Gut Health
Gut health is a measure of how efficiently your gastrointestinal tract digests food, absorbs nutrients, and keeps its trillions of microbes in balance. A well-tuned gut powers your immunity, metabolism, and the gut-brain axis that shapes mood and cognitive function.
Why Your Gut Matters
Your gastrointestinal tract houses 70 % of your immune system, manufactures vitamins, and produces mood-shaping neurotransmitters.
A healthy gut balances beneficial and harmful microbes to properly break down food, absorb nutrients, produce vitamins, and support mental wellbeing and disease prevention.
The moment your microbiome becomes imbalanced, your energy declines, your immunity weakens, your hormones misfire, and your brain loses clarity.
At All Naturopath, we combine cutting-edge testing with food-first, evidence-based care to restore a thriving microbiome and calm digestion.
The Spectrum of Gut Disorders
| IBS (Irritable Bowel Syndrome) | Dysregulated gut-brain signalling and motility. | Bloating, cramps, pain, stool pattern swings. |
| SIBO (Small-Intestinal Bacterial Overgrowth) | Excess microbes migrate into the small bowel. | Gas within 90 min on breath test, malabsorption of nutrients. |
| Dysbiosis/Low Diversity | Loss of beneficial species and a decline in short chain fatty acids (SCFA). | Food sensitivities, low mood, skin flares. |
| ↑ Intestinal Permeability (“Leaky Gut”) | Loosened tight junctions leak antigens. | Brain-fog, joint pain, multiple intolerances. |
| IBD (Crohn’s Disease and Ulcerative Colitis) | Auto-inflammatory mucosal damage. | Blood/mucus in stool, urgency, weight loss. |
| Gastroesophageal Reflux Disease (GERD)/Reflux | Acid and bile splash upward. | Heart-burn, chronic cough, hoarse voice. |
Is Your Gut Sending an SOS?
- Abdominal pain and cramping
- Daily bloating, or visible distension and gas
- Alternating constipation and diarrhoea
- Unexplained fatigue or iron/B-12 deficiency
- Food reactions that seem to “spread” over time
- Skin breakouts, rosacea or eczema linked to meals
- Anxiety, brain fog or poor sleep after eating
- Heartburn and acid reflux
- Mood changes, like stress, anxiety, or low mood.
The Root Cause
Consuming an Ultra-processed Diet
Ultra-processed foods (UPFs) are low in fibre, which is the primary food source for beneficial gut bacteria. Without enough fibre, these microbes starve, leading to a less diverse and abundant microbial community.
Additives and Emulsifiers: Many UPFs contain artificial additives, such as emulsifiers, which can damage the protective mucus layer in the gut and increase inflammation.
Unhealthy Fats: UPFs often contain trans fats and refined vegetable oils that can further reduce microbial diversity and promote an unhealthy shift in gut bacteria.
Alcohol: Excessive consumption disrupts the balance of the gut microbiome.
Micronutrient Gaps
Micronutrient deficiencies in zinc, vitamin D, omega-3 fatty acids, and polyphenols can impair gut health by damaging the gut lining, disrupting gut microbiota balance, and affecting nutrient absorption.
Zinc: A crucial nutrient for gut barrier integrity and a balanced microbial environment. A deficiency can lead to gut dysbiosis (an imbalance of gut microbes) and increase susceptibility to infections.
Vitamin D: Present in the gut, Vitamin D receptors play a role in regulating the gut immune response and maintaining gut barrier function. A deficiency can lead to dysbiosis and an increased susceptibility to gut injury.
Omega-3 Fatty Acids: Omega-3s can influence the composition of the gut microbiota. While studies show varied effects, omega-3 intake is associated with changes in the gut microbial balance, potentially reducing harmful bacteria.
Polyphenols: These plant compounds can selectively stimulate the growth of beneficial gut bacteria like Bifidobacterium and Lactobacillus. A diet lacking in polyphenols means missing out on these positive effects, which can lead to a less favourable gut environment.
Hidden Infections and Overgrowth Conditions
Gut health can be negatively affected by hidden infections such as H. pylori and parasites, bacterial overgrowth in the small intestine, and yeast overgrowth.
H. pylori: Helicobacter pylori penetrates the mucous lining of the stomach and establishes infection, causing inflammation, ulcers, and symptoms like stomach pain, bloating, and gas.
Parasites: Giardia, Cryptosporidium, and Entamoeba histolytica are common parasites transmitted through contaminated food and water that alter gut health by causing diarrhoea, bloating, and other gastrointestinal issues. Other parasites, such as roundworms, tapeworms, and hookworms, interfere with nutrient absorption and cause other infections. The effects on gut health are due to a variety of mechanisms, including altering gut motility, absorption, and microbial composition.
SIBO (Small Intestinal Bacterial Overgrowth): When there is an overgrowth of bacteria in the small intestine, often due to slowed digestion, diarrhoea, bloating, and malnutrition can occur.
Yeast (Candida) overgrowth: This can occur when the gut microbiome is disrupted, such as through dysbiosis or antibiotic use. It can lead to symptoms like bloating, gas, fatigue, and brain fog.
Antibiotic Overuse and
Medication-Induced Acid Loss
Antibiotic Overuse
Disrupts the Gut Microbiome: Antibiotics, especially broad-spectrum ones, can indiscriminately destroy both good and bad bacteria.
Reduces Microbial Diversity: This destruction leads to a significant decrease in bacterial diversity, which is crucial for a healthy gut.
Promotes Antibiotic-resistant Bacteria: The elimination of beneficial bacteria creates an opportunity for antibiotic-resistant strains to thrive.
Increases Susceptibility to Infection: A compromised gut microbiome makes the host more susceptible to infections from pathogens such as Clostridioides difficile.
Medication-Induced Acid Loss
Alters the Gut Environment: Stomach acid helps regulate the gut microbiome. Reducing it can change the gut's environment, impacting the balance of bacteria.
Promotes Bacterial Overgrowth: Medications that suppress acid secretion, such as proton pump inhibitors (PPIs), can lead to bacterial overgrowth in the small intestine (SIBO).
Contributes to Dysbiosis: Both antibiotics and acid-suppressing drugs can directly cause intestinal dysbiosis, an imbalance of gut bacteria.
Chronic Stress and Low Vagal Tone
Chronic stress impairs gut health via the gut-brain axis by reducing vagal nerve tone, disrupting communication between the gut and brain. This low vagal tone impairs the body's "rest and digest" functions, leading to digestive issues like irritable bowel syndrome (IBS), inflammation, and gut dysbiosis. In turn, an unhealthy gut can send signals back to the brain that increase stress and anxiety, creating a negative feedback loop.
Disrupted Communication: The vagus nerve is a major communication channel between the gut and brain. Chronic stress can weaken its function, leading to miscommunication and symptoms like abdominal discomfort, bloating, constipation, or diarrhoea.
Impaired "Rest and Digest" Function: The vagus nerve helps activate the parasympathetic nervous system, which is responsible for rest and digestion. Chronic stress and low vagal tone hinder this "rest and digest" state, negatively impacting digestive processes.
Increased Inflammation: A low vagal tone can lead to increased gut inflammation, which the stress response can exacerbate. This can contribute to gut conditions like irritable bowel disease (IBD) and IBS.
Gut Bacteria Imbalance: Stress can alter the gut microbiome, promoting the growth of harmful bacteria while reducing beneficial ones. This imbalance, or dysbiosis, can contribute to both digestive issues and an increased stress response, creating a vicious cycle.
Altered Gut-Brain Feedback: Poor gut health caused by stress can send signals back to the brain, potentially triggering mood changes, anxiety, and depression. This feedback loop means that gut irritation can lead to emotional stress, which in turn further stresses the gut.
Environmental Mould and Mycotoxins
Mycotoxins are well known for disrupting tight junctions, damaging the gut barrier, and causing leaky gut. This allows undigested food proteins, toxins, and LPS (an endotoxin produced by gut bacteria) to enter the bloodstream and increase inflammation.
When mycotoxins enter the gut, they can kill or suppress many of our beneficial bacteria, such as Lactobacillus and Bifidobacterium. This can allow opportunistic bacteria to survive more easily.
Mould and mycotoxins can affect the digestive system, with common symptoms including gas and bloating, abdominal pain and cramping, diarrhoea, constipation, heartburn, reflux, nausea, and food sensitivities and reactions.
Comprehensive Testing at All Naturopath
Advanced PCR Stool Profile
An advanced PCR stool profile is a comprehensive, DNA-based test that uses Polymerase Chain Reaction (PCR) technology to identify bacteria, viruses, parasites, and fungi in a stool sample and analyse key digestive and immune markers. These tests go beyond traditional stool cultures to provide a more sensitive and specific analysis of gut health, offering insights into microbial imbalances, inflammation, and overall gut function. The results help clinicians understand potential root causes of gastrointestinal and other chronic symptoms and inform treatment decisions.
Inflammatory Markers Panel
Calprotectin: Measures a protein produced by white blood cells, indicating intestinal inflammation.
C-Reactive Protein (CRP): An acute-phase protein measured in the blood. Elevated levels indicate inflammation anywhere in the body.
Secretory IgA (sIgA): Measures an antibody found in various bodily fluids, with high levels indicating immune system function and gut barrier integrity.
Lactulose and Glucose Breath Tests
Lactulose and glucose breath tests are non-invasive methods to diagnose Small Intestinal Bacterial Overgrowth (SIBO) and Intestinal Methanogen Overgrowth (IMO) by measuring hydrogen and methane gas levels in your breath after you drink a sugar solution.
The glucose test is better for detecting SIBO in the upper small intestine. At the same time, the lactulose test can diagnose overgrowth in both the upper and lower small intestine and also measure the time it takes for food to pass through the digestive tract. An elevated gas level indicates bacterial overgrowth.
Food Reaction Panel
IgE Blood Test: Measures antibodies associated with immediate allergic reactions that typically occur within minutes to a couple of hours after eating a food.
Oral Food Challenge (OFC): The gold standard for diagnosing food allergy. The challenge involves a person eating a suspected allergen under supervision to monitor the reaction.
Zonulin Test
Zonulin is a protein that helps control the "tight junctions" between intestinal cells, which act as a gatekeeper for the gut barrier. A blood or stool sample is taken and analysed, with elevated zonulin levels indicating that the "tight junctions" of the intestinal lining are opening too easily.
Lactulose-Mannitol Permeability Assay
In this test, you drink a solution that contains a large sugar (lactulose) and a small sugar (mannitol). Several hours later, we collect your urine and measure the lactulose-to-mannitol ratio; this ratio indicates how effectively your intestinal barrier keeps large molecules out while allowing small ones through.
Genetics Test
Genetic insights provide information about predispositions and should always be discussed with a healthcare professional in context.
MTHFR Testing: Identifies variations in the MTHFR gene that affect how the body processes folate. Variants can lead to less efficient folate metabolism, potentially impacting homocysteine levels and the body's ability to clear histamine.
DAO/HNMT Testing: Genetic testing can identify variants in the diamine oxidase (DAO) or histamine N-methyltransferase (HNMT) genes, which are crucial for the breakdown of histamine. Variants can impact histamine clearance, potentially contributing to histamine intolerance or other symptoms.
Other Genetic Markers: Some comprehensive gut health panels also test for other genetic markers, such as FUT2, HLA-DQ2.5/DQ8, and TLR4, to assess risks related to microbial balance, gluten sensitivity, and immune response.
Our Treatment Framework
Food-First Medicine
- Diversity Diet: Consuming 30+ plant foods per week to increase SCFA-producing groups.
- Targeted Eliminations: Low-FODMAP, gluten-light or dairy-free trials, then structured re-challenge.
- Resistant Starch Hacks: Cooked, then cooled rice or potatoes feed the beneficial bacteria Bifidobacterium. The cooling process transforms some of the digestible starch into resistant starch, which acts as a prebiotic.
- Mindful Meal Rhythm: A 12-hour overnight fast and deep breathing before eating has been shown to activate the vagus nerve.
Lifestyle and Gut-Brain Reset
- Stress-Mapping and Breathwork: Observing and recording personal stress triggers and implementing breathwork, humming, singing and gargling, activates the parasympathetic nervous system via the vagus nerve.
- Sleep Optimisation: Routinely getting 7-9 hours of sleep every night and utilising darkness signals to release melatonin and promote microbiome rhythmicity.
- Progressive Exercise: Brisk walking and strength training improve transit and diversity.
Evidence-Based Botanicals and Nutraceuticals
- Enteric-Coated Peppermint Oil: Antispasmodic, prokinetic (enhances gastrointestinal motility). A meta-analysis of peppermint oil was superior to placebo for the treatment of irritable bowel syndrome (IBS).
- Herbal Antimicrobials (Berberine, Oregano oil, Neem): Reduce SIBO gas and rebalance flora. 2024 open-label trial cleared breath test in ≥ 60 % hydrogen-SIBO.
- L-glutamine: Seals tight junctions, calms inflammation. Randomised data confirm permeability repair within 8 weeks.
- Targeted Probiotics: Restore gut barrier, lower IBS cytokines. 2025 RCT improved epithelial integrity.
- Post-Biotic Butyrate: Fuels colonocytes, moderates immunity. SCFA review links butyrate to barrier integrity and metabolic health.
Ready to Rebuild Your Gut?
Angela La Leggia has a specialist focus with over 20 years of experience restoring gut microbiome balance.
She investigates your gut through a functional, root-cause lens, linking your digestion, immunity, skin and mood. Using the latest clinical data and research, Angela creates evidence-based protocols.
At All Naturopath, your goals inform every decision, ensuring truly patient-centred care. Angela starts with “food-first” medicine, then incorporates evidence-based botanicals and nutraceuticals, collaborating with your GP and gastroenterologists to diagnose, treat and support your gut health.
Call us today on 0402 926 675 for an appointment!