Conditions & the gut

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.

Highly heterogeneous, so findings are less consistent than in IBD. This is where the contested parasites — Blastocystis and Dientamoeba — show up most, with genuinely mixed evidence.

Associations point to fewer butyrate producers and less Akkermansia — but many early findings were confounded by metformin, which itself reshapes the microbiome.

Home to famous but disputed claims. The Firmicutes/Bacteroidetes ‘obesity ratio’ is widely cited and largely unsupported — a useful lesson in skepticism.

Some of the strongest, mechanism-backed associations in the field — certain species are enriched in tumors and appear to actively drive them.

The gut-brain link is real but largely correlational and animal-model-heavy. Treat these as intriguing signals, not established causes.

A case where the microbiome story is causal and actionable: antibiotics collapse diversity, C. difficile overgrows, and restoring the community (e.g., faecal transplant) cures most cases.

A heavily-studied gut-brain condition. Note Akkermansia goes UP here but down in metabolic disease — proof that ‘good’ and ‘bad’ depend entirely on context.

Acute diarrheal infection — the one setting where specific organisms are direct causes rather than subtle associations, spanning viruses, parasites and bacteria.