: Movement = Happy microbes! 
    How does movement influence your gut? Exercise is not just for fitness, it boosts gut motility and microbial diversity. Try low-impact activities like walking, swimming, or yoga to keep your gut health on track.
  • Prioritise Sleep: Burning the midnight oil? Your gut needs rest, too! Poor sleep disrupts gut flora. This is because your gut microbiome regenerates at night. Aim for 7–9 hours of quality sleep daily to maintain a healthy gut environment.

See how small changes in lifestyle led to big gut health transformations from our client review:

“For years, I struggled with gut issues, like bloating and acid reflux, which significantly affected my daily life. After starting the Nirva diet plan, I noticed remarkable improvements within just 4 weeks.”

-Sushil Gaikwad, a Nirva Health client.

 

D. Avoid Gut Disruptors

Be mindful of some everyday choices which could be silently hurting your gut health. Let us know them in detail.

  • Limit Antibiotics: The problem with the use of antibiotics is that they don’t discriminate between good and bad bacteria. It is always better to use them only when necessary.
  • Reduce Alcohol Intake: Excessive drinking of alcohol can irritate your gut lining and impact digestion. Opt for moderation, and remember to hydrate well!
  • Avoid Artificial Sweeteners: Some sugar substitutes like aspartame or sucralose may negatively impact gut bacteria. Stick to natural sources of sweetness like fruit and honey for a healthier balance.

E. Supplements and Natural Remedies

Beyond all the above methods, certain supplements and natural remedies may also come in handy at times to improve your gut flora.

  1. Digestive Enzymes: Your body naturally produces digestive enzymes to break down food and absorb nutrients.  However, sometimes your gut needs an extra little support!  Digestive enzyme supplements play a key role in reducing strain on your gut and smooth digestion.
  2. Omega-3 Fatty Acids: Research suggests that omega-3 supplementation may positively impact gut health by promoting the production of beneficial short-chain fatty acids, which reduce inflammation and promote a balanced microbiome.
    Sources: Salmon, walnuts, or fish oil supplements.
  3. L-Glutamine: L-glutamine is the most abundant amino acid in the human body, which is vital for various metabolic processes.  Its supplementation helps to repair and strengthen the gut lining, preventing a “leaky gut.

Did you know?

“The intestine utilises about 30% of total glutamine, indicating that it is a key nutrient for the intestine and competes with other tissues for glutamine from the body amino acid pool and dietary sources.”

  1. Herbal Teas: A warm cup of chamomile, ginger, or peppermint tea can calm your gut and soothe bloating as they are proven digestive relaxants.  Sip your way after meals to gut bliss!

Benefits of Improving Gut Flora

Taking care of your microbiome is one of the simplest ways to improve your overall health.

Here is why you should care about your gut health:

  • Enhanced Digestion: Experience lightness by reducing bloating, gas, and constipation.
  • Stronger Immunity: A well-balanced gut defends against infections and chronic illnesses
  • Improved Mental Health: Boosts mood and cognitive function via the gut-brain connection
  • Weight Management: Supports healthy metabolism and reduces cravings for unhealthy foods
  • Reduced Inflammation: Alleviates symptoms of inflammatory conditions like arthritis or IBS

Advanced Treatments for Severe Imbalances

If gut imbalances persist despite lifestyle changes and natural remedies, it is time to look for more advanced treatments. Science takes gut health to the next level with specialised treatments as follows.

A. Fecal Microbiota Transplantation (FMT):

Imagine getting a gut microbiome makeover!

FMT is an ultimate gut reset, which involves transferring healthy gut bacteria from a donor into the digestive system of someone with gut issues to restore microbiome balance. It has been successfully used in the treatment of Clostridium difficile infection (CDI) and is also recommended for conditions such as inflammatory bowel disease (IBD) and metabolic disorders such as obesity. 

B. Personalised Gut Health Plans:

Your gut is unique! So should be your treatment.

Based on microbiome testing, tailored diets and supplements target individual needs. Whether you need probiotics, fibre adjustments or enzyme support, this specified and targeted approach ensures your gut gets what it requires.

C. Targeted Antibiotic or Antimicrobial Therapy:

At times, an overgrowth of harmful bacteria like Small Intestinal Bacterial Overgrowth (SIBO) disrupts gut health. In such cases, a carefully designed antibiotic or antimicrobial therapy helps to eliminate bad bacteria without affecting the beneficial ones.

Wrapping up

Your gut health is a longtime investment. Hence, improving your gut flora should be a gradual process and not a quick fix!

Making mindful choices like eating nourishing foods, staying active, and managing stress can create long-term balance. Feed your gut well by introducing probiotics and healthier foods into your routine. Research shows that a diverse microbiome contributes to better digestion, immunity, mental health, and overall well-being. 

Trust the process, and your gut will thank you!

Stay consistent with gut-friendly habits, and don’t hesitate to consult a healthcare professional if you have any persistent symptoms.

For personalised guidance for managing gut issues naturally, talk to our experts at Nirva Health.

Book your appointment here.

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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.