Top Gut Health Supplements That Support Your Microbiome

Your gut is more than just a digestive organ. It’s a dynamic, living ecosystem that influences almost every aspect of your health. The gut microbiome, made up of trillions of bacteria, yeasts and other microbes, plays a vital role in nutrient absorption, immune defence, hormone regulation and even brain function. When the microbiome is balanced, it supports energy, mental clarity, mood stability, skin health and a strong immune response. When it’s out of balance, due to stress, poor diet, medications or environmental factors, it can contribute to issues like bloating, fatigue, food sensitivities, anxiety and inflammatory disease.

The insights in this article are provided by Vivere's Head of Nutrition, Yusra Serdaroglu Aydin, a registered dietitian with a background in nutrition, food engineering and culinary arts. Her approach is grounded in science and shaped by a strong understanding of personalised nutrition and the human microbiome. Here, she shares the most effective, evidence-based supplements for a healthier gut, alongside their natural food sources and usage recommendations.

• Symptoms like bloating, fatigue and food sensitivity are common signs of microbiome imbalance

• Probiotics and prebiotics are foundational supplements for gut support

• Specific ingredients like ginger, curcumin, L-glutamine and magnesium offer targeted benefits

• Personalised microbiome testing reveals what your gut needs

• The most effective supplement routines are personalised, monitored over time and combined with dietary and lifestyle changes

Many people are unaware that their symptoms are connected to poor gut health. Some of the most common signs of microbial imbalance include [1]:

• Persistent bloating, gas or irregular bowel movements

• Food intolerances or sensitivities that seem to be increasing over time

• Frequent fatigue, brain fog or low mood

• Skin issues like acne, eczema or rosacea

• Compromised immunity or frequent infections

• Sugar cravings or blood sugar imbalances

• Poor sleep quality and hormonal fluctuations

These symptoms suggest your gut microbiome may be under strain. Fortunately, targeted lifestyle changes and high-quality supplements can help support your gut and restore its essential functions.

Probiotics are live microorganisms that help restore and maintain a healthy gut microbiome. They support digestion, immunity and inflammation control by replenishing beneficial bacteria and improving microbial balance [2]. There are many strains of probiotics, each with specific health benefits.

Benefits [3]:

• Improve bowel regularity and reduce bloating

• Replenish gut flora after antibiotic use

• Support immune system function

• May reduce symptoms of IBS, IBD and traveller’s diarrhoea

• Enhance mood and mental well-being via the gut-brain axis

Food sources: Kefir, live yoghurt, sauerkraut, kimchi, miso, tempeh, kombucha
Take supplements: After antibiotics, during digestive flare-ups, after travel, when immunity is low, after illness
Usage recommendation: Take daily on an empty stomach or before meals; store in the fridge if required; choose strains like Lactobacillus and Bifidobacterium that are clinically supported

Prebiotics are non-digestible fibres that serve as food for your beneficial gut bacteria. They increase microbial diversity and help your microbiome produce key metabolites like short chain fatty acids [4].

Benefits [5]:

• Feed good bacteria and improve overall microbial diversity

• Support bowel regularity and improve stool consistency

• Increase short-chain fatty acid production

• Strengthen gut barrier and support immune tolerance

Food sources: Garlic, onions, leeks, asparagus, artichokes, oats, green bananas, chicory root, legumes
Take supplements: When fibre intake is low, after antibiotics, during gut repair, when seeking microbial diversity
Usage recommendation: Start with small doses to avoid bloating; can be mixed into smoothies, yoghurts or water; best taken with meals

Polyphenols are plant compounds that act as antioxidants and microbiome modulators. They reduce gut inflammation, protect the intestinal lining and increase beneficial bacteria [6].

Benefits [7]:

• Inhibit the growth of harmful microbes

• Support the growth of Akkermansia muciniphila and other beneficial bacteria

• Reduce oxidative stress and intestinal inflammation

• Enhance gut barrier integrity and metabolic health

Food sources: Blueberries, raspberries, blackberries, olive oil, green tea, dark chocolate, turmeric, pomegranate
Take supplements: When inflammation is present, when diet lacks variety or colour, during metabolic stress
Usage recommendation: Take polyphenol extracts with healthy fats for absorption; combine with black pepper (piperine) to enhance bioavailability

Digestive enzymes help break down proteins, fats and carbohydrates into absorbable nutrients and therefore help to create the right environment for a healthy gut microbiome. They support the digestive process and reduce symptoms related to food intolerances or digestive discomfort [8].

Benefits [9]:

• Relieve bloating, gas and indigestion

• Improve nutrient absorption

• Reduce reactions to dairy and gluten in sensitive individuals

• Assist in breaking down large meals or heavy foods

Food sources: Pineapple (bromelain), papaya (papain), fermented foods, raw honey, sprouted grains
Take supplements: When experiencing persistent bloating, heaviness, or gas after meals, for specified food intolerances
Usage recommendation: Take right before meals; choose the enzyme based on dietary needs and concerns – it is always best to speak with a healthcare provider

Fibre helps regulate bowel movements, supports satiety and feeds beneficial bacteria. Soluble fibre forms a gel in the gut, while insoluble fibre adds bulk to stools [10].

Benefits [11]:

• Regulates bowel habits and relieves constipation

• Helps feed beneficial microbes (prebiotic effect)

• Supports detoxification and gut transit time

• Improves blood sugar balance and cholesterol

Food sources: Flaxseeds, chia seeds, oats, legumes, leafy greens, broccoli, green powders
Take supplements: If you suffer with constipation or have a low fibre intake then a supplement may be beneficial
Usage recommendation: Always take fibre supplements with at least 250–300ml of water; psyllium is best before meals; greens powders can be added to smoothies or water in the morning

These natural botanicals soothe the gut, reduce inflammation and help relieve digestive discomfort. Each offers unique benefits for nausea, cramping, and microbiome health [12].

Benefits [13]:

• Reduce nausea, gas and abdominal pain (especially peppermint)

• Calm gut muscle spasms and reduce IBS symptoms

• Lower inflammation in the gut lining (curcumin, ginger)

• May reduce microbial overgrowth in the small intestine

Food sources: Fresh ginger, peppermint tea, turmeric root, herbal infusions, turmeric latte
Use when: Cramping, nausea, gas, bloating, IBS, inflammation
Usage recommendation: Use enteric-coated peppermint to avoid reflux; curcumin supplements should include black pepper or liposomal formulations; ginger can be consumed as capsules or tea with meals

L-glutamine is an amino acid that fuels your gut and immune cells, supports muscle growth and repair, and also helps your body produce an important antioxidant that protects your cells from damage [14].

Benefits [15]:

• Repairs gut lining

• Reduces inflammation and permeability

• Support and restore a positive gut microbiome

• It may help treat depression

Food sources: Chicken, beef, pork, fish, eggs, dairy - cow’s milk, cheese and yogurt, red cabbage, sweetcorn, nuts and seeds
Take supplements: For leaky gut, after antibiotics or infections, sugar cravings
Usage recommendation: Best taken on an empty stomach for best effect

Magnesium is a critical mineral that supports muscle relaxation, nerve function and bowel regularity. It’s also involved in over three hundred of biochemical reactions throughout the body, supporting systems such as muscle, nerve, and digestive health [16].

Benefits [17]:

• Relieves constipation by relaxing intestinal muscles

• Reduces stress-related gut dysfunction

• Enhances sleep quality, which supports gut repair

• Helps regulate mood and anxiety

Food sources: Pumpkin seeds, almonds, dark chocolate, spinach, black beans, avocado
Take supplements: For constipation, stress, poor sleep, muscle tension, mood swings
Usage recommendation: Magnesium citrate supports bowel movement; magnesium glycinate is calming and better for stress; take in the evening with or after food for improved sleep and gut relaxation

Supplements are only part of the equation. For a truly healthy gut, consider:

• Eating a wide variety of at least 30 different plant-based foods each week, such as vegetables, fruits, legumes, nuts, seeds, and whole grains

• Avoiding ultra-processed foods and artificial additives

• Sleeping at least 7–8 hours a night

• Managing stress through breathwork, nature, or mindfulness

• Exercising regularly, especially low-impact movement like walking or yoga

• Drinking filtered water and limiting alcohol

You can’t optimise what you don’t measure. Vivere’s gut microbiome test gives you a detailed profile of your microbial ecosystem.

This enables:

• Identification of key microorganisms

• Early detection of trends linked to chronic disease risk

• Personalised supplement and nutrition strategies

• Monitoring of progress over time

Pairing microbiome analysis results with professional dietary guidance ensures that your supplement routine is not just effective but tailored to your biology.

"Supporting your microbiome with the right supplements can lead to real improvements in digestion, immunity, energy and even mental wellbeing. While whole foods should always be the foundation, targeted supplements like probiotics, prebiotics, polyphenols, enzymes, and many more offer strategic support, especially when personalised to your individual needs. By combining scientific insights with practical, food-first approaches, we can harness the power of the microbiome to live better, for longer."

Vivere helps you take control of your health with personalised insights from state-of-the-art gut microbiome testing, nutritional guidance, science-backed supplements and expert support. Sign up today and start living better, for longer.

[1] Gut microbiota dysbiosis in functional gastrointestinal disorders: Underpinning the symptoms and pathophysiology - PMC

[2] Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation - PMC

[3] The Potential Impact of Probiotics on Human Health: An Update on Their Health-Promoting Properties - MDPI

[4] Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications - PMC

[5] Fiber and Prebiotics: Mechanisms and Health Benefits - ResearchGate

[6] Dietary Polyphenol, Gut Microbiota, and Health Benefits - PMC

[7] The Interactions between Polyphenols and Microorganisms, Especially Gut Microbiota - MDPI

[8] Digestive Enzyme Supplementation in Gastrointestinal Diseases - PMC

[9] A Multi-Digestive Enzyme and Herbal Dietary Supplement Reduces Bloating in a Single Use in Healthy Adults: A Randomized, Placebo-Controlled, Cross Over Study - Taylor & Francis

[10] Dietary fiber: Essential for a healthy diet - Mayo Clinic

[11] Therapeutic Benefits and Dietary Restrictions of Fiber Intake: A State of the Art Review - PMC

[12] A review on chinese herbal medicine used as carminative - Science Direct

[13] A Scoping Review of the Clinical Evidence for the Health Benefits of Culinary Doses of Herbs and Spices for the Prevention and Treatment of Metabolic Syndrome - MDPI

[14] Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions - PMC

[15] The role of glutamine in supporting gut health and neuropsychiatric factors - Science Direct

[16] Magnesium Fact Sheet for Health Professionals - NIH

[17] Magnesium and Human Health: Perspectives and Research Directions - PMC