digestive health

SIBO — small intestinal bacterial overgrowth and the root cause of persistent bloating

SIBO is one of the most underdiagnosed drivers of IBS-like symptoms bloating, abdominal distension, gas, pain, and altered bowel habits caused by bacteria from the large intestine colonising the small intestine, where they do not belong. In the small intestine, these bacteria ferment carbohydrates before absorption, producing hydrogen and methane gas. The symptoms are often labelled as IBS for years before SIBO is investigated. Nutritional support addresses the preparation for SIBO treatment, the treatment phase itself, and critically the prevention of relapse.

Whichever SIBO type you're dealing with — hydrogen, methane, or hydrogen sulfide — I tailor your nutritional support to it, through treatment and, most importantly, to address what's driving relapse.

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SIBO is a structural problem, not just a dietary one. The pathogenic bacteria are in the wrong location. Dietary change alone reduces symptoms but does not clear the overgrowth antimicrobial treatment (antibiotic or herbal) is the primary intervention. Nutritional support reduces bacterial substrate before treatment, supports the gut during treatment, and most importantly addresses the root causes that allowed the overgrowth to develop, preventing the relapse that affects the majority of SIBO cases without this step.

The three SIBO types

Hydrogen, methane, and hydrogen sulfide — different presentations, different approaches

Hydrogen-dominant SIBO

Bacteria ferment carbohydrates producing hydrogen gas — typically presenting with diarrhoea, urgency, and loose stools alongside bloating. The most common and most responsive to dietary intervention during treatment.

Methane-dominant SIBO (IMO)

Archaea produce methane — characterised by constipation, significant abdominal distension, and bloating that can be visibly dramatic. Methane slows intestinal motility directly. Responds to a different treatment approach from hydrogen SIBO.

Hydrogen sulfide SIBO

Associated with rotten egg-smelling gas, often severe symptoms, and a distinct low-sulfur dietary approach during treatment. An emerging area of SIBO understanding with specific nutritional implications.

Root causes + nutritional phases

What drives SIBO — and the nutritional approach across all phases

Root causes

Impaired motility — the primary driver

Between meals, your gut runs a natural 'cleaning wave' called the migrating motor complex (MMC), whichsweeps bacteria out of the small intestine so they don't build up. When this wave is disrupted by stress, an under active thyroid, nerve damage from a past infection, or structural issues; bacteria can accumulate instead of clearing out. This is why addressing motility is so important for preventing SIBO from coming back.

Root causes

Low stomach acid + PPI use

Stomach acid is a first-line defence against bacteria surviving into the small intestine. Hypochlorhydria from chronic PPI use, ageing, or H. pylori allows far more bacteria through. Where PPI use is a contributing factor, addressing the underlying reason for it (often GERD) is part of the broader picture.

Pre-treatment

Elemental diet or low-FODMAP preparation

A 2-week elemental diet (pre-digested formula that provides minimal bacterial substrate) can significantly reduce bacterial load before antimicrobial treatment, improving treatment outcomes. Low-FODMAP reduces symptom burden during treatment by limiting fermentable carbohydrate substrate.

During treatment

Low-fermentation dietary support

Reducing the substrate available for bacterial fermentation during antimicrobial treatment limiting high-FODMAP foods, excess fibre, and sugars that feed the overgrowth. Adequate protein and nutrient-dense whole foods maintained throughout to support the gut lining and immune function.

Post-treatment

Microbiome rebuilding — carefully phased

After SIBO clearance, the microbiome needs rebuilding but introducing prebiotics and probiotics too early can feed residual bacteria and cause relapse. A structured, phased reintroduction of fermentable foods, prebiotics, and then probiotics timed appropriately after treatment is the post-treatment nutritional plan.

Long-term

Relapse prevention — the most important phase

SIBO recurs in the majority of cases without addressing root causes particularly motility. Meal spacing (allowing the MMC to activate between meals no grazing), prokinetic nutritional support, adequate stomach acid, and addressing underlying drivers are the structural relapse prevention strategies.

Ayurvedic perspective

Apana Vata and the displaced microbiome

SIBO can be understood in Ayurveda as a disruption of Apana Vata — the downward-moving subdosha governing the appropriate directional movement of contents through the digestive system. When Apana Vata is disturbed, the normal downward clearance is impaired and bacteria accumulate where they should not.

Restoring directional movement

The Ayurvedic approach to SIBO focuses on restoring the proper downward movement of Apana Vata — through regular meal timing (which activates the MMC equivalent in Ayurvedic terms), avoiding grazing between meals, warm easily digestible foods, and Agni-kindling digestive spices that support motility and reduce fermentation. Triphala a classical Ayurvedic three-fruit formulation has gentle motility-supporting and gut-regulating properties relevant to SIBO management.

Vishama Agni — the irregular digestive fire

From an Ayurvedic perspective, SIBO creates Vishama Agni pattern unpredictable digestion, bloating that varies day to day, irregular bowel habits. The Vata-aggravated digestive fire that creates this irregularity is addressed through grounding dietary practices: regular mealtimes, warm and cooked foods, avoiding raw and cold inputs that aggravate Vata and impair the already compromised digestive motility.

My integrative approach

What working together looks like

SIBO assessment + root cause identification

Full digestive history, symptom pattern, review of existing testing or discussion of breath testing options, and root cause assessment — impaired motility, low stomach acid, structural factors, post-infectious history.

Pre-treatment dietary preparation

Preparing the gut for antimicrobial treatment — reducing bacterial substrate through dietary modification to improve treatment efficacy.

Nutritional support during treatment

Dietary support during the antimicrobial treatment phase — maintaining nutrient adequacy while reducing fermentable substrate.

Post-treatment microbiome rebuilding

Phased reintroduction of fermentable foods, prebiotics, and probiotics — timed appropriately to avoid reseeding before adequate clearance.

Long-term relapse prevention

Addressing root causes, meal timing for MMC activation, prokinetic nutritional support, and the dietary practices that make the gut environment inhospitable to re-overgrowth.

Suspect SIBO may be driving your digestive symptoms?

Book a free 15-minute call a conversation about your gut picture and whether SIBO investigation is indicated.

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The entire contents of this website are based upon the opinions of Manjiri Nadkarni (Manjiri Nadkarni Consulting) and is meant for educational purposes only and does not constitute medical/ psychological advice . Please note that Manjiri Nadkarni is not a dietitian, physician or other licensed healthcare professional in Canada. She is a Doctor of Ayurvedic Medicine - MD (Ayurveda) (licensed and regulated in India but not Canada), Registered Holistic Nutritionist as well as Oncology Nutrition Consultant.

The content on this website is not intended to diagnose or treat any diseases. The information on this website is NOT intended as medical or psychological nor is it intended to replace the care of a qualified health care professional. Always consult with your primary care physician or licensed healthcare provider for all diagnosis and treatment of any diseases or conditions, for medications or medical advice as well as before changing your health care regimen.