Gut Microbiome 101: What It Is, Why It Matters, and How to Support It

The Gut Microbiome: What It Is, How to Test It, and How to Improve It with the Right Diet

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As some of you may know, twelve years ago, I was very ill with Crohn's disease. I had two horrendous years before I got better. For the past ten years, I haven't had any flare-ups.

Back then, I didn't know much about the Gut microbiome and how it affected your overall health. Today, I know our gut is home to trillions of bacteria that impact everything from digestion to immune health and even mental well-being. A balanced gut microbiome can help prevent chronic disease, improve metabolism, and enhance overall health. But how do we know if our gut microbiome is healthy? And if it's not, what can we do to fix it?

This article serves as a guide as we explore the science of the gut microbiome, how to test it (including the powerful metagenomic sequencing method), and the most effective foods and supplements to support gut health, including probiotics, prebiotics, and postbiotics.

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1. What is the Gut Microbiome and Why is It Important?

The gut microbiome consists of trillions of microbes living in your digestive tract, including bacteria, viruses, fungi, and archaea. These microbes:

✅ Help digest food and absorb nutrients

✅ Support immune function

✅ Regulate inflammation

✅ Influence mood and mental health (via the gut-brain axis)

✅ Play a role in weight management and metabolism

A healthy microbiome is diverse and balanced between beneficial and neutral microbes. An imbalanced microbiome (dysbiosis) is linked to IBS, autoimmune disorders, obesity, diabetes, heart disease, and even depression (Mohajeri et al., 2018).

By the way, the disease I was struggling with is an autoimmune disease (Crohn's disease).

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2. How to Test Your Gut Microbiome

Metagenomic Sequencing: The Most Accurate Gut Test

Metagenomic sequencing is the gold standard for gut microbiome testing. Unlike traditional stool tests, which only detect broad bacterial groups, metagenomic sequencing analyzes the entire DNA of your gut bacteria.

✅ What It Tells You:

•Exact bacterial species in your gut

• Their functions (e.g., whether they produce beneficial compounds like butyrate)

• Presence of pathogenic bacteria

• Personalized dietary recommendations

✅ Who Should Consider It?

• People with IBS, IBD, bloating, diarrhea, or constipation

• Those recovering from antibiotics or infections

• People with autoimmune conditions

• Anyone wanting personalized gut health insights

Together with a genetic test that looks at health markers and a wide panel blood test, I think a Gut Microbiome test is the most important test to take.

When I started Get Body Data, I knew these were the three tests I wanted. If you know how your body functions, your most essential blood markers, and the condition of your gut microbiome, you know almost everything that's going on in your body.

‍3. What to Eat for a Healthier Gut Microbiome

But let's say that you don't want to do a test and you just want to improve your gut microbiome. Is that possible? Of course!

Research shows that diet is the most powerful way to improve gut health (Perler et al., 2022). The best gut-friendly foods include:

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a. Prebiotic Foods (Fuel for Good Bacteria)

Prebiotics are types of fiber that feed beneficial bacteria and help them grow.

Best Prebiotic Foods:

• Onions & Garlic – Support beneficial gut bacteria like Bifidobacterium

• Oats & Mushrooms – Contain beta-glucans, which help increase butyrate production

• Legumes (Lentils, Beans, Chickpeas) – Contain resistant starch for gut bacteria

• Green Bananas & Cooled Potatoes – Provide resistant starch that supports SCFA production

b. Probiotic Foods (Live Beneficial Bacteria)

Probiotics are live microorganisms that restore gut balance.

Best Probiotic Foods:

• Yogurt & Kefir – Contain Lactobacillus and Bifidobacterium

• Sauerkraut & Kimchi – Rich in probiotic lactic acid bacteria

• Miso & Tempeh – Provide fermented soy-based probiotics

• Kombucha – A fermented tea that increases microbial diversity

c. Postbiotics (The End Products of Fermentation)

Postbiotics are bioactive compounds that bacteria produce after digesting prebiotics. These include:

• Short-Chain Fatty Acids (SCFAs) – Improve gut lining and immune function

• Lactate & Butyrate – Reduce inflammation

• Polyphenols (from Berries, Green Tea, Dark Chocolate) – Boost Akkermansia muciniphila, a bacteria that helps regulate metabolism (Żółkiewicz et al., 2020)

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Probiotics, Prebiotics, and Postbiotics: How They Work Together

Type

What It Does

Where to Get It

Probiotics: Live bacteria that restore gut balance --> Yogurt, kefir, kimchi

Prebiotics: Fibers that feed probiotics --> Onions, oats, legumes

Postbiotics: Bacterial metabolites that support gut health --> SCFAs, polyphenols

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How They Work Together:

1️⃣ Prebiotics feed probiotics, helping them grow.

2️⃣ Probiotics produce postbiotics (like butyrate), which strengthen the gut lining and reduce inflammation.

3️⃣ The cycle repeats, leading to a balanced, healthy microbiome.

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--> Practical Takeaways for Better Gut Health

✅ For a healthier gut:

• Eat fiber-rich foods (onions, garlic, legumes) for prebiotics.

• Include fermented foods (yogurt, kefir, kimchi) for probiotics.

• Consume polyphenols (berries, green tea) to boost postbiotic production.

• Reduce processed foods and artificial sweeteners to prevent dysbiosis.

• Consider a gut microbiome test if you have ongoing gut issues.

Final Thoughts

Your gut microbiome is constantly changing, and the foods you eat directly shape its composition.

• If you're struggling with digestive issues, inflammation, or poor metabolism, gut testing (especially metagenomic sequencing) can provide personalized insights.

• Eating the right foods—fiber, fermented foods, and polyphenols—can significantly improve gut health.

• A combination of prebiotics, probiotics, and postbiotics helps create a thriving gut environment.

PART 2

Best Probiotic Supplements Based on High-Quality Research

Probiotic supplementation can have significant health benefits, but not all probiotic strains are equally effective. Based on the latest high-quality research, here are the most effective probiotic supplements and their benefits.

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1. Multi-Strain Probiotics Are the Most Effective

A 2020 study found that multi-strain probiotics containing both Lactobacillus and Bifidobacterium were the most effective for reducing gastrointestinal symptoms and improving gut barrier function (Miles, 2020).

✅ Best Multi-Strain Probiotic Supplements (Lactobacillus + Bifidobacterium):

• Visbiome – One of the most researched high-potency probiotics (450 billion CFUs)

• VSL#3 – Clinically studied for gut disorders like IBS and IBD

• Garden of Life Raw Probiotics – Contains multiple strains + prebiotics

These multi-strain probiotics help restore gut balance and support immune function.

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2. Lactobacillus-Based Probiotics for Gut Barrier & Inflammation

A study found that Lactobacillus salivarius CPN60 improved gut health, increased butyrate production, and reduced harmful bacteria in rats with colitis (Gupta et al., 2020).

✅ Best Lactobacillus-Based Probiotics:

• Culturelle Digestive Health – Contains Lactobacillus rhamnosus GG, proven to support gut integrity

• Align Probiotic – Contains Bifidobacterium infantis, which reduces bloating and inflammation

These probiotics may help people with digestive disorders like IBS and IBD.

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3. Probiotics for Gut Stability & Digestive Balance

A study on Lactobacillus plantarum HNU082 (Lp082) found that continuous supplementation with a prebiotic (galactooligosaccharide) increased gut microbiome stability (Ma et al., 2020).

✅ Best for Gut Stability & Digestive Balance:

• Jarrow Formulas Ideal Bowel Support 299v – Contains Lactobacillus plantarum 299v, which enhances gut stability

• Seed Probiotic – Contains multiple strains + prebiotics for long-term gut health

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4. Probiotics for Athletes & Active Individuals

A 2022 systematic review found that probiotics reduce exercise-related gut symptoms and improve gut barrier function (Łagowska et al., 2022).

✅ Best Probiotics for Athletes:

• OMNi-BiOTiC POWER – Designed for gut permeability & inflammation

• Klean Probiotic – Contains Lactobacillus and Bifidobacterium strains for digestion & immunity

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5. Probiotics for Metabolic & Blood Sugar Support

A study found that probiotics improve glucose metabolism and lipid levels in diabetes patients (Khalil et al., 2021).

✅ Best Probiotics for Metabolism:

• Pendulum Glucose Control – Designed for blood sugar regulation

• Thorne FloraMend Prime Probiotic – Supports gut-brain-metabolism balance

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6. Bifidobacterium-Based Probiotics for Immune Function

A study found that Bifidobacterium lactis BL04 combined with bacteriophages improved immune response and gut health (Grubb et al., 2020).

✅ Best Bifidobacterium-Based Probiotics for Immunity:

• Florastor – Contains Saccharomyces boulardii, beneficial for diarrhea prevention

• BioGaia Protectis – Contains Bifidobacterium lactis, proven to enhance immunity

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Key Takeaways: Choosing the Best Probiotic for You

Health Goal

Best Probiotic Strains

Top Supplement

Overall Gut Health: Multi-strain (Lactobacillus + Bifidobacterium) --> Visbiome, VSL#3

Gut Barrier & Inflammation: Lactobacillus salivarius, L. rhamnosus --> Culturelle, Align

Gut Microbiome Stability: Lactobacillus plantarum + prebiotics --> Jarrow 299v, Seed Probiotic

Athlete’s Gut Health: Multi-strain probiotics --> OMNi-BiOTiC POWER, Klean Probiotic

Metabolic & Blood Sugar Support: Bifidobacterium, Akkermansia --> Pendulum Glucose Control, Thorne FloraMend

Immune Function: Bifidobacterium lactis BL04 --> Florastor, BioGaia Protectis

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Final Advice

• For gut disorders (IBS, IBD): Choose multi-strain probiotics like Visbiome or VSL#3.

• For bloating and digestion: Look for Lactobacillus rhamnosus (Culturelle) or Bifidobacterium infantis (Align).

• For metabolism & blood sugar: Consider Pendulum Glucose Control with Akkermansia.

• For general gut balance: Seed Probiotic or Garden of Life provide a mix of probiotics + prebiotics.

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