A healthy gut is critical to health and wellbeing, imbalances and dysfunction here can impact every system in the body and create all sorts of problems. In my case when I committed to being fully gluten free, a lot shifted. The joint pains eased. The brain fog lifted. My energy returned. The mouth ulcers, abdominal pain and GI problems settled. That experience taught me something simple and important: health starts in the gut.
In this article I share why gut health is so important and the simple 5 step approach used by functional medicine practitioners to restore balance and health in the gut.
Why functional medicine often starts with the gut
Functional medicine begins with a simple question: what is causing these symptoms? Instead of chasing labels (diagnoses), we look for root causes and patterns. Daily inputs such as food, sleep, movement, light and stress act as signals that switch processes in your body up or down. Your body is not a set of separate parts. It is a set of connected systems that speak to each other all day. When one system slips, others are pulled with it.
The gut is the root of health. It breaks down food, absorbs nutrients, trains the immune system, makes key signalling chemicals and sends constant messages to the brain. When the gut is unsettled, dysfunctions and imbalances can show up in energy, mood, skin, joints and sleep. That is why we often start here and go food first. The food you eat is a lever you control every day, and small changes can shift several systems at once.
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The 5R approach, in context
One of the most useful frameworks I learnt on AFMCP is the 5R approach to gut health. It gives you a framework you can use to systematically optimsie your gut health. Here are the 5Rs:
- Remove what irritates or infects the gut, so inflammation can settle.
- Replace what is missing for digestion, so food is broken down cleanly.
- Reinoculate with friendly microbes and the fibres they feed on.
- Repair the gut lining with nutrients that soothe and rebuild the barrier.
- Rebalance daily rhythms, because stress and sleep drive gut function.
When is it useful? This approach can be used by people with a wide range of gut and every health problems. It is particularly good when you have common IBS-type symptoms such as: bloating, non-specific abdominal pain, reflux, loose or hard stools, and discomfort after meals. It also helps after antibiotics, periods of high stress, travel bugs or a run of ultra-processed eating.
Why does it work? The sequence reduces triggers, improves digestion at the top of the chain, restores the microbiome, supports the intestinal barrier and calms the gut–brain axis. Small daily changes and improvements will stack up. Over a few weeks many people feel steadier.
Your simple 5R plan for this week’s sunday reset
Keep it food first, safe and practical. Choose one from each of Remove, Replace and Reinoculate. Add Repair or Rebalance if you have the bandwidth. Aim for tiny steps you can repeat and incorporate long term in your daily routine.
1) Remove
Remove the things which are harming your gut and your microbiome. Lighten the load so your gut can settle.
Try:
- Swap one ultra-processed meal for a whole-food bowl: protein, two fistfuls of veg, olive oil.
- Skip alcohol on weeknights.
- If you know foods which trigger your symptoms try eliminating them for 7 days and observe. Common culprits are milk, gluten/wheat, eggs, soy and ultra processed foods.
- If you want to go deeper you might want to work with a functional medicine practitioner who can run tests to see if you have any ‘bad’ bacteria or parasites which may need treatment.
2) Replace
Support the mechanics of digestion so food breaks down cleanly and absorbs well. In FM we start with “meal hygiene” before supplements.
Try:
- Slow eating: sit down, breathe, chew 15–20 times, put cutlery down between bites.
- Bitter signals: add rocket, watercress or radicchio to your main meal to nudge stomach acid and bile flow.
- Hydration timing: sip fluids between meals; avoid large gulps with food if you bloat.
- If meals feel heavy or you see undigested food, discuss a short trial of digestive enzymes with a clinician.
- Avoid self-prescribing HCl/betaine if you have reflux, ulcers or take NSAIDs. Get advice first.
3) Reinoculate
Rebuild balance by feeding and adding beneficial microbes. Food first with plenty of fibre (which feed your friendly bacteria) and fermented foods. If you want to try probiotics start with small amounts, then build.
Try:
- One fermented food daily: live yoghurt or kefir; non-dairy options like sauerkraut, kimchi or kombucha. Start with 2–3 forkfuls.
- Prebiotic fibre add-ons: 1 tbsp ground flax or chia; ¼ tin beans or lentils; onions, leeks, garlic, asparagus; cooked-and-cooled potatoes or rice for resistant starch.
- Plant diversity goal: aim for 20–30 different plants a week across veg, fruit, herbs, nuts, seeds, pulses.
- If very sensitive, introduce fibres gradually and increase water. Consider gentler options first (oats, cooked carrots, ripe bananas).
4) Repair
Soothe inflammation and give the gut lining what it needs to rebuild. Think protein, colour, and targeted support where appropriate.
Try:
- Protein at each meal plus two fistfuls of colourful veg at lunch and dinner.
- Omega-3s 2–3 times a week (salmon, mackerel, sardines) or a quality supplement, most people tolerate 1 to 2 grams per day of fish oil.
- Broth or quality stock in a mug 3–4 times this week, or use a collagen powder if tolerated.
- If already supplementing, discuss L-glutamine, zinc carnosine, or DGL with a clinician or functional medicine practictioner. Avoid liquorice products if you have high blood pressure or are on certain meds.
- Reduce gut irritants for now: excess alcohol, frequent NSAIDs, and large spicy/fatty meals, especially at night.
5) Rebalance
Tidy up the gut–brain axis and daily rhythm. Stress, sleep and movement change motility, microbiome tone and symptom thresholds.
Try:
- A 10-minute walk after your main meal to smooth blood sugar levels and improve the movement of the food through the gut (motility).
- A fixed sleep window and 5–10 minutes of morning light to anchor circadian rhythm.
- Five minutes of slow breathing before bed (box breathing 4-4-4-4).
- Mindful meals: no screens for the first 10 minutes; breathe, chew, notice.
- Caffeine window: all coffee before midday. Keep 3–4 alcohol-free nights.
If any of these steps flare symptoms, scale back and go slower. If you hit red flags (unintentional weight loss, blood, fever, night pain, persistent vomiting), speak to a clinician and consider using IFM’s Find a Practitioner to get support.
Make it stick
This week’s plan
Pick the changes you want to make from the list above, or pick your own, aim for one Remove, one Replace and one Reinoculate. Add Repair or Rebalance if life allows. Keep choices small enough to do daily.
Track one signal for 7 days
Choose one symptom you are struggling with, make a simple diary or tracker and note it each evening, for example:
- Bloating after dinner (0–10)
- Heartburn (0–10)
- Abdominal discomfort (0–10)
You are looking for a gentle shift towards better, not perfection.
One tiny next step
At your next meal, sit down and chew. Fifteen slow chews per mouthful. Concentrate of the flavour and texture of the food. Mindful eating improves digestion, try it, and notice the difference.
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Disclaimer
This article is education, not medical advice. Speak to your clinician before making changes, especially if you take medication or have a diagnosed condition.
