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Step 5 - Month 4 | Restore the Microbiome

If you’re someone who feels okay after eating, but then gets bloated or gassy hours later, you’re likely dealing with microbial imbalance. This is the stage where your food is being handled by trillions of bacteria in your large intestine. When things are balanced, those bacteria quietly finish off the leftovers, make vitamins, and produce short-chain fatty acids that nourish your gut.

 

But when they’re out of balance, or when food arrives half-digested, they get overwhelmed and start to ferment what shouldn’t really be there. That’s when you feel the gurgling, the bloating, or the sudden wind hours after meals.

 

What It Feels Like

 

You might notice:


  • Bloating that worsens as the day goes on.

  • Gas or cramping three to eight hours after meals. (Gas within 1 hour of eating is almost never the microbiome, it’s upper gut timing.)

  • A noisy, gurgling belly.

  • Irregular stools: sometimes loose, sometimes constipated.

  • Feeling better when you fast or eat simply, but worse when you add variety.

 

Three Common Imbalances

 

1. Overgrowth | Too much in the wrong place: When bacteria move higher into the small intestine, they ferment food before it’s ready. This creates gas, bloating, burping, and fullness soon after eating. It can happen after long-term stress, constant snacking, or sluggish stomach acid and bile, all of which slow the normal clearing waves between meals. Restoring the upstream steps and reducing your eating window is often all that's needed.

 

2. Depletion | Not enough good bacteria or diversity: After antibiotics, restrictive diets, or illness, the gut can lose its strength. The large intestine becomes quiet and underpopulated. Stools may be pale, soft, or incomplete. Energy and mood often drop too. The solution isn’t to take endless probiotics, but to feed the terrain that lets the right microbes grow again by eating whole, unprocessed foods your body tolerates and using broths, fats, and minerals to rebuild the lining.

 

3. Dysbiosis | The wrong strains leading the team: Sometimes the total number of microbes looks fine, but the balance is off. Yeasts, inflammatory bacteria, or methane-producers take over. This often happens after high-sugar, high-stress, or when acid and bile flow slows and gut movement weakens.

 

Why It Happens

 

It’s easy to blame “bad gut bacteria,” but usually the microbes are just reacting to the environment they’re given. If the terrain is off, no supplement will work, and the same symptoms keep circling back. Common triggers include:


  • High-stress living | Which changes gut motility and microbe balance, and weakens the immune system. (Step 2 | Calm the System)

  • Low stomach acid | The most overlooked trigger. It lets food arrive partly undigested and allows microbes to survive in the upper gut. (Step 3 | Reset Your Stomach Acid)

  • Weak bile flow | Bile keeps the small intestine sterile. Without it, bacteria migrate upward. (Step 4 | Balance Bile + Enzymes)

  • Diets that are overloaded | Too many fermented foods, excess carbohydrates, large fibre loads, and ultra-processed foods.

  • Migrating Motor Complex (MMC) is switched off | Overgrowth often resolves by restoring the MMC, our guts cleaning system. See below for more information.

  • Environmental | Sterile environment, chlorinated water, and no natural exposure to soil and animals.

  • Medications | Antibiotics, acid blockers, and certain hormones reshape the microbiome long term.

 

Migrating Motor Complex | Your Gut's Cleaning Cycle

 

Between meals, your gut runs a quiet “cleaning cycle” called the migrating motor complex (MMC). You can think of it as a slow wave that moves through the small intestine, sweeping away leftover food, bile, and bacteria so they don’t sit and ferment. When this wave is working well, the small intestine stays relatively clear and the microbiome is mostly contained to the large intestine where it belongs.

 

You’ll often feel the MMC as a rolling, wave-like gurgle or a shifting feeling a couple of hours after eating. It’s not true hunger, it’s the clean-up phase. That wave usually lasts ten to twenty minutes, then settles. If you eat during that time, even something small like a lolly, a biscuit, a milky coffee, a sip of juice, or even chewing gum, the body switches straight back into digestion and the cleaning cycle stops halfway through.

 

This is why constant snacking can quietly drive overgrowth. The gut never gets to finish its sweep, so food and microbes linger in the small intestine and start to ferment. Over time, that can show up as late bloating, gas hours after meals, loose stools, or the classic “I feel better when I don’t eat” pattern.

 

The simplest way to support your MMC is to eat proper meals and leave gaps between them. Aim for three to four hours with only water, mineral water, herbal tea, or electrolytes without sugar in between. Let your gut gurgle, move, and reset without interruption. Two or three calm meals in a ten-hour window is often enough to give the cleaning wave time to do its job. For anyone with SIBO, IBS, bloating, or a history of antibiotics, protecting this rhythm can be just as powerful as any supplement.

 

When it’s time to eat, you don’t need to rush your gut out of the cleaning cycle. A soft transition is all it needs. 10 - 15 minutes before your meal,  a small dose of bitters can help your stomach acid and bile wake up without interrupting the cleaning wave too early. When you're ready to eat, take a moment to slow your system down, a couple of steady breaths, relaxed shoulders, feeling settled. This switches on the vagus nerve. From here, let your senses do the rest. Smelling your food and taking a quiet moment to notice the meal gently tells your gut, “We’re getting ready now.” It’s a simple rhythm, but it's all that's need to keep your MMC intact and your digestion calm and steady.

 

How to Rebalance Naturally

 

This part isn’t about killing off bacteria or taking loads of probiotics, it’s about creating an environment where the right ones can thrive. Once that terrain is stable, the microbes will follow.


  1. Continue Steps 2 - 4 | Calm eating, and stomach acid and bile flow support all help to keep the microbiome balanced and where they belong.

  2. Keep meals simple and fresh | Eat unprocessed, lower carbohydrate food that’s been cooked recently. Avoid reheating the same thing for days.

  3. Limit “gut boosters” temporarily | Fermented foods, probiotics, and high-fibre powders and diets can make things worse if your microbiome is still off. Focus on stabilising first.

  4. Continue bone broth and glycine | They help restore the gut lining, which is the foundation the microbiome grows on.

  5. Eat until satisfied, not stuffed | Overfilling the gut leaves too much food for bacteria to ferment later so keep meals slightly smaller.

  6. Move daily | Even a short walk helps digestion and keeps food moving forward instead of sitting still and fermenting.

  7. Support the MMC - don't snack | The gut needs time to clean itself between meals. Two or three main meals within a 10 hour window is ideal. Even tiny snacks or sips of juice will turn off the cleaning cycle. Use bitters 10 - 15 minutes before meals to wake the digestive system back up.

 

A Word on Probiotics

 

Probiotics are often thrown in too early. They sound harmless, but if the gut isn’t ready, they can make things worse. Adding new bacteria into a gut that’s still stagnant, depleted, or is inflamed, is like planting seeds in poor quality soil, they won’t take, and sometimes they rot. In people with microbiome overgrowth  or histamine intolerance they can make things worse.

 

Probiotics can be useful, but they belong later, once acid, bile, and rhythm are stable, and the gut has been cleared of overgrowth. Even then, they work best when chosen precisely (strain by strain) and for a clear purpose, often after stool testing through a qualified practitioner. For many, the real reset happens not through capsules but through rhythm and clean food.

 

Fibre | Friend or Foe

 

Fibre is often praised as a cure-all, but in truth, it’s only healing in the right phase of repair. For some guts, it restores order. For others, it pours fuel on a fire. Think of fibre as food for microbes. That’s fine when your microbes are balanced, but if there’s overgrowth, low acid, or sluggish bile, feeding them too early just means feeding the wrong team.

 

In the early phases, when rhythm is off, bile is sluggish, or stomach acid is low, fibre can cause real trouble. It can lead to fermentation, slow clearance and colon irritation. It often worsens microbiome overgrowth, histamine intolerance, diarrhoea, and chronic bloating. Fibre is generally not helpful until at least step 6, when acid, bile, and timing have been restored and stools are moving cleanly again.

 

If It’s Working

 

You’ll notice less bloating, more predictable bowel movements, and less gurgling several hours after meals. The belly and body feels quiet and calm again, and sleep often deepens.

 


If You’re Still Struggling

 

If bloating improves but you start noticing bowel urgency, morning looseness, or lower gut irritation, it’s usually a sign that the colon needs attention. That’s where we’re headed next: Step 6 | Steady the Colon.


 
 
 

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