Why your microbiome matters in IBD

Your gut is home to trillions of bacteria, fungi, and other microorganisms that make up the gut microbiome, a living ecosystem that plays a critical role in digestion, nutrient absorption, immune regulation, and inflammation control. When this ecosystem is in balance, it supports overall health. When it’s disrupted, a state called dysbiosis, it can fuel chronic inflammation and worsen conditions like Ulcerative Colitis (UC) and Crohn’s disease

For people with IBD, the microbiome is directly linked to how the gut lining functions, how the immune system behaves, and how severe flare-ups become. This connection is part of what we call the Gut Health Triangle: microbiome health, gut barrier integrity, and inflammation control. All three corners of this triangle work together, and all three can be influenced by the food you eat.

But here’s the key: the best foods for your microbiome aren’t always the same at every stage of IBD. What you can tolerate in remission (CARE) might be very different from what you can handle during a flare (FLARE) or in the post-flare recovery window (REPAIR). Knowing how to fuel your microbiome at the right time can make the difference between supporting recovery and accidentally setting back your progress.

In this guide, we’ll look at the foods that help your microbiome thrive, the ones that can cause more harm than good, and how to adapt your diet to your IBD stage, so you can support gut healing without adding unnecessary strain.

What your microbiome thrives on

A healthy microbiome is like a well-fed garden; it needs the right fuel to grow beneficial bacteria and keep harmful ones in check. For people with Ulcerative Colitis (UC) or other forms of Inflammatory Bowel Disease (IBD), feeding that “garden” is a balancing act. Too much of the wrong thing, or even too much of the right thing at the wrong time, can tip you into discomfort or even trigger symptoms.

Below are the core food groups that have been shown to support microbiome health, along with stage-specific guidance for FLARE, REPAIR, and CARE.

Fibre, but at the right time

Fibre is the microbiome’s favourite fuel. It’s fermented by gut bacteria into short-chain fatty acids like butyrate, which nourish the cells lining your colon and help regulate inflammation. But there’s a catch: not all fibre is easy on an inflamed gut.

Why it matters in IBD:

• Soluble fibre (found in oats, peeled apples, carrots) forms a soothing gel in the gut and feeds beneficial bacteria.

• Insoluble fibre (in raw greens, whole nuts, and seeds) can be rough on an already sensitive intestinal lining, especially during a flare.

Stage-based guidance:

• FLARE: Keep fibre very low. Focus on low-residue foods that reduce mechanical irritation, such as white rice, well-cooked peeled vegetables, and tender protein.

• REPAIR: Slowly reintroduce soluble fibre. Start with well-cooked carrots, pumpkin, zucchini (peeled), or oatmeal.

• CARE: Aim for a wide variety of fibre types to support a diverse microbiome. Include soluble, insoluble, and resistant starch sources as tolerated.

Resistant starches and gentle prebiotics

Not all carbohydrates are created equal when it comes to microbiome health. Resistant starches are a type of carbohydrate that resists digestion in the small intestine, travelling to the colon where they become prime fuel for beneficial bacteria. This fermentation process helps produce short-chain fatty acids like butyrate, which support gut barrier integrity and help regulate immune responses, both key in Ulcerative Colitis (UC) and other IBD conditions.

Examples of resistant starches:

• Cooked and cooled white potatoes

• Green (unripe) bananas

• Cooked and cooled rice or oats

• Legumes (in CARE stage only, unless otherwise tolerated)

Gentle prebiotics, non-digestible fibres that feed good bacteria, can be especially helpful in the REPAIR and CARE stages. One example is isomaltooligosaccharide (IMO), a low-FODMAP prebiotic used in the Proviscera CARE formula. It’s designed to feed beneficial strains without triggering bloating, gas, or other common prebiotic side effects.

Stage-based guidance:

• FLARE: Avoid resistant starch and prebiotics; the goal is to reduce bacterial fermentation until inflammation settles.

• REPAIR: Introduce small amounts of resistant starches and low-FODMAP prebiotics to begin rebuilding microbial diversity.

• CARE: Include a variety of resistant starch sources regularly to maintain microbiome balance and resilience.

(Cleveland Clinic – Nutritional Plan for UC and Crohn’s)

Polyphenol-rich foods

Polyphenols are plant compounds with powerful antioxidant and anti-inflammatory properties, and your microbiome loves them. Many beneficial gut bacteria can use polyphenols as fuel, and in return, they transform these compounds into bioactive molecules that help regulate inflammation, protect the gut lining, and even support immune balance.

For people with Ulcerative Colitis (UC) or Inflammatory Bowel Disease (IBD), this two-way relationship can be a valuable tool for long-term gut health. However, the way you introduce polyphenol-rich foods should still be stage-appropriate.

Examples of polyphenol-rich foods:

• Blueberries and blackberries (pureed during REPAIR for easier digestion)

• Green tea

• Extra virgin olive oil

• Pomegranate

• Cocoa (unsweetened)

Stage-based guidance:

• FLARE: Limit polyphenol-rich foods unless they’re very gentle (e.g., small amounts of well-steeped green tea, extra virgin olive oil drizzled over soft foods).

• REPAIR: Begin introducing berries in pureed or well-cooked form and small amounts of pomegranate juice.

• CARE: Include a variety of polyphenol sources regularly to help maintain microbial diversity and support anti-inflammatory pathways.

Foods that disrupt your microbiome

Just as some foods help beneficial bacteria flourish, others can tip the microbiome into dysbiosis, encouraging the growth of strains linked to inflammation, gut barrier damage, and symptom flares in Ulcerative Colitis (UC) and Inflammatory Bowel Disease (IBD).

These aren’t always “bad” foods for everyone, but during certain stages of IBD, they can set back recovery or make symptoms worse.

Ultra-processed foods

Why they’re a problem:
Many ultra-processed foods contain emulsifiers, artificial sweeteners, preservatives, and stabilisers that can alter the gut microbiome. Some emulsifiers, like carboxymethylcellulose and polysorbate-80, have been shown in studies to increase gut permeability and trigger low-grade inflammation.

Examples:

• Packaged snack cakes, biscuits, and pastries

• Flavoured crisps and chips

• Processed meats with additives

• Ready-made sauces with long ingredient lists

Stage-based guidance:

• FLARE: Avoid completely; these add unnecessary stress to the gut.

• REPAIR: Continue avoiding while the microbiome and gut barrier are still fragile.

• CARE: Limit to occasional treats, always balancing with whole, minimally processed foods.

(Direct impact of commonly used dietary emulsifiers on human gut microbiota)

Excess refined sugar and alcohol

Why they’re a problem:
Refined sugars can feed inflammatory bacterial strains and encourage overgrowth of yeast species like Candida. Alcohol, meanwhile, can thin the gut lining and disrupt microbiome composition, even in small amounts.

Examples:

• Sugary sodas and energy drinks

• Sweets and confectionery with added sugars

• Beer, wine, and spirits

Stage-based guidance:

• FLARE: Avoid entirely, both sugar and alcohol can worsen symptoms and inflammation.

• REPAIR: Keep sugar low and alcohol minimal to prevent microbiome setbacks.

• CARE: Small amounts of natural sweeteners (e.g. honey, maple syrup) may be tolerated, but alcohol should still be limited.

Problematic FODMAPs (for some)

FODMAPs, short for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols, are certain types of carbohydrates that can ferment rapidly in the gut, producing gas and drawing water into the bowel. While they can be healthy for many people, in the context of Ulcerative Colitis (UC) or Inflammatory Bowel Disease (IBD), they may trigger bloating, cramping, and diarrhoea, especially when the gut lining is still healing.

Examples of high-FODMAP foods:

• Onions, garlic, cauliflower, and mushrooms

• Certain legumes (beans, lentils, chickpeas)

• Apples, pears, and stone fruits

• Sweeteners like sorbitol, mannitol, and xylitol

Stage-based guidance:

• FLARE: Avoid high-FODMAP foods to reduce gas, bloating, and bowel urgency.

• REPAIR: Gradually reintroduce low-FODMAP versions of these foods, monitoring tolerance.

• CARE: Slowly expand variety, many people can tolerate moderate FODMAP intake in remission, but it’s individual.

Matching your diet to your stage

The best foods for your microbiome, and the ones to avoid, aren’t fixed. They shift depending on whether you’re in an active flare (FLARE), recovering post-flare (REPAIR), or in long-term remission (CARE). Choosing stage-appropriate foods is one of the most effective ways to protect the gut barrier, support microbiome diversity, and control inflammation in Ulcerative Colitis (UC) and Inflammatory Bowel Disease (IBD).

FLARE phase

Priority: Calm inflammation and reduce mechanical and fermentative stress on the gut.

• Focus on:

• Low-residue, low-fibre foods (white rice, peeled and well-cooked carrots, pumpkin, tender chicken, fish)

• Healthy fats in small amounts (extra virgin olive oil, avocado oil)

• Gentle hydration with broths and diluted electrolyte solutions
  

• Avoid:

• High-fibre foods (especially raw vegetables and whole grains)

• Probiotic supplements (can overstimulate an inflamed gut)

• High-FODMAP foods, sugar, alcohol, and ultra-processed foods

REPAIR phase

Priority: Restore microbiome diversity while supporting gut lining recovery.

• Focus on:

• Soluble fibres (oats, peeled apples, pumpkin, zucchini)

• Resistant starches (cooled potatoes, green bananas, cooled rice)

• Gentle prebiotics (low-FODMAP options like IMO)

• Omega-3-rich foods (salmon, sardines, flaxseed oil)
  

• Avoid:

• Sudden introduction of multiple new fibre sources

• Large portions of high-FODMAP foods

• Ultra-processed foods that can trigger dysbiosis

CARE phase

Priority: Maintain microbiome resilience and reduce inflammation risk long-term.

• Focus on:

• A wide variety of plant-based foods for fibre diversity

• Fermented foods (yoghurt, kefir, sauerkraut) if tolerated

• Polyphenol-rich foods (berries, pomegranate, green tea, olive oil)

• Balanced intake of prebiotics and probiotics for ongoing microbial support
  

• Avoid:

• Slipping back into a low-diversity diet

• Overreliance on processed snacks or high-sugar treats

Practical tips for feeding your microbiome daily

Knowing what to eat is only half the story; the real change happens when you make it part of your daily routine. For those living with Ulcerative Colitis (UC) or Inflammatory Bowel Disease (IBD), consistency matters, but so does flexibility. Your gut will have good days and sensitive days, and the right food strategy adapts to both.

1. Rotate plant foods
The microbiome thrives on variety. Even small swaps, like alternating between pumpkin, carrots, and zucchini, can introduce new fibres that feed different bacterial species.

2. Prep foods for easier digestion
Cooking methods matter. Steaming, roasting, peeling, or pureeing vegetables can make fibre gentler on the gut while still providing prebiotic benefits.

3. Track your tolerance
A simple food journal can help identify which foods feel supportive and which trigger symptoms. This is especially helpful when reintroducing fibre or high-FODMAP foods in the REPAIR and CARE phases.

4. Hydrate strategically
Adequate fluids support digestion, nutrient absorption, and mucosal health. Aim for water, diluted herbal teas, or electrolyte solutions, especially if you’ve experienced diarrhoea during a flare.

5. Introduce changes gradually
Jumping from a low-fibre FLARE diet straight into a high-diversity CARE diet can overwhelm the microbiome and cause discomfort. Add one new fibre-rich or fermented food at a time, watching for tolerance.

Where Proviscera fits in

Food is the foundation of microbiome health, but during Ulcerative Colitis (UC) and Inflammatory Bowel Disease (IBD), diet alone often isn’t enough to fully restore balance. This is where targeted supplementation, aligned with your IBD stage, can make the process more effective and predictable.

FLARE – Calming inflammation before rebuilding

• In an active flare, the microbiome is often unstable, and the gut lining is inflamed.

• Proviscera FLARE delivers high-dose, gut-targeted anti-inflammatories like Qing Dai, curcumin, and Boswellia, alongside omega-3s and zinc carnosine to protect and support the gut lining.

• No probiotics are included at this stage; adding them too soon can cause unnecessary stress to an inflamed system.

REPAIR – Restoring microbiome diversity and gut barrier integrity

• Once symptoms have eased, REPAIR works on all three corners of the Gut Health Triangle: microbiome, gut barrier, and inflammation.

• Contains tapered doses of Qing Dai, curcumin, and Boswellia, plus L-glutamine, tributyrin, omega-3s, and zinc carnosine for gut lining support.

• Includes targeted probiotics clinically relevant to IBD, plus gentle low-FODMAP prebiotic IMO to feed beneficial strains without triggering discomfort.

CARE – Maintaining resilience long-term

• CARE supports a stable microbiome, ongoing gut barrier health, and inflammation control in remission.

• Combines targeted probiotics (six clinically studied strains) with prebiotic IMO for daily microbial support.

• Curcumin, omega-3s, tributyrin, and zinc carnosine help protect the gut lining and keep inflammation in check.

When paired with the right foods for your stage, these formulas help break the cycle of inflammation, dysbiosis, and barrier damage, setting the stage for a more stable, resilient gut.

FAQs

1. Should I take probiotics during a flare?
Not usually. During a flare, the gut is inflamed and more reactive. Adding probiotics too soon can worsen symptoms. It’s better to wait until the REPAIR phase, when inflammation has calmed, before introducing targeted strains.

2. Can I eat fermented foods with UC or Crohn’s?
Some people tolerate fermented foods like yoghurt, kefir, or sauerkraut well in CARE, but they can be too stimulating during a flare. Start small in REPAIR and monitor how you feel.

3. What’s the difference between prebiotics and probiotics?
Probiotics are live bacteria that can benefit your gut. Prebiotics are the fibres and compounds that feed those bacteria. Both are important, but timing matters.

4. How quickly can diet changes affect the microbiome?
Research suggests noticeable shifts can happen in just a few days, but lasting diversity comes from consistent, long-term changes.

5. Is a plant-based diet better for IBD?
A varied, plant-rich diet can help maintain microbiome diversity, but it should be tailored to your stage and tolerance. Some plants need to be peeled, cooked, or pureed during sensitive periods.

Long-term gut health starts here 

Your microbiome is a powerful ally in managing Ulcerative Colitis (UC) and Inflammatory Bowel Disease (IBD), but only if you feed it the right way, at the right time. By aligning your diet with your IBD stage, you can give beneficial bacteria what they need to thrive while avoiding foods that can disrupt the balance.

The FLARE, REPAIR, and CARE phases of the Proviscera protocol are designed to work alongside this stage-based approach, calming inflammation, supporting gut barrier integrity, and restoring microbial diversity step by step.

If you’re unsure where to start, take the Proviscera Quiz or reach out to us at clinic@proviscera.com for guidance. The right foods, the right supplements, the right timing, that’s how you fuel a microbiome that fuels you back.