Reboot the Gut

Reboot the Gut


Restore balance, calm inflammation, and support your microbiome with simple, science-informed changes.

The gut is far more than a digestive tube. It is an ecosystem, an immune organ, and a metabolic control centre. When it's out of balance, it can affect mood, weight, hormones, energy, skin and even sleep. This page explores practical, evidence-informed ways to "reboot" your gut and support long-term health.

Explore methods below:


Low FODMAP for IBS:

A Forgotten Tool


From years in clinical practice, as well as my own family's health journeys, I've rarely seen patients with Irritable Bowel Syndrome (IBS) offered the Low FODMAP diet as an option – yet it can be life-changing for some.

The Low FODMAP protocol involves temporarily removing certain fermentable carbohydrates that can trigger bloating, pain, diarrhoea or constipation, and then reintroducing them in a structured way.

Following a Low FODMAP diet for 6–8 weeks can give the gut a chance to settle. During the reintroduction phase, you learn which FODMAP groups trigger symptoms. Interestingly, once the gut calms, some previously problematic foods can become tolerable again.

Important: Always speak to your GP or a dietitian before starting the Low FODMAP diet, especially if you have other medical conditions or are underweight.


Gut Reset for Everyone

Rebooting the Gut Even Without IBS

Many people experience low-grade gut dysfunction without a formal diagnosis: bloating, irregular bowel habits, sugar cravings, fatigue or "brain fog". Often, this reflects an unhappy microbiome rather than a dramatic disease.

One of the most effective ways to reboot the gut is simply to clean up the diet:

Simple Gut-Friendly Changes

  • Remove or drastically reduce ultra-processed foods

  • Cut back on refined sugars and white flours

  • Minimise seed oils (e.g. sunflower, soybean, rapeseed blends in UPFs)

  • Increase leafy greens, fibre and polyphenol-rich plants

  • Choose grass-fed or minimally processed animal foods where possible

  • Use extra virgin olive oil as your main fat and grass fed butter!

  • Add fermented foods such as kefir, sauerkraut, kimchi, kombucha and live yogurt

This is not a fad; it's closer to how our ancestors ate – whole foods, natural fats, and plenty of fibre and fermentation.


Ultra-Processed vs Ancestral

Ultra-Processed Diets vs the Ancestral Microbiome


Historically, human diets were rich in fibre, resistant starch, polyphenols and naturally fermented foods. Today, many diets are dominated by ultra-processed foods containing additives, emulsifiers, refined sugars and altered fats.

This shift can:

  • reduce microbial diversity

  • lower beneficial short-chain fatty acids (SCFAs)

  • slow gut motility

  • weaken the mucosal barrier

  • promote low-grade inflammation

Not surprisingly, conditions like obesity, type 2 diabetes, fatty liver and autoimmune diseases have risen alongside these changes in how and what we eat.


Fasting for Gut Repair

Fasting as a Tool for Gut Repair


Fasting gives the gut a chance to rest and reset. It can support:

  • autophagy (cellular clean-up processes)

  • improved microbial diversity

  • reduced inflammation

  • better insulin sensitivity

  • less bloating and dysmotility

  • more stable energy and appetite

Types of Fasts That May Help

  • Intermittent fasting (14–16 hours):
    A daily eating window and an overnight fast to give the gut a break.

  • 24-hour fasts (e.g. dinner-to-dinner):
    Once a week or fortnightly; a gentle metabolic and gut reset.

  • 36-hour "gut reset" fasts (occasional):
    Deeper rest and autophagy for some individuals, when medically appropriate.

Women, especially in perimenopause and menopause, may benefit from fasting protocols tailored to female physiology and hormonal rhythms. I discuss this in more detail in my hormone and menopause sections. Always seek advice from your own medical professional before implementing fasting, especially longer fasts. 


Fermented Foods vs Probiotics


Fermented foods are one of the most powerful – and underused – tools for gut repair. They often provide a wider range and higher volume of beneficial bacteria than many commercial probiotic capsules.

Examples include:

  • kefir

  • sauerkraut

  • kimchi

  • kombucha

  • miso

  • live natural yogurt

These foods deliver live microbes in a matrix of fibre, organic acids and bioactive compounds. Probiotic supplements can be useful, but usually offer a limited number of strains in isolation. If tolerated, fermented foods are an excellent daily foundation.


After Antibiotics

Rebuilding the Gut After Antibiotics


Antibiotics can be lifesaving, but they also disrupt the ecosystem of the gut. After a course of antibiotics, it's worth focusing intentionally on gut repair:

  • emphasise fermented foods

  • aim for fibre diversity (lots of different plants)

  • consider prebiotics (e.g. inulin, GOS, beta-glucan) if tolerated

  • prioritise omega-3 fats

  • include polyphenol-rich foods (berries, olives, herbs, green tea, cacao)

  • avoid ultra-processed foods during the recovery phase

Some people develop IBS-like symptoms after antibiotics; a structured approach to diet and microbiome support can be very helpful.


Exercise & Gut Motility

Movement, Motility and the Microbiome


Movement is a simple but often overlooked gut therapy. Physical activity:

  • improves gut motility and helps prevent constipation

  • reduces transit time

  • positively influences microbial diversity

Even a daily walk can make a noticeable difference. Resistance training adds extra benefit by improving metabolic health, which in turn supports a healthier microbiome.


The Gut–Brain Axis

The Gut–Brain Axis: Mood, Sleep and Stress


The gut and brain are in constant conversation via the vagus nerve, hormones and immune messengers. Gut microbes produce or influence neurotransmitters such as GABA, serotonin and dopamine precursors.

When the gut is out of balance, you may notice:

  • anxiety or irritability

  • lower stress tolerance

  • poor sleep

  • mood swings

  • cognitive "fog"

This is why IBS often coexists with anxiety, and why stress flares digestive symptoms. Rebooting the gut can be a key part of supporting mental and emotional wellbeing.


Gut & Menopause

Gut Health in Perimenopause and Menopause


During perimenopause and menopause, hormonal shifts reshuffle multiple microbial ecosystems:

  • the gut microbiome (including the estrobolome)

  • the vaginal microbiome (often less Lactobacillus)

  • the urogenital microbiome (influencing UTIs and urgency)

These changes are linked to:

  • weight and metabolic changes

  • inflammation

  • mood and sleep disruption

  • pelvic and bladder symptoms

Rebooting the gut in midlife can support metabolic resilience, hormone balance and symptom relief. I explore this in more depth on my menopause pages.


Metabolism, Immunity & the Gut

Metabolism, Immunity and the Gut


Around 70% of the immune system sits in and around the gut. Beneficial bacteria produce short-chain fatty acids that help regulate inflammation, glucose metabolism and insulin sensitivity.

When the microbiome is imbalanced (dysbiosis), it can contribute to:

  • obesity

  • insulin resistance

  • PCOS

  • fatty liver

  • autoimmune tendencies

This is why gut repair isn't just about comfort – it's central to metabolic and immune health.


Key Nutrients for Gut Reboot

Nutrients That Support a Gut Reboot


Some of the key nutritional factors that support gut repair and microbial balance include:

  • Fibre diversity: aim for a variety of plant foods each week

  • Polyphenols: berries, olives, herbs, spices, green tea, cacao

  • Omega-3 fats: oily fish or high-quality supplements

  • Magnesium: supports motility, muscle function and relaxation

  • Potassium: from leafy greens and whole foods to support electrolyte balance

  • Fermented foods: daily, if tolerated

  • Vitamin D: supports immune and epithelial (gut lining) health


Where to Start


Rebooting the gut doesn't have to be complicated. You don't need to do everything at once. Start with one or two changes:

  • clean up the diet

  • add one fermented food

  • try a gentle fasting window

  • increase your daily steps

Over time, these small steps can transform how your digestive system – and the rest of your body – feels.

This page is a starting point, not a replacement for medical advice. Always speak to your GP or a qualified professional before making major dietary or fasting changes, especially if you have underlying health conditions.