Gut health protocol
The antimicrobial diet
Your body is home to a large community of microbes that keep you well. When that balance is disturbed, dysbiosis sets in and undesirable microbes overgrow, bringing bloating, diarrhoea, mood changes, and fatigue. This diet leans on medicinal foods to restore balance, and unlike very restrictive plans it is safe for the long term.
The purpose of an antimicrobial diet
Increase the medicinal foods that help eradicate undesirable microbial growth, while temporarily reducing the foods that promote it.
Support the supplemental interventions used to clear microbial overgrowth.
Protect and nourish the intestinal microbiome to optimise overall health and prevent recurrent infections.
Most of us have taken antibiotics or other medications at some point. While sometimes necessary, studies show they can disturb the delicate ecosystem of the gut and place stress on the liver. Stress, poor diet, and high alcohol intake do the same. Luckily, the plant world offers natural antimicrobials that target undesirable microbes while protecting the beneficial strains vital for gut function, immunity, and wellbeing.
How do I know this diet is right for me?
The antimicrobial diet is a safe, sustainable, and gentle way of combatting pathogenic overgrowth. Before integrating natural remedies, consult your practitioner to make sure they are appropriate for you. In pregnancy and lactation, where strong herbal interventions are not suitable, this diet is an effective and safe alternative.
Rather than strict restriction, it avoids refined sugars and processed foods and only briefly reduces some other groups, so you are still starving the undesirable microbes while protecting the diverse microbiome you need for good health. Some clinical situations call for stronger restrictions, so check with your practitioner about what suits your situation.
What to expect
As harmful microorganisms die off, they release inflammatory toxins that can feel uncomfortable, but it passes. No two people react the same way. In the short term you may notice aches and pains, headaches, skin breakouts or rashes, changes in bowel movements, food cravings, and fatigue. These point to progress toward restoring gut balance, but talk to your practitioner about easing any unwanted symptoms.
Make your own antibiotic tonic
Not suitable in pregnancy or lactation
Ingredients
- 1/2 cup fresh thyme, chopped
- 1/2 cup fresh rosemary, chopped
- 1/2 cup fresh ginger, chopped
- 1/2 cup garlic cloves, chopped
- Pinch of lemon rind
- 2 tbsp manuka honey (high UMF)
- Apple cider vinegar
- A large glass jar with a lid
Method
- Let the chopped garlic sit for about 10 minutes to release more allicin, the compound behind its antibacterial properties.
- Add all the herbs to the jar and fill with apple cider vinegar.
- Seal, gently shake, and place in a cool, dark cupboard.
- Shake once a day for 6 weeks, then strain the tincture into a glass dropper bottle.
- Take one dropper full three times a day in a glass of water.
Foods to eat more, eat less, and avoid
As a guide, choose organic produce and lean toward a plant-based diet. Reduce carbohydrates such as good-quality breads, rice, and starchy vegetables, but do not cut them out entirely.
| Eat more More | Eat less Less | Avoid Avoid |
|---|---|---|
| Clove, turmeric, oregano, coriander, thyme, cinnamon, cumin, fennel, and caraway, all with significant antibacterial and antifungal properties. | Refined grains: wheat, spelt, barley, semolina, rice, quinoa, buckwheat, millet, teff. | Processed and snack foods: sweets, ice cream, chocolate, custard, jelly, chips, biscuits, crackers, cereals, baked goods. |
| Pomegranate, with broad-spectrum antimicrobial activity and high polyphenol levels. | Dairy-containing foods: milk, cream, sweetened yoghurt, cheeses. | Refined sugars (white, brown, raw), rice malt syrup, maple syrup, corn syrup, molasses. |
| Garlic, ginger, and onion, traditional antimicrobial agents with high antioxidant and anti-inflammatory properties. | Red meats and processed or preserved meats: deli meats, sausages, salami, ham, bacon, beef, lamb, pork. | High-sugar and dried fruits: mango, grapes, bananas, oranges, cherries, pears, watermelon. |
| Cruciferous vegetables (broccoli, brussels sprouts). | Stock powders and sauces: barbecue, honey mustard, sweet and sour. | Fast food, takeaway, and alcohol. |
| Other vegetables: leafy greens, asparagus, artichoke, zucchini, celery, kale, eggplant. | Legumes: chickpeas, beans, lentils. | |
| Avocado, berries, rockmelon, papaya. | Vegetable, sunflower, and canola oil, margarine and butter alternatives. | |
| Nuts, seeds, seaweed, lean protein, and eggs. | Fruit juices and high-sugar smoothies, coffee, soft drink, whey-based protein powders. |
Feeling peckish?
By swapping sugary choices for nutrient-dense, high-fibre alternatives, you send pathogens a clear message to find food elsewhere.
- Handful of organic pumpkin and sunflower seeds.
- Papaya (and its seeds) topped with a thin layer of manuka honey.
- Mixed nuts roasted in antimicrobial spices and a hint of salt.
- Baba ghanoush dip with cucumber and carrot sticks.
- Coconut yoghurt with pomegranate seeds.
- Home-made pesto (herbs, garlic, pumpkin seeds, walnuts, lemon juice).
A sample antimicrobial day
Breakfast
Option 1: Scrambled eggs on good-quality toast with oregano, spinach, and red onion cooked in coconut oil, with 1/2 avocado.
Option 2: Chia and hemp seed pudding on unsweetened coconut or almond milk, topped with pumpkin seeds, walnuts, and pomegranate.
Lunch
Option 1: Roasted asparagus, eggplant, and zucchini on leafy greens with a garlic, ginger, and lemon vinaigrette and coriander.
Option 2: Dahl with turmeric, cinnamon, cumin, fennel, and garlic, with a natural yoghurt dressing and pomegranate.
Dinner and drinks
Option 1: Salmon baked in turmeric and cumin with roasted broccoli, cauliflower, brussels sprouts, onion, and garlic, on quinoa.
Option 2: Chicken stir-fry with ginger, garlic, tamari, and mixed greens, topped with coriander.
Antimicrobial herbal teas (green, hibiscus, moringa, cinnamon, turmeric) and 2L filtered water.
Adapted for Elemental Health and Nutrition from the Orthoplex and Bio Concepts antimicrobial diet resource.
Frequently asked questions
What is the antimicrobial diet?
The antimicrobial diet uses medicinal foods to help rebalance the gut microbiome when there is dysbiosis, an overgrowth of less desirable microbes. Unlike many restrictive plans, it is considered safe for the long term. The idea is that the plant world offers natural antimicrobials that target undesirable microbes while still protecting beneficial strains, so the diet increases these medicinal foods while reducing foods that promote unwanted growth, and supports the gut's overall balance.
What foods have natural antimicrobial properties?
Foods emphasised for their antimicrobial properties include spices like clove, turmeric, oregano, coriander, thyme and cinnamon, pomegranate for its broad-spectrum action and high polyphenols, and traditional antimicrobials such as garlic, ginger and onion. Cruciferous vegetables, leafy greens, asparagus, artichoke, berries, nuts and seeds round out the plan. Foods to reduce include refined grains, dairy, red and processed meats, refined sugar and fruit juice, with processed foods and alcohol avoided.
Can you follow the antimicrobial diet long term?
Yes, unlike many strict elimination diets, the antimicrobial diet is described as safe for the long term, and even suitable during pregnancy and lactation where stronger herbal interventions would not be appropriate. Because it works by adding medicinal foods and gently reducing others rather than eliminating broad food groups, it can be sustained ongoing. Some people experience temporary die-off effects like aches, headaches or fatigue as the microbiome shifts, which can be discussed with a practitioner.
Reviewed by Rohan Smith, BHSc Nutritional Medicine · Elemental Health & Nutrition, Adelaide. Last reviewed 13 June 2026.
Important: This summary is general information, not personalised medical advice, diagnosis, or a treatment protocol. Speak with a qualified practitioner about your individual situation. Book a consultation →