Condition

Inflammatory bowel disease (IBD)

10 associated organisms · Crohn’s and ulcerative colitis show some of the most reproducible shifts of any condition — and uniquely, changes across all five domains: fewer anti-inflammatory bacteria, more Candida and Malassezia, fewer protective parasites, and a disturbed phage community.

Symptoms of Inflammatory bowel disease (IBD) can need medical evaluation. Treat these associations as background context only — please see a doctor rather than self-treating.
Organisms associated with Inflammatory bowel disease (IBD)
Faecalibacterium prausnitzii Beneficial Reduced in Inflammatory bowel disease (IBD)
Species

Depletion of this anti-inflammatory butyrate producer is among the most consistently replicated IBD findings.

Well-replicated source: curated sample
Overall diversity Community metric Reduced in Inflammatory bowel disease (IBD)
Community metric

Reduced richness is a hallmark of active disease across nearly all cohorts.

Well-replicated source: curated sample
Roseburia Beneficial Reduced in Inflammatory bowel disease (IBD)
Genus

Butyrate producers decline alongside Faecalibacterium, weakening anti-inflammatory tone.

Moderate evidence source: curated sample
Escherichia coli Opportunist Elevated in Inflammatory bowel disease (IBD)
Species

Adherent-invasive strains are enriched, especially in Crohn’s — a strain-level, not species-level, story.

Moderate evidence source: curated sample
Candida albicans Opportunist Elevated in Inflammatory bowel disease (IBD)
Yeast · species

Enriched in Crohn’s and shown to amplify pro-inflammatory cytokines, creating a vicious circle with inflammation.

Moderate evidence source: curated sample
Malassezia restricta Contested Elevated in Inflammatory bowel disease (IBD)
Yeast · species

Expanded in Crohn’s and shown to worsen colitis in mice via the IBD-linked CARD9 gene; tracks treatment escalation.

Moderate evidence source: curated sample
Saccharomyces cerevisiae Beneficial Reduced in Inflammatory bowel disease (IBD)
Yeast · species

This generally protective yeast is depleted in Crohn’s and correlates with the beneficial bacteria that are also lost.

Moderate evidence source: curated sample
Helminths (soil-transmitted) Contested Reduced in Inflammatory bowel disease (IBD)
Helminths (worms)

Largely absent in industrialized populations where IBD is common; their immunomodulation may be protective, and controlled exposure has been trialed as therapy.

Moderate evidence source: curated sample
Blastocystis Contested Reduced in Inflammatory bowel disease (IBD)
Protozoan (protist)

Consistently LESS common in IBD than in healthy people, hinting at a protective or health-marker role rather than a harmful one.

Moderate evidence source: curated sample
Bacteriophages Regulator Mixed in Inflammatory bowel disease (IBD)
Phage community

Virome disturbance is real and can even worsen colitis in mice, but reports conflict — some find loss of protective mucosal phages, others expansion.

Moderate evidence studies conflict source: curated sample
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