SIBO: When your gut microbes move into the wrong neighbourhood
- Dr. Khush Mark PhD
- 4 days ago
- 5 min read
Updated: 3 days ago
Ever had that kind of bloating where you look (and feel) about seven months pregnant, even though the only thing you are actually expecting is relief from your jeans button? That is one of the classic signs of SIBO, Small Intestinal Bacterial Overgrowth. This is when bacteria set up shop in the wrong part of your gut aka the small intestine.
First a little bit on the microbiome
The gut microbiome is the community of trillions of bacteria, yeasts, and other microbes that live mostly in your large intestine, a bustling ecosystem that:
Helps digest food you can not fully break down yourself
Produces vitamins like vitamin K and some B vitamins
Trains and regulates your immune system
Influences hormones, mood, and metabolism
Provides short-chain fatty acids, vital for bowel health
A balanced microbiome is like a well-tended garden, diverse, resilient, and full of the right species in the right places with some weeds too!
Why does SIBO occur?
The small intestine should be relatively low in bacteria because its job is to absorb nutrients. But sometimes, bacteria migrate upwards from the colon or simply overgrow when the small intestine’s natural defences are weakened.
Common triggers include:
Low stomach acid (from stress, ageing, or long-term use of acid blockers) food is not 'sterilised' properly and not only do bacteria sneak through but digestion is compromised.
Sluggish motility (the migrating motor complex, your gut's 'rhythmic wave', slows down) bacteria are not 'swept' along into the colon.
Frequent antibiotics or gut infections that disrupt the normal balance and open the door for the wrong species.
Chronic stress puts the digestive system on 'pause', lowering stomach acid and slowing motility, because when you have to escape a 'wild beast in the jungle', the body cannot deal with digestion!
Structural issues (like adhesions or scarring in the gut) create pockets for bacteria to thrive.
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Symptoms of SIBO
SIBO symptoms overlap with IBS, but there are a few tell-tale signs:
Severe bloating: the 'I look 7 months pregnant after dinner' look
Excessive gas (sometimes sulphurous, rotten egg smell)
Abdominal pain or cramping
Diarrhoea, constipation, or both
Fatigue and brain fog from nutrient malabsorption and toxins)
Nutrient deficiencies: low B12, iron, or fat-soluble vitamins like A, D, E, K
Left unchecked, SIBO not only makes you uncomfortable, it can also affect energy, hormones, immunity, and even mood.
The treatment of SIBO
At the New School, we believe in addressing the root cause(s). We do not take the 'Kill Bill' approach., but restore balance and function so the overgrowth doesn’t keep coming back.
A comprehensive gut test helps
The breath test is the frontline way to diagnose SIBO and distinguish between hydrogen, methane, and hydrogen sulphide overgrowth. But on its own, it doesn’t tell us the whole story.
A comprehensive stool analysis (CSA) or a full functional gut test shows the 'bigger picture'. These tests do not directly diagnose SIBO, but they give us crucial context about why the overgrowth happened in the first place and what might keep it coming back.
With a comprehensive gut panel, we can check for:
Stomach acid function, markers like protein breakdown or microbial overgrowth patterns can hint at low gastric acid, which is a major risk factor for SIBO.
Bile production and flow, bile keeps the small intestine antimicrobial; poor bile output can allow bacteria to creep upwards.
Microbiome diversity, is the colon’s ecosystem rich and balanced, or lacking protective species?
Gut lining health, stool markers for inflammation (calprotectin, lactoferrin), intestinal permeability, or secretory IgA and/or zonulin can show if the mucosal barrier is inflamed or 'leaky'.
Digestive capacity, enzyme function (elastase, fat in stool) reveals how well food is being broken down/digested.
Remember that breath tests only tell us what’s happening right now (the type of SIBO). A stool/gut test tells us why it happened and what to do so SIBO doesn’t keep coming back.
Here’s how nutritional medicine and natural approaches support recovery:
1. Starve and reset
Low FODMAP diet (short term): reduces fermentable carbohydrates that bacteria love to feast on.
Elemental diets (in very stubborn cases): provide pre-digested nutrients while starving bacteria.
2. Clear the overgrowth
Antimicrobial herbs: oregano oil, berberine, garlic (allicin), neem, and thyme have all been studied for their ability to reduce bacterial overgrowth.
3. Support digestion
Digestive enzymes: help break down food so it doesn’t ferment in the small intestine.
Betaine HCl (if stomach acid is low): supports sterilisation of food and prevents bacteria from sneaking in.
Bile support (ox bile, bitters like gentian or dandelion root): keeps fat digestion smooth and discourages bacterial stagnation (check out our Liver gall bladder cleanse HERE)
4. Restore motility
Prokinetic herbs & nutrients: ginger, motility-supporting bitters, 5-HTP, can help the migrating motor complex.
Meal spacing: leave 3–4 hours between meals gives your gut’s natural 'clean-up wave' time to sweep bacteria down into the colon.
5. Rebuild the microbiome
Probiotics: careful use of spore-based or specific strains (like Saccharomyces boulardii) can help once the overgrowth is reduced.
Prebiotic foods: slowly reintroduce foods like onions, garlic and beans, which feed the right bacteria once balance is restored.
Our students integrate all the above learning into the clinics, which may also include functional tests for certain clients as needed. Here is what Rakhee (Cohort 2022-2024) shares about the clinics:
Student clinics is where the theory becomes practice, allowing us to directly work with clients on their healing journeys. Knowledge alone is not enough, applying nutrition, coaching and Rapid Relief Homeopathy in real life situations is what truly makes the difference.
Daily habits that make a difference
Beyond supplements and herbs, the everyday basics are powerful tools for healing:
Chew your food thoroughly: digestion starts in the mouth, and less work for the gut means less fermentation.
Eat mindfully: sitting, breathing, and eating slowly helps switch on your parasympathetic 'rest and digest' mode.
Stay hydrated: water helps motility and prevents constipation, which worsens SIBO.
Manage stress: meditation, walking, or simply pausing before meals helps restore digestive signalling.
Prioritise sleep and circadian rhythm: your gut microbes follow light-dark cycles too, and disrupted sleep worsens the imbalance.
SIBO is NOT just about bacteria 'gone rogue', it is usually a sign that your digestive system, stomach acid, motility, microbiome, and lifestyle needs attention. The good news is that with the right combination of diet, supplements, herbs, and mindful daily habits, you can not only ease the bloat but also rebuild a healthier, more resilient gut.
To health!
From the team at the New School Of Nutritional Medicine
Learn about the Founder & Principal of the New School of Nutritional Medicine, Dr Khush Mark PhD, HERE.
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