Reboot your biome

Rebooting your biome involves removing specific foods from your diet (Remove and Repair Phase), and then reintroducing them back into your diet (Reintroduction phase) along with introducing prebiotics and probiotics to boost your biome. This process can be particularly helpful for people who have been experiencing gut related symptoms such as bloating, mild Irritable Bowel Syndrome (IBS), abdominal cramps etc.

However, those who are doing the diet for general health and weight loss reasons, and who don’t have specific gut related symptoms can usually skip the Remove and Repair Phase and go straight on to the Reintroduction Phase to boost the health of their gut biome.

If you do have gut symptoms it is important to keep a detailed food diary during this process and to record your symptoms. This will help you identify whether or not your symptoms are of dietary origin, and what foods (if any) are upsetting your gut.

Please note: This approach isn’t suitable for everyone, and we don’t recommend embarking on this process if you are underweight, suspect you have a food allergy, have other significant medical problems, are suffering from unexplained weight loss or change in bowel habit, bleeding, or are frail or unwell. If you have any concerns, we recommend talking to your health professional first. See FAQs for exclusions.


This phase, designed for those with gut symptoms, usually takes about 4 weeks. It may involve removing specific common foods that can cause symptoms such as gluten or dairy, or a particular food suspected of being related to the symptoms. We advise only addressing a maximum of a few foods at a time.

We also suggest general measures regarding foods to avoid and others to add which are known to reduce symptoms and improve gut health. These are detailed in the book.


Many people will go straight to Phase 2, without needing to eliminate any foods. For those who have removed food substances and done the gut healing program in Phase 1, the Reintroduction program in Phase 2 involves gradually including the foods that you eliminated during the repair phase.

In general, the Reintroduction Phase involves moving towards healthier ways of eating that will be good for you, your gut and your gut bacteria. This means introducing more prebiotic foods to feed the bacteria, such as onions, chicory and apples, along with probiotic foods such as fermented foods like live yoghurt or fermented vegetables, which top up the healthy bacteria in your gut.

During this phase you should introduce foods one at a time with a gap of at least three days between each added food. This applies to both new foods and reintroductions.  More details on how to re-boot your biome can be found in the Clever Guts Diet book.

If symptoms recur after completion of this plan, you can complete the process again. However, if your symptoms are particularly troublesome and not settling as expected, we recommend you see a health professional.

If you are going to reboot your biome, we recommend you keep a regular food and symptoms diary as a record. This can also be useful to show your health professional. 

Click to download your food and symptoms diary.