Inflammatory bowel disease & the microbiome

Inflammatory bowel disease (IBD) is complex, chronic, and deeply individual. This guide draws on the latest clinical evidence to help you understand what is happening in your gut — and what an integrative approach can offer alongside conventional care.

What is inflammatory bowel disease?

IBD is a chronic gastrointestinal condition characterised by persistent inflammation of the digestive tract. It affects millions of people worldwide and is most commonly divided into two main forms: Crohn’s Disease and Ulcerative Colitis (UC). Together, these conditions make up the vast majority of IBD cases.¹²

Own work, This file was derived from: Patterns of Crohn’s Disease.svg by Samir, vectorized by Fvasconcellos, CC BY-SA 3.0, via Wikimedia Commons

Crohn’s Disease

Crohn’s disease can affect any part of the gastrointestinal tract from the mouth to the anus, though it most commonly involves the last segment of the small intestine. Inflammation can affect the entire thickness of the bowel wall — and characteristically appears in “skip lesions” with patches of inflamed tissue separated by healthy segments.¹²

Ulcerative colitis

Ulcerative Colitis affects only the colon and rectum, with inflammation confined to the mucosa and submucosa- the innermost lining of the large intestine. Unlike Crohn’s, the ulceration in UC is continuous in nature and typically begins in the rectum, spreading proximally through the large bowel.¹²

Signs & symptoms of IBD

Both Crohn’s and UC share a similar set of intestinal symptoms, though severity and pattern vary considerably¹²:

• Abdominal pain and cramping
• Chronic diarrhoea
• Rectal bleeding
• Urgency to have a bowel movement
• Fatigue and low energy
• Unintentional weight loss
• Constipation (can alternate with diarrhoea)
• Nausea and reduced appetite

Extra-intestinal symptoms

IBD is a systemic condition, and inflammation can manifest beyond the gut:²⁴

• Musculoskeletal: Peripheral arthritis (type 1 & 2), axial spondyloarthritis, arthralgia
• Ocular: Uveitis, episcleritis
• Dermatological: Erythema nodosum, pyoderma gangrenosum

Complications of IBD

• Anaemia — iron deficiency, vitamin B12 deficiency, or anaemia of chronic disease
• Other nutrient deficiencies, especially folate (vitamin B9), vitamin D, zinc and magnesium
• Osteoporosis
• Intestinal strictures and fistulas
• Venous thromboembolism
• Increased long-term risk of colorectal cancer

How does IBD develop?

IBD arises from a complex interplay between genetic predisposition and environmental triggers. No single cause has been identified; the current evidence points to a multifactorial model:²⁵

• Genetics: A family history of IBD increases risk, though genes alone are insufficient
• Gut microbiome: Disruption to the balance of gut bacteria (dysbiosis) is both a contributor and consequence
• Environmental: Long-term medication use and environmental pollutants
• Stress: Chronic psychological stress is linked to flare onset and worsening disease activity
• Infections: Bacterial and viral infections can trigger or worsen flares
• Diet: Ultra-processed food consumption and low dietary diversity are associated with increased IBD risk²⁰²¹²³

A 2021 prospective cohort study published in the BMJ found that ultra-processed food intake was significantly associated with an increased risk of developing IBD, while a traditional whole-food dietary pattern was protective.²³

The role of the gut microbiome in IBD

The gut microbiome — the community of trillions of microorganisms living in the digestive tract — plays a central role in the development, perpetuation, and potential resolution of IBD.⁷⁹¹⁰

Microbiome patterns in Crohn’s Disease

These patterns can be seen on a stool microbiome test:

• Decreased microbial diversity overall
• Reduced butyrate-producing bacteria (particularly Faecalibacterium spp.)
• Reduced Akkermansia spp.
• Increased hexa-LPS-producing bacteria
• Increased oral species migrating to the gut
• Elevated Escherichia coli

Microbiome patterns in Ulcerative Colitis

These patterns can be seen on a stool microbiome test:

• Decreased microbial diversity
• Increased oral species in the gut
• Reduced Faecalibacterium spp.
• Elevated Escherichia coli and Proteobacteria signals

Pathogens and active flares

Infections are significantly more common during active IBD flares than during remission.⁶

• Clostridioides difficile has been identified in up to 26% of patients with active disease
• Non-C. difficile enteric infections are found in approximately 16–18% of symptomatic IBD tests
• UC cases show a higher prevalence of pathogenic E. coli strains, including EAEC and EPEC, compared to non-IBD controls
• Both Crohn’s and UC have higher rates of Campylobacter spp. compared to healthy individuals

Elevated E. coli enrichment (Proteobacteria dominance) has been associated with reduced responsiveness to anti-TNF medication in Crohn’s disease.³⁴ This highlights why understanding the microbiome may directly inform treatment decisions.

The microbiome in remission

Reaching clinical remission does not mean the microbiome has normalised. Even in remission, the gut microbiome in IBD patients remains impaired compared to healthy controls, with lower levels of beneficial SCFA-producing bacteria and higher inflammatory taxa.⁹¹⁰

• IBS-like symptoms can persist despite mucosal healing due to motility changes, visceral hypersensitivity, or SIBO⁹¹⁰¹³
• Baseline microbiome features can help predict future therapy intensification and relapse risk³⁴
• Higher Escherichia at the time of remission is associated with increased risk of relapse³⁵

Why microbiome testing can be helpful

Standard investigations for IBD — including blood tests, faecal calprotectin, and colonoscopy — are essential for diagnosis and monitoring. However, they do not provide insight into the specific microbial imbalances, immune function, and digestive markers that may be driving ongoing symptoms, contributing to flares, or preventing remission.

Comprehensive microbiome testing offers a deeper layer of clinical information that can meaningfully complement conventional care.

Microba’s Microbiome Explorer Comprehensive Test

Microba’s Microbiome Explorer Comprehensive is an advanced, clinically validated stool test providing a detailed analysis of the gut ecosystem. For individuals with IBD, it offers insight into areas that standard tests miss:

What It Measures	Clinical Relevance for IBD
Gut Microbiome Composition	Identifies which bacterial species are present and their relative abundance, compared to a healthy cohort — including key species relevant to IBD such as Faecalibacterium, E. coli, and pathogenic strains like EPEC and EAEC.
Inflammation Markers (Calprotectin & Lactoferrin)	Calprotectin >200 µg/g is strongly suggestive of active IBD and supports escalation of care. Lactoferrin >7.2 µg/g confirms active neutrophil-mediated mucosal inflammation.¹⁴¹⁵
Immune Function (Secretory IgA)	Secretory IgA is the gut’s first line of immune defence. Abnormal levels — low or high — can indicate immune dysregulation common in IBD.
Digestive Function (Pancreatic Elastase)	Provides insight into pancreatic enzyme output, helping identify why nutritional deficiencies may be persisting despite dietary changes.
Pathogen Screening	PCR-based detection of clinically relevant pathogens, including C. difficile, EPEC, EAEC, Campylobacter, and Dientamoeba fragilis, which may mimic or exacerbate IBD symptoms.
Microbial Functional Markers	Reports on hexa-LPS-producing microbes (systemic inflammation drivers), butyrate and propionate producers (mucosal healing support), hydrogen sulphide, trimethylamine, methane-producing archaea, and beta-glucuronidase activity.

When to consider microbiome testing

• Baseline assessment — establishing the microbial landscape before beginning treatment
• During a suspected flare, to identify whether infection is contributing and to guide antimicrobial or probiotic strategies
• Monitoring therapy response — tracking microbial shifts after dietary, supplement, or medication changes
• In apparent remission — to identify residual microbial imbalances that may predict relapse or explain ongoing IBS-like symptoms
• Annual monitoring — to track long-term microbial stability and guide preventative interventions

Repeat testing over time allows practitioners to track changes in key markers like faecal calprotectin, E. coli abundance, and butyrate-producing species — providing early warning of microbial regression before symptoms worsen. This proactive approach may help prevent escalation to more aggressive treatments.¹³

Diet & Lifestyle in IBD

No single diet has been found to consistently decrease flare rates in all adults with IBD. Dietary approaches should always be personalised to the individual’s disease state, tolerances, and nutritional status.

The Mediterranean Diet

A recent consensus from the American Gastroenterological Association highlights the Mediterranean diet as beneficial in IBD management:²³²⁴

• A wide variety of fresh fruits and vegetables
• Monounsaturated fats (olive oil, avocado)
• Complex carbohydrates and legumes
• Lean proteins, particularly small oily fish rich in omega-3
• Low intake of ultra-processed foods, added sugar, emulsifiers, and salt

Crohn’s Disease Exclusion Diet (CDED)

The Crohn’s Disease Exclusion Diet is a structured, evidence-based three-phase protocol designed to reduce gut inflammation in Crohn’s disease. When combined with Partial Enteral Nutrition (PEN), it has been shown to induce remission and promote favourable microbial changes:²⁴²⁶

• Increased Faecalibacterium prausnitzii
• Increased Bifidobacterium spp.
• Reduced E. coli and Fusobacterium

CDED + PEN has been shown to have better patient compliance than Exclusive Enteral Nutrition (EEN) due to the inclusion of whole foods, with comparable remission rates.

Integrative support alongside medical care

Integrative care for IBD works alongside — not instead of — conventional medicine. Gastroenterology remains essential for diagnosis, monitoring, and medical management. The goal of integrative support is to reduce the inflammatory burden, support the microbiome, restore nutritional status, and address the environmental and lifestyle factors that contribute to disease activity.

Evidence-Based Nutraceuticals

Here’s a selection of supplements that could be helpful in IBD. This is not an exhaustive list, and it doens’t mean all of these should be taken. It’s important to work with a trained practitioner who can advise which supplements are right for you and at what doses – this is crucial as low levels often don’t have the therapeutic effect.

SUPPLEMENT	PURPOSE & EVIDENCE
Curcumin (C3 complex)	An RCT found curcumin combined with mesalamine induced remission in mild-to-moderate UC. Anti-inflammatory and antioxidant support.²⁷
Fish oil (EPA + DHA)	Omega-3 fatty acids support inflammatory resolution and have been shown to improve colonic differentiation markers and reduce inflammatory signalling in UC.²⁸²⁹
Saccharomyces boulardii	Shown to reduce faecal calprotectin in active UC and to support microbial resilience.³¹
L. gasseri KS-13 / B. bifidum G9-1 / B. longum MM2	This three-strain combination has been shown to induce a less inflammatory cytokine profile and reduce E. coli overgrowth.³²³⁸
Glutamine + PHGG + Zinc carnosine	Supports mucosal gut healing, barrier integrity, and epithelial repair. Glutamine is the primary fuel source for enterocytes.
GOS (Galacto-oligosaccharides)	A prebiotic fibre shown to modulate the faecal microbiome and immune function.³⁰
Vitamin D	A 2024 systematic review found vitamin D supplementation effective in supporting the IBD disease course and immune functioning.³⁷

Ready to take action?

If you have persistent symptoms that don’t respond to the usual advice and treatment, please get in touch. The good news is that with the right testing, a personalised dietary and supplement plan, real improvement is possible.

Book a free 20-minute inquiry call today, and let’s have a chat.