What Causes Gut Dysbiosis and How to Fix It

Understanding Gut Dysbiosis (and Why It Matters in IBD)

If you’ve been diagnosed with Ulcerative Colitis (UC), Crohn’s or another form of Inflammatory Bowel Disease (IBD), chances are you’ve heard the word dysbiosis tossed around, maybe in a clinic, maybe in a podcast, maybe in your own 2 am research spiral. It’s one of those words that sounds vague but feels important. And in the world of IBD, it is.

Gut dysbiosis refers to an imbalance in the microbial ecosystem of the gut,  the trillions of bacteria, viruses, and fungi that collectively make up your microbiome. When that ecosystem becomes disrupted, it can trigger or worsen inflammation, break down the gut lining, and leave you feeling like your digestive system is constantly working against you.

But here’s the part that’s often overlooked: fixing dysbiosis isn’t as simple as taking a probiotic and hoping for the best. In IBD, especially, the path to microbial recovery has to match where your body is in its healing journey. Because dysbiosis doesn’t stand alone, it’s tightly linked to inflammation and intestinal permeability, the other two corners of what we call the Gut Health Triangle.

In this blog, we’ll explore:

• What causes dysbiosis (especially in people with UC and Crohn’s)

• Why timing matters when trying to correct it

• And how the Proviscera protocol supports microbiome recovery in the right stage, at the right time

Let’s start with the basics and work our way back to balance.

What Exactly Is Gut Dysbiosis?

The Basics

Gut dysbiosis is the scientific term for what happens when the balance of your gut microbes goes off track. Under normal conditions, your microbiome is made up of a diverse community of beneficial bacteria that work together to support digestion, protect the gut lining, and help regulate immune responses. Around 70% of your immune system lives in the gut, and your microbes play a big part in keeping that system calm, focused, and non-reactive.

When dysbiosis sets in, that harmony breaks down. You might see a drop in microbial diversity, a loss of beneficial strains, or an overgrowth of less helpful (or even harmful) species. These changes can lead to poor digestion, immune overactivation, and a breakdown of the intestinal barrier, the perfect storm for people with IBD.

Dysbiosis and IBD: A Two-Way Street

Here’s where it gets even more complex: dysbiosis doesn’t just make IBD worse; IBD makes dysbiosis worse, too. The inflammation that characterises a UC or Crohn’s flare damages the gut lining and alters the microbial environment. That makes it harder for beneficial bacteria to survive, and easier for the wrong ones to thrive.

And when dysbiosis takes hold, it can trigger even more inflammation, weakening the barrier further and deepening the cycle.

This is why dysbiosis is one corner of the Gut Health Triangle, interconnected with inflammation and intestinal permeability. You can’t treat one without acknowledging the others. And you can’t fix dysbiosis by targeting microbes alone. It requires a phased, whole-system approach that meets your gut where it’s at.

What Causes Gut Dysbiosis?

Common Culprits in IBD

For people living with Ulcerative Colitis or Crohn’s, dysbiosis doesn’t usually come out of nowhere. It’s often the result of repeated hits to the gut ecosystem, some obvious, some invisible, that shift the balance over time. Here are the most common drivers of gut dysbiosis in IBD:

• Antibiotics: While sometimes necessary, antibiotics can wipe out both harmful and beneficial bacteria, leaving your microbiome stripped of its natural defences and diversity.

• Active Inflammation: The inflammatory process itself changes the gut environment. It makes the colon more hostile to beneficial bacteria and more favourable to pro-inflammatory species. That shift can happen during even a short-lived flare.

• Medications: Immunosuppressants, corticosteroids, and biologics may alter the microbiome as a side effect, sometimes helpful, sometimes disruptive. Their impact varies depending on the type and duration.

• Diet: A low-fibre, ultra-processed diet deprives good bacteria of the fuel they need to thrive. Additives like emulsifiers and artificial sweeteners can also negatively influence microbial balance and gut barrier integrity.
  
  

• Stress and Poor Sleep: Chronic stress and disrupted circadian rhythms affect the gut-brain axis, the two-way communication system between your gut and brain, which in turn influences microbial populations.

• Infections: A single bout of food poisoning, gastroenteritis, or even a cold can destabilise your microbiome and tip it into dysbiosis, especially if you’re already in a vulnerable state.

• Environmental Exposures: Toxins, pollutants, and endocrine disruptors in everyday products may have subtle, chronic effects on the gut microbiome over time.

Signs Your Gut Might Be in Dysbiosis

In People With IBD

The signs of gut dysbiosis aren’t always dramatic, and they don’t always show up in the gut. That’s part of what makes it tricky to pin down. But if you’re living with IBD, there are some patterns worth paying attention to:

• Your symptoms don’t match your inflammation markers. You’re not flaring, but things still feel “off”, maybe bloating, cramping, or fatigue that doesn’t fully resolve.

• You’re reacting to foods that used to feel safe. Increasing food sensitivities or post-meal discomfort can be a clue that your microbiome isn’t buffering digestion the way it should.

• Gas, bloating, and irregularity are common. Even outside of flares, these symptoms can indicate microbial imbalance, especially if they appear after antibiotics or a change in medication.

• Your skin is flaring up. Acne, rashes, or eczema-like symptoms can be downstream effects of microbial imbalance and intestinal permeability.

• You’re getting sick more often. A disrupted microbiome can reduce immune resilience, leading to frequent colds, lingering infections, or just a general sense of being run down.

• You’re foggy, flat, or fatigued. The gut-brain axis plays a huge role in mood, energy, and mental clarity, and dysbiosis often shows up here before it becomes obvious in the gut.

How It’s Measured (And Why Symptoms Still Matter)

Dysbiosis can be measured through comprehensive stool tests, which analyse microbial diversity, short-chain fatty acid production, and the presence of harmful or beneficial strains. But stool isn’t the only lens.

Other diagnostics also use blood (to look at immune and inflammatory markers) and urine (to detect microbial metabolites) to build a fuller picture of how the gut microbiome is functioning systemically. 

And while lab tests can be informative, they’re still just one piece of the puzzle. In clinical practice, symptoms and context matter just as much. That’s why the Proviscera protocol doesn’t rely on testing alone. It’s designed to meet your gut where it is, during a flare, after a flare, or in remission, with the right tools for the stage you’re in.

How to Fix Gut Dysbiosis

When it comes to rebuilding a healthy microbiome, timing matters. Especially if you’re living with Inflammatory Bowel Disease (IBD), trying to “fix” dysbiosis during the wrong phase, like the middle of a flare, can actually set you back.

The truth is: not every gut is ready for probiotics. Not every gut needs fibre right away. And not every symptom means it’s time for bacterial intervention.

That’s why the Proviscera system follows a staged approach, tailored to what your body can tolerate and benefit from at each point in your recovery. We don’t throw everything at the problem at once. We work in sync with your gut’s capacity to heal.

FLARE: Calm the Storm First

When you're in an active flare, dysbiosis is present, but it’s not the first priority.

The gut is inflamed, immune signalling is heightened, and the mucosal lining is often damaged. In this state, introducing probiotics or aggressive prebiotics can add to the chaos. The terrain is simply too unstable.

The Proviscera FLARE protocol is designed to:

• Reduce inflammation with high-dose curcumin, Qing Dai, and Boswellia

• Protect the gut lining with zinc carnosine and omega-3 fatty acids

• Not include probiotics, deliberately, to avoid overloading a reactive gut

While FLARE doesn’t directly rebuild the microbiome, it sets the stage by stabilising the environment.

REPAIR: Begin Microbiome Recovery Gently

Once flare symptoms have eased, your gut enters a critical but often overlooked window, the post-flare recovery phase. This is where true dysbiosis support begins.

The Proviscera REPAIR protocol was built for this moment. It addresses all three corners of the Gut Health Triangle, inflammation, gut lining, and microbiome, but in a balanced, post-flare-friendly way.

What’s Inside the REPAIR Probiotic (31.5 billion CFUs/day):

• Bifidobacterium longum  – 10.5 billion CFUs
  A foundational species shown to reduce inflammation and promote gut barrier function.

• Bacillus subtilis – 7 billion CFUs
  A spore-based strain that enhances microbial resilience and helps rebalance the ecosystem after a flare. Hardy, stable, and well tolerated.

• Weizmannia coagulans – 7 billion CFUs
  Supports microbial diversity and soothes common post-flare symptoms like bloating and irregularity.

• Lactiplantibacillus plantarum – 7 billion CFUs
  Reduces intestinal permeability, calms inflammation, and supports mucosal healing.

Additional Gut Repair Agents:

• L-Glutamine – fuels epithelial cells and supports barrier repair

• Tributyrin – a source of butyrate to nourish the colon and regulate immune activity

• Zinc Carnosine – helps seal the gut lining and reduce permeability

Tapered Anti-Inflammatory Support:

• Curcumin, Qing Dai, and Boswellia - included at tapered, post-flare doses to gently continue inflammation control while promoting repair

REPAIR is the foundation-laying phase. It’s where the microbiome starts to rebuild, the gut lining begins to seal, and the immune system starts learning how to calm down again. You’re no longer in a flare, but you’re not in the clear yet. REPAIR bridges that gap.

CARE: Maintain Microbial Balance in Remission

Once you’ve stabilised and your symptoms are minimal or absent, you move into the CARE stage, a maintenance phase focused on resilience, long-term immune support, and microbiome diversity.

The CARE protocol is designed for daily maintenance: to keep inflammation low, support immune resilience, and prevent the slow creep of dysbiosis from returning.

What’s Inside the CARE Probiotic (35 billion CFUs/day):

• Bifidobacterium longum – 10 billion CFUs
  One of the most clinically studied strains for reducing gut inflammation and regulating immune responses.

• Bacillus coagulans – 5 billion CFUs
  A spore-forming strain that survives harsh conditions, balances the microbiome, and requires no refrigeration.

• Lactobacillus plantarum – 5 billion CFUs
  Supports mucosal recovery by sealing leaky junctions in the gut lining.

• Bifidobacterium lactis – 5 billion CFUs
  Enhances microbial diversity, improves bowel regularity, and boosts immune function.

• Lactobacillus acidophilus  – 5 billion CFUs
  Promotes digestion, nutrient absorption, and overall gut health.

• Lactobacillus reuteri – 5 billion CFUs
  A mucosal-protective strain that supports long-term lining integrity by boosting mucin production.

Daily Anti-Inflammatory Support:

• Tributyrin continues to fuel colon cells and maintain barrier function

• Curcumin + Zinc Carnosine – help reduce inflammation and maintain tight junction integrity

CARE is your long-term support system. It helps you stay in remission, handle day-to-day triggers with more ease, and prevent small setbacks from spiralling into full-blown flares. It’s reinforcement for a gut that’s working hard behind the scenes to stay balanced.

Beyond Supplements: Lifestyle Support for a Balanced Gut

Supplements are powerful, but they’re only one part of the picture. If you’re living with Ulcerative Colitis (UC) or Crohn’s, your microbiome is constantly responding to your environment, not just what’s in your medicine cabinet. That’s why supporting microbial diversity and stability through daily habits is just as important as choosing the right protocol.

Diet: Diversity Over Perfection

There’s no single “IBD diet,” but one principle applies almost across the board: the more plant diversity you can tolerate, the better for your microbiome. That doesn’t mean stuffing yourself with raw kale mid-flare; it means gently increasing variety over time, based on your current stage.

• Aim for 30+ different plant types per week (grains, vegetables, fruits, nuts, seeds, herbs)

• Include prebiotic-rich foods if tolerated (e.g. cooked onion, garlic, oats, bananas, leeks)

• Avoid ultra-processed foods and additives like emulsifiers, which can worsen dysbiosis and permeability

• Consider polyphenol-rich foods like blueberries, green tea, olive oil, and fresh herbs, which feed beneficial bacteria and support gut barrier function

Tip: During FLARE, focus on simple, soothing foods. As you move into REPAIR and CARE, you can start reintroducing more variety with guidance from your symptoms (and ideally a practitioner).

Stress and Sleep: The Microbial Underdogs

The gut-brain axis is a hardwired, two-way communication channel. Your nervous system and your microbiome are constantly in conversation, and when stress is high or sleep is broken, that conversation starts to go sideways.

• Chronic stress can increase gut permeability and reduce microbial diversity

• Poor sleep disrupts circadian rhythms, which in turn affect microbial cycles

• People with IBD often report flare-ups after periods of emotional strain or sleep deprivation

Simple strategies that help:

• A consistent bedtime (even on weekends)

• Morning sunlight exposure to anchor your circadian rhythm

• Short daily stress relief rituals (breathwork, journaling, movement, etc.)

Movement: Gentle is Powerful

Exercise has been shown to positively shift the gut microbiome, increasing diversity and supporting immune regulation. But in IBD, the goal isn’t intensity, it’s consistency.

• Walking, yoga, Pilates, and swimming are all low-impact options that support circulation and lymphatic flow

• Resistance training (with guidance) can help rebuild strength after a flare

• Aim for movement that feels energising, not depleting

Note: During a flare, it’s okay to rest. Even gentle stretching or short walks count. The point is to reconnect with your body and gradually rebuild trust in what it can do.

There’s No One-Size-Fits-All Timeline

Gut dysbiosis isn’t a quick fix, and in IBD, it’s rarely a stand-alone problem. It’s part of an interconnected cycle with inflammation and leaky gut, each one feeding into the other. That’s why isolated efforts (like taking a random probiotic or cutting out a few foods) often fall short.

The key is to work with your gut, not against it and to support it in the right way, at the right time.

• During a flare, the focus is on calming inflammation and stabilising the gut lining.

• In the post-flare window, you can start the real work of microbial repair, but gently, and with the right tools.

• In remission, the goal is to build resilience and reduce the risk of relapse by supporting long-term balance.

The Proviscera protocol was built around these phases, FLARE, REPAIR, and CARE, because your gut doesn’t heal in a straight line. It heals in layers.

Whether you’re currently flaring, just coming out of one, or trying to stay in a stable place, there’s a version of support that fits you. And if you’re unsure where to start? We can help, just reach out to clinic@proviscera.com or take our assessment to get personalised guidance based on your current symptoms.

FAQs About Gut Dysbiosis and IBD

Can dysbiosis cause a UC flare?

Yes. Dysbiosis can increase inflammation and permeability, both of which may trigger a flare. That said, it also worsens during a flare, so it’s often both a cause and a consequence.

Should I take probiotics during a flare?

Not usually. When your gut is inflamed, even “good” bacteria can provoke unwanted immune responses. That’s why the Proviscera FLARE protocol skips probiotics entirely and focuses on calming the system first.

When should I start taking probiotics again?

Once your flare has settled and you’ve entered a post-flare recovery window, your gut is typically more receptive. This is where the REPAIR protocol comes in; it uses four targeted strains chosen specifically for IBD recovery.

How do I know which stage I’m in?

It depends on your current symptoms, how recently you flared, and whether you’re on any medications. You can take our assessment or contact clinic@proviscera.com for support.

Can I test for dysbiosis?

Yes, stool, blood and urine tests provide helpful markers. However, testing isn’t always necessary. In many cases, symptoms and clinical history are just as telling.

What if I’ve been on antibiotics recently?

Recent antibiotic use is a common trigger for dysbiosis. If you’re post-flare or symptom-stable, the REPAIR protocol is often a good place to start to help rebuild the microbial terrain.