- If probiotics made you worse, that was diagnostic. It suggests bacterial overgrowth in the small intestine, where bacteria should be sparse.
- IBS is a description, not a diagnosis. It names your symptoms. It does not tell you what is causing them, and something usually is.
- A meaningful share of IBS is SIBO — bacteria growing where they do not belong, fermenting your food before you absorb it.
- Order matters more than ingredients. Remove, repair, then reinoculate. Reversing that sequence is the single most common reason gut protocols fail.
- Reflux is more often too little stomach acid than too much, which is why long-term acid suppression can worsen the underlying problem.
Why the probiotic made it worse
This is the single most common story patients tell us, and what I want you to know is that it was useful information rather than a failure.
Your small intestine is supposed to be relatively sparse in bacteria. The colon is where the dense microbial population belongs. Small intestinal bacterial overgrowth is what happens when bacteria colonise the small intestine in numbers that do not belong there.
Those bacteria ferment carbohydrate before you absorb it, and fermentation produces gas. That is the bloating — often within thirty to ninety minutes of eating, often worse with healthy high-fibre food, and often described as looking six months pregnant by evening.
Now add a probiotic. You are introducing more bacteria into a segment already overpopulated. For a genuine subset of people that predictably worsens bloating and gas — and rather than being a sign the probiotic was wrong, it is a fairly strong clue about what is actually happening.
What is actually going on
IBS is a description of symptoms. Underneath it sit four mechanisms, and most people have more than one.
SIBO — bacteria in the wrong place, fermenting carbohydrate and producing gas. Hydrogen-dominant tends toward diarrhoea; methane-dominant tends toward constipation and is often the more stubborn.
Dysbiosis — the right neighbourhood, wrong population. Insufficient beneficial species, overgrowth of opportunists, sometimes fungal overgrowth. Comprehensive stool testing shows this directly.
Intestinal permeability — the junctions between intestinal cells loosen, allowing partially digested proteins and bacterial fragments to reach immune tissue. Around seventy percent of your immune system lives in that lining, which is why gut problems so often present as systemic ones.
Insufficient digestive capacity — low stomach acid or inadequate enzyme and bile output. Stomach acid is also a barrier: it is one of the mechanisms that keeps the small intestine sparse. Suppress it long enough and you remove a defence against the overgrowth causing the symptoms in the first place.
The testing that finds it
One thing I tell every patient about food sensitivity panels: IgG food testing is widely sold and poorly supported. IgG antibodies to food often indicate exposure rather than reaction, and we see patients who have eliminated thirty foods on the strength of one. We would rather do a structured elimination and reintroduction, which costs nothing and tells you more.
The order that makes it work
Almost every failed gut protocol we see failed on sequence rather than on ingredients.
1. Remove. Address the overgrowth or pathogen, and remove the foods genuinely driving a response for you. Herbal antimicrobials — berberine, oregano, allicin, neem — have head-to-head evidence against rifaximin in SIBO. This phase runs two to six weeks.
2. Repair. Rebuild the lining before repopulating it. L-glutamine, zinc carnosine, aloe, deglycyrrhizinated liquorice and collagen peptides. Support digestion properly so food is broken down rather than fermented. Four to eight weeks.
3. Reinoculate. Now the probiotics, and now the fermented foods and prebiotic fibre. Introduced into a small intestine that is no longer overgrown and a lining that can handle them, these do exactly what they are supposed to.
Do that in reverse — probiotics and fibre first, into an overgrowth, through a permeable lining — and you get worse. Which is precisely the experience most people describe when they arrive.
L-glutamine is a standard part of gut repair and we use it routinely. We do not use it in anyone with a history of colorectal cancer, because glutamine is a preferred fuel for those tumour cells. This is the kind of screening that should happen before a supplement protocol, not after.
The ten levers that change gut health
Ranked by how much difference they make and how often the problem sits there.
Identify SIBO Before Anything Else
If bacterial overgrowth is present, every other intervention is compromised — fibre feeds it, probiotics add to it, and prokinetics matter more than diet. Establishing this first changes the entire sequence and is why breath testing comes early.
What the evidence showsSmall intestinal bacterial overgrowth produces hydrogen and methane through carbohydrate fermentation proximal to the colon, generating the bloating that characteristically appears 30 to 90 minutes after eating and worsens with fermentable fibre.Restore Digestive Capacity
Food that is not broken down is food that gets fermented. Adequate stomach acid, enzymes and bile flow are upstream of nearly every symptom on this page — and stomach acid is also one of the defences keeping the small intestine sparse.
What the evidence showsGastric acid is a primary barrier limiting bacterial colonisation of the small intestine. Long-term acid suppression is associated with increased SIBO prevalence, and digestive enzyme insufficiency leaves substrate available for fermentation.Remove Before You Add
Herbal antimicrobials have head-to-head evidence against rifaximin in SIBO. Two to six weeks of properly targeted removal, before any probiotic or prebiotic goes near the situation.
What the evidence showsA comparative trial found herbal antimicrobials — including berberine, oregano and neem — equivalent to rifaximin for SIBO eradication as measured by breath testing.Repair the Lining
L-glutamine, zinc carnosine, DGL and collagen peptides rebuild the barrier that keeps immune tissue from seeing what it should not. This phase is why gut work resolves joint and skin symptoms that seemed unrelated.
What the evidence showsL-glutamine is the preferred fuel for enterocytes, and zinc carnosine has trial data for mucosal repair. Increased intestinal permeability allows luminal antigens to reach gut-associated lymphoid tissue, where roughly 70 percent of immune tissue resides.Reinoculate Last
Probiotics, fermented foods and prebiotic fibre — introduced once the terrain can receive them. Same interventions, opposite result, purely because of when they arrive.
What the evidence showsProbiotic and prebiotic introduction into an overgrown small intestine increases fermentation and symptoms. The same interventions delivered after eradication and mucosal repair produce the opposite result.Support Motility
The migrating motor complex is the wave that sweeps the small intestine clean between meals, and it only runs when you are not eating. Constant grazing suppresses it, which is one of the most common reasons SIBO returns after successful treatment.
What the evidence showsThe migrating motor complex sweeps the small intestine between meals and is suppressed by eating. Impaired motility is the primary mechanism of SIBO recurrence, and prokinetic support reduces relapse rates.Address the Nervous System
The gut-brain axis is bidirectional and not a metaphor. Sustained sympathetic dominance reduces digestive secretions, slows motility and increases permeability. Eating in a genuine rest-and-digest state is a real intervention.
What the evidence showsThe gut-brain axis is bidirectional through vagal, endocrine and immune signalling. Sympathetic dominance reduces gastric acid and pancreatic enzyme secretion, slows motility and increases intestinal permeability.Structured Elimination, Not IgG Panels
A proper elimination and reintroduction identifies your genuine triggers. IgG food panels frequently indicate exposure rather than reaction, and we routinely see people who have eliminated thirty foods unnecessarily on the strength of one.
What the evidence showsIgG antibodies to food reflect exposure and immune tolerance rather than clinical reaction, and professional allergy societies do not support IgG testing for food sensitivity. Structured elimination and reintroduction remains the reference method.Screen for Coeliac First
Before any gluten trial, always. Once you have removed gluten the test becomes unreliable, and coeliac disease is a diagnosis with lifelong implications you want made properly rather than guessed at.
What the evidence showsCoeliac serology becomes unreliable after gluten withdrawal, requiring reintroduction for accurate testing. Coeliac disease carries lifelong implications for screening and family testing that warrant definitive diagnosis.Correct What Malabsorption Cost You
Ferritin, B12, vitamin D, magnesium and zinc are all commonly depleted by years of poor absorption. Correcting them is part of gut treatment rather than separate from it, and it is often what finally resolves the fatigue.
What the evidence showsMalabsorption from mucosal damage produces measurable deficiencies in iron, B12, vitamin D, magnesium and zinc. Correcting these is frequently what resolves the fatigue that accompanied the gut symptoms.What patients commonly experience under our care
When patients receive the proper guidance, here is what they commonly experience under our care.
- Weeks 1–3 — bloating. Usually the first to shift once the overgrowth is being addressed. Patients describe being able to eat without watching their abdomen distend through the afternoon.
- Weeks 3–6 — regularity and reflux. Bowel habit normalises as the microbial picture changes, and reflux frequently improves once digestion is properly supported — which surprises people who assumed they had too much acid.
- Weeks 6–12 — food tolerance and systemic symptoms. This is when the barrier work shows. Foods that previously caused reactions become tolerable again, and the joint, skin and energy symptoms that seemed unrelated often settle alongside.
- Months 3–6 — retest and stability. Repeat stool analysis or breath testing to confirm. Ferritin, B12 and vitamin D climbing as absorption recovers. The goal is a gut that tolerates a wide diet again, not a permanently narrow one.
If your gut has been running your life, it does not have to keep doing so. Schedule a consultation and let my team find out what is actually going on in there — and then treat it in the order that works. You will be cared for by a team who takes the whole picture seriously, not just the symptom you walked in with.
Comprehensive stool analysis, SIBO testing where indicated, and a protocol sequenced in the order that works.
Common questions
Why do probiotics make my bloating worse?
It suggests small intestinal bacterial overgrowth. Your small intestine should be relatively sparse in bacteria, and if it is already overpopulated, adding more predictably increases fermentation and gas. Rather than a sign the probiotic was poor quality, it is a useful clue about what is happening — and a reason to test before continuing.
What is SIBO and how do I know if I have it?
Small intestinal bacterial overgrowth is bacteria colonising the small intestine in numbers that do not belong there, fermenting carbohydrate before you absorb it. The classic picture is bloating within thirty to ninety minutes of eating, worse with healthy high-fibre foods, and worse on probiotics. It is confirmed with a hydrogen and methane breath test.
Is IBS a real diagnosis?
IBS is a real and validated clinical description, but it describes symptoms rather than causes. Underneath an IBS label there is usually something identifiable — SIBO, dysbiosis, bile acid malabsorption, coeliac disease or genuine food triggers. Being given the label is the start of the investigation rather than the end of it.
Should I get a food sensitivity test?
We would generally say no to IgG food panels. IgG antibodies to a food often reflect exposure rather than reaction, and the panels routinely produce long lists of foods people then eliminate unnecessarily. A structured elimination and reintroduction costs nothing and identifies genuine triggers far more reliably.
Do I need to be on a low FODMAP diet forever?
No, and staying on it long term is counterproductive. Low FODMAP is a diagnostic and symptom-management tool for a limited period, typically two to six weeks, because it starves the fermenting bacteria. Long term it also starves the beneficial ones and reduces microbial diversity. The goal is always reintroduction.
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- Deng Y, Misselwitz B, Dai N, Fox M. Lactose intolerance in adults: biological mechanism and dietary management. Nutrients. 2015;7(9):8020–8035.
This article is educational and reflects the published literature as of August 2026. It is not a diagnosis or a treatment recommendation for any individual, and any decision about your care belongs in a conversation with a licensed practitioner who has seen your history and your labs.