Part 2: The Gut Microbiome — Who’s Really Running the Show

Sometimes I laugh thinking about the fact that I’m really just a walking science project — carrying my gut around the world while it quietly runs the show.

Once you really sit with that idea, it’s both wildly fascinating and slightly humbling. Inside each of us lives an entire ecosystem — trillions of microbes — depending on us to feed it, care for it, and not completely ignore it. That’s a big responsibility when you think about it.

And hey… if you ever feel lonely, it’s also a little comforting to know you’re never actually alone. 😉

We are, in many ways, the vessel

The gut microbiome isn’t just about digestion. These microbes influence:

• How we break down food

• How our immune system functions

• How inflamed (or calm) our bodies are

• How we regulate mood

• How we experience cravings and hunger

They communicate constantly with the brain through chemicals, hormones, and electrical signals — especially via the gut–brain axis and the vagus nerve, the superhighway connecting what’s happening in the gut to how we feel emotionally and physically.

This means the gut isn’t a passive pipe.

It’s a communication hub.

Electrical.

Chemical.

Responsive.

Wild, right?

Diversity matters more than perfection

One of the most important markers of gut health is microbial diversity — having many different types of bacteria, not just a lot of one “good” strain.

And here’s the reassuring part: diversity doesn’t come from perfection. It comes from consistency.

Consistent meals.

Consistent rhythms.

Consistent nourishment.

Not extremes. Not constant fixing. Not chasing the newest trend.

The gut doesn’t ask us to be perfect.

It asks us to be steady.

Probiotics… or no probiotics? (Why more isn’t always better)

If you’ve ever taken antibiotics — or even just thought about your gut microbiome — you’ve probably heard this advice:

“You need probiotics.”

Full stop.

No nuance.

No explanation.

But let’s slow that down for a moment.

What are probiotics, actually?

Probiotics are live microorganisms intended to support gut health. They can come from:

• Supplements (capsules, powders, liquids)

• Foods, like yogurt, kefir, sauerkraut, kimchi, miso, and other fermented foods

In theory, they help by introducing beneficial bacteria into the gut.

In practice… it’s more complicated.

Why probiotics seem like the obvious answer

The logic feels simple:

• Antibiotics reduce bacteria

• Probiotics add bacteria

• Balance restored… right?

Sometimes.

But the gut isn’t a fish tank you can just refill.

It’s a living ecosystem, and ecosystems care far more about conditions than additions.

Why some people feel worse on probiotics

This is something many people experience but rarely hear validated:

“Every time I take probiotics, my bloating gets worse.”

That doesn’t mean your gut is broken.

It often means:

• The bacteria were added too soon

• The strains weren’t a good match

• The gut environment wasn’t ready to host them

• Or bacteria were already living where they didn’t belong (hello, small intestine)

In those cases, probiotics can feel less like support and more like throwing a housewarming party before the plumbing works.

After Xifaxan: less urgency, more patience

Xifaxan is different from most antibiotics because it’s minimally absorbed and often used to reduce bacterial overgrowth where it doesn’t belong — particularly in the small intestine.

After treatment, the gut is often:

• Quieter

• Less inflamed

• More receptive

That doesn’t mean it’s empty.

It means it’s resetting its rhythm.

And sometimes the most supportive move is to not rush in with probiotics at all.

Yes — really.

Food first: letting the microbiome rebalance naturally

For many people, the gut does best post-Xifaxan when supported with:

• Regular meals

• Simple, whole foods

• Gentle fiber

• Adequate protein

• Good hydration

• A calm nervous system

When conditions are right, beneficial bacteria often repopulate on their own, guided by what you eat and how consistently you live.

No capsule required.

This can feel counterintuitive in a culture that loves supplements — but sometimes restraint is the most restorative choice.

When probiotics

can

be helpful

Probiotics aren’t bad.

They’re just situational tools, not defaults.

They may help when:

• Chosen for a specific purpose (not “gut health” in general)

• Introduced slowly

• Used for a defined period

• Matched to symptoms (diarrhea, constipation, post-infectious changes)

And even then, how you feel matters more than what the label promises.

If a probiotic makes symptoms worse, that’s information — not failure.

The bigger lesson the gut keeps teaching us

This is one of the quiet truths the microbiome reveals:

Healing isn’t about adding more.

It’s about creating the right conditions.

The gut doesn’t respond well to force.

It responds to consistency, safety, and patience.

Sometimes the most loving thing we can do for our bodies is to stop interfering and let them recalibrate.

🍯 Honey Note

What we feed thrives.

What we neglect fades.

And that turns out to be true with food, with bodies… and with life itself.

There’s something this whole conversation about probiotics and the microbiome keeps teaching me — and it has very little to do with bacteria. For years, I believed that if something felt off, the answer must be to do more: add another supplement, try harder, control the outcome. But the gut has a way of humbling that instinct. Sometimes healing doesn’t come from adding or forcing — it comes from trusting, from creating steady conditions, and then letting go. Letting the body remember its own intelligence. And I’m realizing that this lesson shows up everywhere in life: in food, in relationships, in love. The more I stop gripping, the more things seem to settle — naturally, quietly, and with far more peace than I ever found through control.

Warmly,

MaryNell (Honey) 🐝