Your Gut Microbiome: The Tiny Organisms That Run the Show

So far in our Gut Health Series, we’ve taken you through the full digestive journey—starting with how your body breaks food down, why stomach acid and enzymes are essential, and how your gut lining keeps the good in and the bad out.

Now, we’re diving into the part of gut health everyone talks about—but often oversimplifies:

🦠 The microbiome

Yes, you’ve likely heard all the buzz—probiotics, fermented foods, “gut-friendly” everything. But what exactly is the microbiome? And how does it actually impact your health?

When we talk about the gut microbiome, we’re referring to the vast inner world of microbes—mostly in your colon. And vast is no exaggeration: your gut contains up to 10 times more microbial cells than human ones.

This complex ecosystem does far more than coexist with us. It works with us—breaking down food, supporting immunity, and influencing everything from metabolism to mood.

And it’s not just bacteria that live there. Your microbiome is a diverse community made up of:

• Bacteria – The stars of the show. Beneficial strains like Lactobacillus, Bifidobacterium, and Akkermansia aid digestion, produce vitamins, support immunity, and keep pathogens in check.
• Fungi – Yeasts like Candida and Saccharomyces boulardii support immune balance in small amounts, but can become problematic if they overgrow.
• Viruses – Mostly bacteriophages that regulate bacterial populations and support diversity.
• Archaea – Microbes involved in fermentation and gas regulation, especially methane.
• Other Microorganisms – Includes protozoa and other single-celled species that can support or disrupt balance depending on the gut environment.

Together, this inner ecosystem helps shape how you feel, think, digest, and defend against illness. When your gut microbes are diverse and in balance, it works like a well-tuned team—keeping your gut (and the rest of you) in sync.

A healthy, balanced microbiome helps:

• Break down fiber into short-chain fatty acids to fuel your gut lining and reduce inflammation

• Produce essential vitamins like B12, K2, and folate

• Support your immune system and help it respond appropriately

• Influence neurotransmitter production (like serotonin and dopamine)

• Keep harmful microbes in check

• Play a role in metabolism, hormones, and even weight regulation

Your microbes may be small—but their impact is anything but.

Your microbiome is a dynamic filter between you and the outside world. When that filter is off, your whole system feels it.

Everything you bring into your body will either help your microbiome or hurt it. Unfortunately, our modern lifestyles are not very friendly to our microbiome, so it’s good to understand what can impact its happiness.

While microbes can be found throughout the body (skin, lungs, reproductive system), the majority live throughout your digestive system. In a healthy gut, the majority of your microbiome lives in the large intestine (colon)—where they help break down fiber, produce short-chain fatty acids, and support immune and gut lining health.

This natural setup keeps digestion efficient, nutrient absorption smooth, and immune reactions in check.

Tip: A balanced microbiome isn’t just about the types of microbes you have—it’s also about where they live and how they behave.

The good news? Your microbiome is incredibly responsive to your daily choices. Here’s how to show it some love:

• Avoid unnecessary antibiotics and ultra-processed foods
• Cut down on alcohol, artificial sweeteners, and excess sugar
• Choose clean, low-toxin food and water when possible

• Prioritize sleep and rest—your gut microbes follow a circadian rhythm too
• Reduce stress through breathwork, movement, nature, or stillness
• Get outside and let your body interact with the real world—microbial exposure isn’t something to fear

When it comes to gut health, these three often get tossed around together—but they each play a distinct role:

🥦 Prebiotics
Think of prebiotics as microbe food. They’re certain types of fiber (found in plants!) that your beneficial gut bacteria ferment to stay alive and thriving. Examples include garlic, onions, leeks, bananas, oats, apples, and asparagus. A diverse, plant-rich diet is your best source.

🦠 Probiotics
These are the actual live microbes—the good bacteria—that support gut health. You’ll find them in fermented foods like yogurt, kefir, sauerkraut, kimchi, and miso. Supplementing with probiotics can also help in some cases, but they’re not a one-size-fits-all solution.

✨ Postbiotics
These are the beneficial byproducts created when your gut bacteria break down prebiotic fibers. Think short-chain fatty acids (like butyrate), which help maintain the gut lining, regulate inflammation, and support immune health. You can’t eat postbiotics directly—they’re made inside your gut.

Bottom line?
Prebiotics feed the probiotics, and together they create postbiotics. Supporting all three is the key to a resilient, balanced microbiome—and whole foods are one of the best ways to do just that.

Whole foods and lifestyle shifts should always be your foundation—but sometimes your gut needs more targeted support. That’s where probiotics come in.

Supplements can help, especially if your microbiome has been disrupted by antibiotics, illness, or stress. But not all probiotics are the same—specific strains offer specific benefits

Top strains to look for include:

• Lactobacillus acidophilus NCFM® - bloating, gut barrier support
• Bifidobacterium lactis HN019 – gut barrier support, bowel regularity, immune function
• Lactobacillus rhamnosus GG (LGG) – gut barrier support and immunity, increases sIgA
• Saccharomyces boulardii (SB) – post-antibiotic support, pathogen control
• Lactobacillus plantarum – relieves IBS and digestive discomfort
• Lactobacillus reuteri – gut immunity, oral health, reduces gut inflammation
• Bifidobacterium longum BB536 – immunity, reduces GI discomfort

We’ve explored how the trillions of microbes in your gut shape your digestion, immunity, and mood. But what do those microbes actually run on?

UP NEXT  ⏭️  In our next post, we’ll zoom in on food—the everyday choices that either nourish or disrupt your microbiome. From fiber to polyphenols, we’ll explore why variety matters, how soil health affects nutrient density, and why real, whole foods may be the most powerful tool for gut balance.