Gut Dysbiosis
Understanding Microbiome Imbalance, Its Impact on Health, and How to Restore Gut Health
By Dr. Alain Frabotta - Integrative Chiropractor, Naturopathic & Functional Medicine Clinician, Educator, Sydney, Australia.
1. A New Frontier in Medicine
For most of medical history, the gut was regarded as a mechanical conduit — a tube that digests and eliminates. Today, systems biology reveals something far more profound: the gut microbiome is a living organ in its own right, a microbial command centre that influences immunity, metabolism, inflammation, and brain function. [1–3]
Within every human lies a rainforest of nearly 100 trillion microorganisms. When this ecosystem thrives in balance, it nurtures health; when disrupted, it becomes a silent driver of disease. This disruption is known as dysbiosis.
Clinical Insight: Dysbiosis is not a disease in itself but an ecological state that underlies many chronic conditions — from irritable bowel syndrome and autoimmunity to fatigue, mood disorders and cardiometabolic disease. [4–6]
2. What Is Dysbiosis?
Dysbiosis refers to an alteration in the gut microbiota characterised by a loss of beneficial microbes, overgrowth of opportunistic species, and a reduction in overall diversity. [4, 7]
A healthy microbiome maintains equilibrium through symbiosis — mutual benefit between host and microbes. When this relationship destabilises, host functions — digestion, barrier integrity, immune tolerance, and even neurotransmitter balance — suffer. [3, 8]
2.1 Microbial Ecology of Health
In a balanced state:
SCFA Production: Beneficial bacteria ferment dietary fibres into short-chain fatty acids (SCFAs) like butyrate, acetate and propionate. These regulate immune tolerance, nourish intestinal cells and reduce inflammation. [9]
Immune Training: Microbes educate the immune system, fostering regulatory T-cells and maintaining mucosal immunity. [10]
Barrier Integrity: Microbial metabolites stimulate mucin and tight junction proteins, thereby preventing intestinal permeability.
Neurochemical Communication: The gut–brain axis transmits microbial signals via the vagus nerve, serotonin pathways and cytokine messaging. [3]
2.2 The Transition to Dysbiosis
When the equilibrium shifts — whether through diet, medication, infection or stress — beneficial fermenters decline while pro-inflammatory and proteolytic species proliferate. The result is reduced SCFAs, increased lipopolysaccharide (LPS), oxidative stress, and immune dysregulation. [5, 9, 11]
Patient Tip: The gut ecosystem can change within days. Even brief exposure to poor diet or antibiotics can shift microbial balance — but positive changes can occur just as quickly with targeted intervention.
3. What Causes Dysbiosis?
Dysbiosis emerges from multiple overlapping influences. Understanding them allows both patients and clinicians to address root drivers rather than symptoms.
3.1 Dietary Disruption
The Western diet — rich in processed foods, refined sugars, saturated fats and low in plant fibre — is one of the most potent triggers of microbiome imbalance. [7, 12]
Refined carbohydrates feed pathogenic fermenters.
Low fibre reduces butyrate production and microbial diversity.
High salt and emulsifiers alter microbial adhesion and promote barrier breakdown.
Clinical Insight: Even moderate dietary changes — increasing plant diversity and reducing ultra-processed foods — can restore beneficial species within four weeks [13].
3.2 Medication and Chemical Exposures
Antibiotics remain the most well-known culprit, reducing microbial diversity and allowing pathogen colonisation. NSAIDs, proton-pump inhibitors and antacids also alter pH and damage the epithelial barrier. [14]
Environmental toxins — pesticides, plastics, heavy metals — further impair microbial resilience and immune balance [15].
3.3 Stress and the Gut–Brain Axis
Psychological stress reduces mucin secretion and changes gut motility and blood flow through the hypothalamic–pituitary–adrenal (HPA) axis. This creates conditions for bacterial overgrowth and barrier damage. [16]
Patient Tip: Meditation, diaphragmatic breathing and vagal-nerve stimulation have been shown to positively modulate microbial composition and reduce stress-induced gut symptoms.
3.4 Infections, Motility and Anatomical Factors
Post-infectious irritable bowel syndrome and small intestinal bacterial overgrowth (SIBO) often follow viral or bacterial enteritis. [17] Surgery, trauma or ileocecal valve dysfunction may disrupt intestinal motility, allowing retrograde bacterial migration.
3.5 Ageing and Immune Senescence
With age, microbial diversity declines, and immune function weakens. Reduced SCFA production and heightened inflammation contribute to frailty and metabolic disorders. [18]
4. Dysbiosis and the Leaky Gut Connection
4.1 Barrier Integrity and Inflammation
A compromised intestinal barrier allows translocation of LPS and antigens into the bloodstream, triggering systemic inflammation. [9, 11] This “leaky gut” state has been associated with metabolic syndrome, autoimmune disease and neuroinflammation. [19]
4.2 The Oral–Gut Axis
Emerging research shows that oral pathogens can colonise the gut, linking periodontal disease with inflammatory bowel disease and cardiovascular risk. [20]
Clinical Insight: Integrative care should include oral health assessment — a neglected yet critical component of gut microbial homeostasis.
5. Diagnosing Dysbiosis: Clinical and Functional Perspectives
Dysbiosis rarely manifests as a single symptom. Instead, it presents as a constellation of digestive irregularities, food intolerances, mood changes, fatigue, and chronic inflammation.
A functional assessment integrates clinical history, dietary analysis, and, where appropriate, laboratory testing.
5.1 Conventional and Functional Testing Options
Comprehensive Stool Analysis – identifies bacterial composition, yeast or parasite overgrowth, inflammatory markers (calprotectin), and SCFA profiles.
Breath Testing – evaluates hydrogen and methane gases to detect SIBO.
Intestinal Permeability Testing – measures absorption of lactulose/mannitol to assess barrier integrity.
Urinary Organic Acids – detects microbial metabolites reflective of dysbiosis.
Advanced Metagenomics (research use) – next-generation sequencing for microbiome diversity mapping.
Clinical Insight: Testing informs but does not replace clinical reasoning. Dysbiosis is dynamic — interpretation must consider diet, medication, stress, and symptom context.
6. Restoring Microbiome Balance: The 4R Clinical Framework
Functional and integrative medicine often uses the 4R model — Remove, Replace, Reinoculate, Repair — as a structured roadmap to restore microbiome homeostasis.
6.1 Remove — Eliminating Root Drivers
Withdraw irritants such as processed foods, refined sugars, alcohol, and excessive animal fats.
Identify and reduce medications that harm the microbiome (PPIs, NSAIDs, unnecessary antibiotics).
Address infections or bacterial overgrowth with targeted herbal or medical antimicrobials, as indicated.
Patient Tip: Even a short 14-day elimination of processed foods and sugars can lower gut inflammation and rebalance key bacterial species.
6.2 Replace — Supporting Digestion and Motility
Optimise gastric acid (betaine HCl if indicated), bile flow, and pancreatic enzyme output.
Include bitters, ginger, and digestive herbs to enhance secretion and peristalsis.
Ensure adequate hydration and dietary fibre to normalise transit time.
Clinical Insight: Adequate stomach acid prevents pathogenic colonisation of the small intestine. Low acid (hypochlorhydria) is an under-recognised contributor to dysbiosis.
6.3 Reinoculate — Rebuilding Beneficial Microbes
Prebiotics: plant fibres such as inulin, fructooligosaccharides (FOS), resistant starch, pectin.
Probiotics: evidence-based strains (Lactobacillus rhamnosus GG, Bifidobacterium longum, Saccharomyces boulardii).
Fermented foods: kefir, kimchi, sauerkraut, miso, yoghurt, tempeh.
Postbiotics: emerging therapeutics using purified microbial metabolites (e.g. butyrate supplements) show promise for barrier repair and immune modulation [21].
Patient Tip: Diversity matters more than quantity. Aim for 30 different plant foods per week to feed a broad microbial network.
6.4 Repair — Restoring the Intestinal Barrier
Key nutrients: L-glutamine (enterocyte fuel), zinc carnosine (tight-junction support), omega-3 PUFAs (anti-inflammatory), vitamin D (immune regulation).
Botanical mucoprotectives: aloe vera, slippery elm, liquorice (DGL).
Polyphenols: turmeric (curcumin), green-tea catechins, and berry anthocyanins enhance SCFA production and antioxidant defence.
Lifestyle: stress management, adequate sleep, movement, and circadian alignment.
Clinical Insight: Repair is a long-term phase. Lasting microbiome resilience requires sustained dietary and behavioural change, not a temporary cleanse.
7. The Mediterranean Model for Microbiome Restoration
A wealth of research confirms that the Mediterranean diet promotes microbial richness, metabolic health, and reduced inflammation [22].
8. Integrating the Naturopathic & Functional Medicine Perspective
Functional medicine views dysbiosis not as an isolated gut issue but as a systems-wide imbalance.
By identifying nutritional deficiencies, inflammatory drivers, and environmental stressors, practitioners can address root causes rather than merely manage downstream disease.
Clinical Insight: Healing the gut often improves multiple domains — energy, immunity, mood, and hormonal balance — reflecting the microbiome’s central role in systemic homeostasis.
+ REFERENCES
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[2] Hentges DJ. Gut flora and disease resistance. In: Fuller R, ed. Probiotics: the Scientific Basis. London: Chapman and Hall; 1992:87- 110.
[3] Holzapfel WH, Haberer P, Snel J, et al. Overview of gut flora and probiotics. Int J Food Microbiol 1998;41:85-101.
[4] Gibson GR. Dietary modulation of the human gut microflora using prebiotics. Br J Nutr 1998;80:S209-S212.
[5] Moore WE, Holdeman LV. Human fecal flora: the normal flora of 20 Japanese-Hawaiians.Appl Microbiol 1974;27:961-979.
[6] Noack J, Kleessen B, Proll J, et al. Dietary guar gum and pectin stimulate intestinal microbial polyamine synthesis in rats. J Nutr 1998;128:1385-1391.
[7] Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 1995;125:1401-1412.
[8] Rinninella, E., Cintoni, M., Raoul, P., Lopetuso, L.R., Scaldaferri, F., Pulcini, G., Miggiano, G.A.D., Gasbarrini, A., Mele, M.C. (2019). Food Components and Dietary Habits: Keys for a Healthy Gut Microbiota Composition. Nutrients, 11, 2393. doi: 10.3390/nu11102393