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Microbiome & Microbial Ecology

Microbes as Pills: When Your Gut Prescribes the Medicine

2025-06-17 · 2 min read

As a doctor, I am trained to recognize inflammation ie redness, swelling, pain, dysfunction, and treat with medications, procedures and/or monitoring.

We now know that the solution to chronic inflammation, or the most powerful medicine, may not always come in a prescription bottle.

It may be in the community of bacteria living inside us.

Series: Our Gut Microbiome and Our Health - Part 5

Author: Dr. Tina Agbaosi, MD – Infectious Diseases | Metagenomics | Kindness is Contagious

Last week, we explored how gut microbes influences inflammation in general.

Today, I want to go deeper, into what we’re learning about specific diseases, the powerful role our microbial partners play, and how rebalancing the gut may offer new hope for people living with inflammatory and autoimmune conditions.

New to the series? Catch up on: ➡️ Part 1, ➡️ Part 2, ➡️ Part 3, ➡️ Part 4.

Microbes as Gatekeepers of Inflammation

Did you know that the composition of your gut microbes could increase or decrease your risk of inflammatory and autoimmune diseases?

Imagine what this could mean for treatment in the future.

So far in this series, we’ve learned that our gut microbiome does more than help us digest food.

📌It trains our immune system.

📌It produces anti-inflammatory compounds.

📌 It even influences whether the immune system turns aggressive or stays calm.

Some bacterial species help produce short-chain fatty acids (like butyrate), which keep inflammation in check. Others can trigger immune overactivity.

This balance matters and might influence whether someone develops or flares with autoimmune disease.

We’ve known for a while that conditions like Crohn’s disease and ulcerative colitis involve gut microbiome disruption, but now we’re seeing links to diseases we never expected:

→ 𝑅𝒽𝑒𝓊𝓂𝒶𝓉𝑜𝒾𝒹 𝒶𝓇𝓉𝒽𝓇𝒾𝓉𝒾𝓈

→ 𝑀𝓊𝓁𝓉𝒾𝓅𝓁𝑒 𝓈𝒸𝓁𝑒𝓇𝑜𝓈𝒾𝓈

→ 𝐿𝓊𝓅𝓊𝓈

→ 𝒫𝓈𝑜𝓇𝒾𝒶𝓈𝒾𝓈

→ 𝐸𝓋𝑒𝓃 𝓉𝓎𝓅𝑒 𝟣 𝒹𝒾𝒶𝒷𝑒𝓉𝑒𝓈

I'm fascinated by fecal microbiota transplantation (FMT).

This is a procedure where we take healthy gut bacteria from one person and give them to someone whose gut bacteria community needs help.

FMT has delivered remarkably successful results (over 90% )in C. difficile infections, and the best part is that we’re now beginning to apply it to other inflammatory diseases.

What truly excites me is how metagenomics is teaching us the "why" behind these successes and who they’re most likely to help.

Metagenomics is basically taking us from guesswork to precision.

A Message of Hope

If you’re living with an autoimmune condition, or caring for someone who is, I want to share something important:

You are not alone in your body. You have trillions of microscopic allies, whose health is intimately connected to your own.

Small Steps, Big Impact

Supporting your microbiome doesn’t have to be complicated: Eat a diverse, fiber-rich diet, Try fermented foods like yogurt or kimchi, Use antibiotics only when necessary.

Think about your body as a whole, not just one organ at a time.

Where This Leads Us

This is more than medicine. It’s a shift in how we understand the body.

It is still unfolding. The research is growing. And so is our understanding.

What questions do you have about your own microbiome?

How has understanding gut health shifted your view on inflammation or healing?

I’d love to hear from you in the comments.

Also, check out the scientific references in the comments to explore further

This concludes our five-part article series on the microbiome