The Role of the Microbiome in Chronic Disease

A Hidden Ecosystem With Visible Impact

We tend to think of chronic diseases as isolated events. An inflamed gut. Aching joints. A sluggish metabolism. A foggy mind. But what if many of these symptoms, and the conditions they belong to, had a shared origin? One that starts deep in the gut?

The human gut microbiome, made up of trillions of bacteria, fungi, and other microbes, plays a crucial role in how our bodies function, repair, and defend themselves. When this ecosystem is balanced, it quietly supports our health. But when it’s disrupted, a state known as dysbiosis, the ripple effects can show up far beyond the gut.

From Ulcerative Colitis (UC) and Crohn’s Disease to type 2 diabetes, autoimmune disorders, and even depression, microbiome imbalance has been linked to a growing list of chronic conditions. And while the research is still evolving, one thing is clear: the microbiome isn’t a side character in chronic disease; it’s often part of the origin story.

In this blog, we’ll unpack how the microbiome contributes to chronic disease, how it interacts with inflammation and intestinal permeability, and why it must be supported strategically, especially in people with IBD. We'll also explore how the Proviscera protocol addresses microbiome repair in a way that respects the timing, terrain, and complexity of the gut.

What Is the Microbiome, Really?

The microbiome is the collection of microorganisms living in and on the human body, and the vast majority of them reside in the gut. These trillions of bacteria, fungi, viruses, and other microbes aren’t passive residents. They help digest food, produce vitamins, regulate immune responses, and even communicate with the brain.

The microbiome is a kind of operating system for your gut. When it’s running smoothly, it keeps everything in balance,  from your digestion to your inflammation levels. But when that system is disrupted, things start to go wrong.

This disruption, known as dysbiosis, can mean a drop in beneficial bacteria, an overgrowth of harmful ones, or a lack of diversity in general. It’s not always dramatic. Sometimes, it’s a subtle, slow background shift that sets the stage for more serious issues.

In people with Inflammatory Bowel Disease (IBD), including Ulcerative Colitis (UC) and Crohn’s, dysbiosis is almost always present. And while it may not be the sole cause of disease, it plays a central role in how flares develop, how symptoms escalate, and how the gut struggles to repair itself.

How Microbiome Imbalance Fuels Chronic Disease

When the gut microbiome falls out of balance, it doesn’t just affect digestion. It alters immune function, increases gut permeability, and triggers inflammation, all of which can contribute to the development and progression of chronic diseases.

Inflammatory Bowel Disease (IBD) and the Microbiome

In people with Ulcerative Colitis (UC) and Crohn’s Disease, the microbiome is often significantly disrupted. Studies consistently show reduced microbial diversity, lower levels of protective species and an increase in pro-inflammatory strains.

This imbalance can weaken the gut lining, allowing particles to leak through, a phenomenon often referred to as “leaky gut.” The immune system, in turn, reacts aggressively, inflaming the intestinal walls and worsening symptoms. It becomes a vicious cycle: inflammation disrupts the microbiome, and a disrupted microbiome fuels more inflammation.

Crucially, certain microbial imbalances may even help trigger a flare, which is why Proviscera’s FLARE protocol holds off on probiotics and instead focuses on calming the system and supporting mucosal repair.

The Gut Health Triangle: Why the Microbiome Can’t Heal Alone

The microbiome is a key player in gut health, but it’s not the only one. At Proviscera, we talk about the Gut Health Triangle, which includes:

1. Dysbiosis (microbial imbalance)

2. Leaky gut (gut barrier dysfunction)

3. Chronic inflammation

These three elements don’t operate in isolation. They feed into one another in a self-perpetuating loop. When one corner is disrupted, the others often follow.

For example, dysbiosis can damage the gut lining, leading to increased permeability. This, in turn, allows bacteria and food particles to leak through, a phenomenon often referred to as “leaky gut.”, activating the immune system and triggering inflammation. That inflammation disrupts the microbiome even further, and the cycle continues.

It’s why single-focus solutions, like taking a probiotic or following an anti-inflammatory diet, often fall short. If you're only addressing one part of the triangle, you're unlikely to see lasting results.

Effective healing means addressing all three corners, but not all at once, and not in the same way for every person. In the context of Ulcerative Colitis, the right intervention depends on where you are in the disease cycle. And that’s exactly how the Proviscera protocol is structured.

Why Stage Matters: Timing Microbiome Support in IBD

When it comes to healing the microbiome in Inflammatory Bowel Disease (IBD), timing is everything.

It’s not just about what you take, it’s about when. The gut is a dynamic environment, and during an active flare, it behaves very differently than it does in recovery or remission. This is why the Proviscera protocol is staged, not stacked. Each phase, FLARE, REPAIR, and CARE, is designed to support the microbiome at the appropriate time, in the context of the Gut Health Triangle.

Let’s break it down.

FLARE: When Inflammation Is High and the Gut Is Under Siege

During an active flare, inflammation is acute, the mucosal lining is compromised, and the gut is highly reactive. This is not the time to introduce probiotics, even the “good” ones. In many cases, doing so can add fuel to the fire.

The FLARE protocol is designed specifically for this volatile window. It focuses on:

• Calming the immune response

• Controlling inflammation through gut-directed natural compounds

• Supporting mucosal healing and protecting the gut lining

This is the phase where you stabilise. The system is too sensitive for microbiome rebuilding, so we don’t push it. No probiotics are used here, by design.

REPAIR: After the Flare: A Window for Recovery

Here, the repair work begins.

In this post-flare window, the gut is still fragile but stable enough to start rebuilding. The REPAIR protocol offers targeted support for all three corners of the Gut Health Triangle:

• It provides gentle microbiome support through a curated probiotic blend, specifically selected for people with IBD. These strains have been shown to promote microbial recovery, reduce inflammation, and assist in restoring microbial diversity, without overwhelming the system.

• It supports the gut lining with nutrients and compounds that strengthen barrier function, reduce permeability, and assist in tissue repair.

• It continues to modulate inflammation at a tapered dose, helping the body transition from flare into full recovery.

This is where probiotics are reintroduced, but carefully, with intention, and only once the gut is ready.

CARE: When the Gut Is Stable and Ready for Long-Term Support

The CARE protocol is designed for remission when symptoms are settled, inflammation is low, and the goal is to maintain balance.

At this stage, the body can benefit from broad-spectrum probiotic support, including a diverse mix of strains for microbial balance, mucosal health, and immune regulation. These probiotics are chosen for their ability to enhance long-term resilience and help protect against future flares.

CARE also includes ongoing anti-inflammatory support to help keep inflammation in check and maintain gut lining integrity over time.

This is about long-term health. About stability. About helping the gut not just recover, but stay well.

Lifestyle Factors That Impact the Microbiome

While the Proviscera protocol forms the clinical foundation of microbiome repair, everyday lifestyle choices also shape the health of your gut ecosystem. These factors alone may not correct deep dysbiosis, especially in conditions like Ulcerative Colitis, but they can either support or sabotage your progress.

Here are some of the biggest players:

Diet
The microbiome thrives on diversity, and that starts with what you eat. Diets high in fibre, plant variety, and polyphenols feed beneficial bacteria. The American Gut Project has shown that people who eat a wider variety of plant foods tend to have more diverse and resilient microbiomes. On the flip side, ultra-processed foods, refined sugars, and emulsifiers can fuel inflammation and feed the wrong microbes. If your food is feeding you, it’s feeding your microbes too.

Stress
The gut and brain are in constant communication via the gut-brain axis. Chronic stress can alter microbial composition, reduce diversity, and even increase gut permeability. This is not as simple as “staying calm”; it’s more about recognising that emotional health and gut health are deeply connected.

Sleep
Sleep isn’t just restorative for you, it’s restorative for your microbes. Disrupted sleep patterns have been shown to negatively impact microbial diversity and increase inflammation. Aim for consistency and quality wherever possible.

Antibiotics and Medications
Antibiotics can be life-saving, but they’re also microbiome-wiping. After a course, your gut may need targeted support to recover, and not all bacteria bounce back on their own. Other medications, like PPIs and NSAIDs, can also alter microbial balance and gut barrier function.

Environment
Your microbes are shaped by the world around you, from the soil on your vegetables to the chemicals in your cleaning products. Over-sanitisation and lack of outdoor exposure. While you don’t need to live on a farm, small changes, like spending more time in nature or eating a variety of whole foods, can have an impact.

It’s important to remember: lifestyle supports the work, it doesn’t replace it. Especially in IBD, clinical-grade intervention is often necessary to correct the core imbalances. But once your microbiome is on the mend, these habits can help sustain and protect it.

Why the Microbiome Needs More Than Just Probiotics

If restoring gut health was as simple as taking a probiotic, many people with IBD would be in remission. But the truth is, probiotics, while valuable, are just one piece of the puzzle.

In a healthy person, adding a few billion CFUs of friendly bacteria might offer a short-term boost. But in someone with Ulcerative Colitis, Crohn’s, or another chronic condition marked by inflammation and barrier damage, the terrain is much more complex.

Probiotics Aren’t Always Helpful, Especially During a Flare
During an active flare, the gut is inflamed, the lining is fragile, and immune activity is heightened. Adding live bacteria at this stage, even well-studied strains, can increase symptoms, not reduce them. This is why Proviscera FLARE doesn’t include probiotics. First, we calm the system. Then, we rebuild.

Strain, Dose, and Delivery All Matter
Not all probiotics are created equal. Many over-the-counter options contain generic strains, low doses, or formulas that don’t survive digestion. Proviscera’s probiotic formulas are:

• Clinically selected for their relevance to IBD

• Dosed at therapeutic levels

• Delivered in enteric-coated capsules to survive stomach acid and reach the gut where they’re needed most

But even the best probiotic won’t be effective if the gut lining is compromised or if inflammation is still raging. That’s why we pair them with anti-inflammatory compounds and gut-lining support in REPAIR and CARE.

The Microbiome Needs a Supportive Environment to Thrive
Think of probiotics as seeds. They can only grow in soil that’s ready to receive them. That “soil” is your gut terrain, and it needs nutrients, reduced inflammation, and structural repair to support a healthy microbial community.

That’s why the Proviscera approach is layered, strategic, and stage-specific.
Because the goal isn’t just to add bacteria, it’s to create the conditions for lasting microbial balance.

The Microbiome Is a Mirror of Chronic Disease

Chronic disease rarely appears out of nowhere. It’s the result of long-term disruptions in how the body regulates inflammation, maintains its barriers, and interacts with its internal ecosystems. The gut microbiome is at the centre of all three, and when it’s out of balance, the entire system feels it.

For people with Inflammatory Bowel Disease, especially Ulcerative Colitis, the microbiome doesn’t just reflect the disease. It helps drive it. Which means that true, lasting relief can’t come from symptom suppression alone. It requires a strategic reset of the gut ecosystem, at the right time, in the right way. When the microbiome is supported wisely, it becomes one of the most powerful levers we have for long-term gut health.

Not sure which stage you're in or where to begin?

Take our assessment or reach out to our clinical team at clinic@proviscera.com for personalised support and guidance on the right next step for your gut.

FAQs

What is dysbiosis?

Dysbiosis refers to an imbalance in the gut microbiome, usually a loss of microbial diversity or a shift toward more harmful, pro-inflammatory strains. It’s been linked to a wide range of chronic conditions, including IBD, and is often both a symptom and a driver of disease.

Can probiotics fix my gut on their own?

Not likely. While probiotics can help restore balance, they’re only effective when the gut environment is ready for them. If inflammation is high or the lining is damaged, probiotics alone won’t make much of a difference, and in some cases, they can make symptoms worse. That’s why we use a phased, terrain-aware approach.

Why aren’t probiotics included in the FLARE protocol?

During an active flare, the gut is inflamed and hyper-reactive. Even beneficial bacteria can cause discomfort or worsen symptoms if introduced too soon. FLARE focuses on calming inflammation and protecting the gut lining, creating a safer foundation for microbiome work later on.

When is the right time to start probiotics?

Once flare symptoms have settled and the gut has had some time to recover. This is usually in the post-flare stage, when inflammation is under control and the mucosa is beginning to heal. That’s where the REPAIR protocol comes in.

Do I need to test my microbiome before starting Proviscera?

You don’t have to. While microbiome testing can be informative, it’s not essential for choosing the right protocol. The Proviscera system is designed around IBD-specific stages and symptoms, not test results alone. If you’re unsure, take our assessment, or our clinical team can guide you based on your symptom profile.

Can the microbiome affect my mood and mental health?

Yes. The gut and brain are connected through the gut-brain axis, and research shows that microbiome imbalances can contribute to anxiety, depression, and cognitive issues. This is especially relevant in IBD, where inflammation and gut dysfunction often spill over into mental health.

What’s the best probiotic for Ulcerative Colitis?

There isn’t one single “best” strain and more isn’t always better. The key is choosing clinically studied strains that are relevant to IBD, delivered in the right dose and format, and introduced at the right time. That’s the approach we take in both REPAIR and CARE.

What are postbiotics, and do I need them?

Postbiotics are the beneficial compounds produced by probiotics, like short-chain fatty acids (e.g. butyrate) that nourish the gut lining and reduce inflammation. While not essential to supplement directly, Proviscera includes ingredients like tributyrin (a butyrate source) to help mimic the benefits of a well-functioning microbiome, especially when yours is still recovering.

Do I need to take prebiotics as well?

Not separately. Once your gut is stable, prebiotics can help feed beneficial bacteria, but they need to be the right type, in the right amount. The Proviscera CARE formula includes a gentle, low-FODMAP prebiotic (IMO) that supports microbial balance without triggering bloating or gas. It’s designed specifically for long-term maintenance in IBD, when your gut is ready for support.