Understanding SIBO
Symptoms of SIBO?
- You bloat within an hour of eating
- Bloating builds through the day
- The healthy foods hit hardest
- A fiber supplement made things dramatically worse, not better
- Your bowel habits lean hard one direction — mostly loose, or mostly constipated.
- Your bowel habits lean hard one direction — mostly loose, or mostly constipated.
- Acne or skin issues
- Mood swings that can be timed with meals
So What's Actually Going On?
Here's what makes SIBO click: nothing is wrong with the bacteria. They're in the wrong room.
Your gut bacteria are supposed to live almost entirely in your large intestine — the last stretch of the pipe. Your small intestine, the long section before it where you actually absorb food, is meant to be relatively sparse.
SIBO is when bacteria move upstream and set up in numbers where they don't belong. Same bacteria, wrong address.
Why the address matters.
Bacteria don't digest carbohydrate the way you do — they ferment it. And fermentation makes gas.In a normal gut that happens in your large intestine, which is wide, stretchy, and built for it. Your small intestine is an inch across, twenty feet long, and coiled. It has nowhere to put a sudden volume of gas.That's the bloating. Not water, not inflammation. Gas, made in a narrow tube that can't expand to hold it.
What Causes SIBO?
Almost every cause runs through one failure: a broken cleaning cycle. Between meals, your small intestine runs a housekeeping wave — the migrating motor complex — sweeping debris and bacteria downstream every 90 to 120 minutes.
That growling in an empty stomach is it working. It only runs when you're not eating; food shuts it off within minutes.Break the sweep, and bacteria that would have been cleared out stay. Here's what breaks it.
- Antibiotics — even years ago.
- Acid reducers — Tums, Prilosec, PPIs.
- Chronic stress - slows gut motility
- Ultra-processed food - Low fiber, emulsifiers, etc
- GLP-1s — Ozempic, Retatrutide, Semaglutides.
- Snacking - constantly eating prevents the gut from clearing bacteria in the small intestine.
- Food poisoning - The antibodies you build against the bug can attack the pacemaker cells
- Abdominal surgery - C-section, appendix, gallbladder.
How To Get Rid Of It?
Clearing it
Rifaximin is the first-line medical treatment. It's a non-absorbed antibiotic — it stays in the gut rather than circulating through your body, which is why it's preferred here. Standard dosing in the SIBO literature is 1200mg daily for two to four weeks, and the ACG guideline builds its treatment recommendation around antibiotics like it.
Methane needs a different approach. Rifaximin alone works poorly against methanogens, so methane-dominant cases (IMO) are typically treated with rifaximin plus neomycin or metronidazole. If you're the constipated type and rifaximin alone didn't touch it, that's likely why — not that you're a treatment failure.
Cost is real. Without insurance coverage a course frequently runs well over $1,000. Worth knowing before you assume the medical route is the easy one.
Elemental diet is the third option: a two-to-three week liquid formula of pre-digested nutrients, absorbed before bacteria can reach them. Effective and genuinely miserable. Usually reserved for people who've failed other routes.
How to treat SIBO Holistically
- Berberine — 500mg, twice daily
A plant alkaloid from goldenseal, barberry, and Oregon grape, with well-documented antimicrobial activity and a long history of use for gut complaints. It appears to shift microbial composition — favoring Bacteroides, Bifidobacterium, and Lactobacillus while reducing E. coli — rather than clearing indiscriminately, and it supports intestinal barrier integrity alongside that.
It's also the single most-studied botanical in this space. A team at Peking University Third Hospital ran the BRIEF-SIBO trial — 180 patients, randomized, berberine at 800mg daily versus rifaximin for two weeks, with breath test normalization as the primary endpoint. That it exists at all tells you where the research interest is. Our 1000mg daily is above that trial's dose, in line with the range used in metabolic research. - NAC — 600mg
N-acetylcysteine breaks disulfide bonds, which is what makes it a mucolytic in respiratory medicine. The same property is why it's used against biofilms — the polysaccharide matrix bacteria build to shield themselves, and a recognized reason overgrowths resist treatment. Biofilm disruption as an adjunct is an active research area rather than settled practice; the mechanism is well-characterized, the clinical trial evidence in SIBO specifically is early. - Quercetin + zinc
Quercetin is a flavonoid that stabilizes mast cells and moderates histamine release — relevant because a fermenting small intestine is an irritated one. Zinc has the better-established role here: zinc carnosine has human data supporting gut barrier integrity, and zinc deficiency measurably impairs it. Together they support the lining while the rest of the protocol works on the environment. - L-glutamine + soothing botanicals
Glutamine is the primary fuel source for enterocytes — the cells lining your small intestine. They preferentially burn it over glucose, which is unusual and makes availability matter during repair. This is among the better-supported ingredients in the formula. The accompanying botanicals are demulcents: they form a soothing layer over irritated tissue. Traditional use, thin trial data, low risk. - 8-strain probiotic, 10 billion CFU, with FOS
The honest note first: probiotics in SIBO are genuinely debated, since adding bacteria to a small intestine that already has too many is a fair objection. The reasoning for including them is that the target is the colon — supporting a robust downstream population is part of why bacteria stay downstream. FOS is a prebiotic fiber feeding that population. If you're mid-flare and highly reactive, this is the component to introduce slowly. - Ginger — 1000mg
This is the one we'd argue matters most, and it's the step nearly every competing formula omits.Everything in the causes section pointed at motility. Ginger is a prokinetic — it accelerates gastric emptying and stimulates the contractions that drive the migrating motor complex. That's the mechanism behind the 40–50% recurrence rate: kill the bacteria, leave the sweep broken, watch it refill. Ginger is standard in the prokinetic protocols practitioners use specifically for relapse prevention, and it's why it's in ours at a meaningful dose rather than a token one.
Everything you need to remove SIBO - Predosed
Everything above, in one protocol
Four jobs, not one: support microbial balance, get through the biofilm, repair the lining, and keep the cleaning wave running.
Most formulas do the first. The Microbiome Balance Formula does all four:
- Berberine — 1000mg daily
- NAC — 600mg
- Quercetin + zinc
- L-glutamine + soothing botanicals
- Ginger - 1000mg
- 8-strain probiotic, 10 billion CFU + FOS
View ProtocolWhat To Eat While You Do This
We recommend low FODMAP for the 30 days.
Why: FODMAPs are the carbs bacteria ferment fastest. Remove the fuel, and an overgrown small intestine makes less gas. Relief is often fast — but you're managing the symptom, not fixing it. That's what the protocol underneath is for.
This is temporary: FODMAPs feed the colonic bacteria you're trying to strengthen, so months of restriction works against you. Weeks 3–4 are for adding foods back — one at a time, small portion, two days apart.
Common high-FODMAP foods
- Vegetables — onion, garlic, leek, shallot, cauliflower, mushrooms, asparagus, artichoke, snow peas
- Fruit — apples, pears, mango, watermelon, cherries, peaches, plums, nectarines, dried fruit
- Grains — wheat, rye, barley. Most bread, pasta, and cereal
- Legumes — beans, lentils, chickpeas, soy
- Dairy — milk, yogurt, ice cream, soft cheeses (lactose)
- Sweeteners — honey, agave, high-fructose corn syrup, and anything ending in -ol: sorbitol, mannitol, xylitol. Check your gum
- Added fibers — inulin, chicory root, FOS. This is the sneaky one. It's in most protein bars and half the products marketed as gut-healthy
- Drinks — apple and pear juice, oat milk, sodas with HFCS
Still fine: meat, eggs, fish, rice, oats, potatoes, carrots, spinach, zucchini, berries, citrus, bananas, hard cheeses, lactose-free dairy. The Monash University app has the full lists and portion sizes.