Is Faecalibacterium prausnitzii good or bad?

It is a beneficial commensal. Healthy levels are generally favourable; low levels are associated with gut inflammation in research and may reflect dysbiosis.

How does the GI-MAP measure it?

The GI-MAP uses quantitative PCR (qPCR) to detect and quantify F. prausnitzii DNA, reporting an actual amount rather than just present/absent.

Faecalibacterium prausnitzii: A Keystone Gut Microbe

Faecalibacterium prausnitzii is an anti-inflammatory, butyrate-producing commensal. The GI-MAP quantifies it as a beneficial-flora marker.

Educational overview · Medically reviewed by Madison Ordway, FDN-P

Key facts

What it is: an anti-inflammatory, butyrate-producing commensal bacterium.
On the GI-MAP: quantified as a beneficial-flora (commensal) marker.
Why it matters: low levels are associated with inflammatory bowel disease in research.
Method: quantitative PCR (qPCR).

Faecalibacterium prausnitzii is one of the most abundant bacteria in a healthy human gut and a major producer of butyrate, a short-chain fatty acid that feeds the cells of the colon. It is considered a keystone, anti-inflammatory commensal, and the GI-MAP (Gastrointestinal Microbial Assay Plus) quantifies it among the beneficial/commensal flora.

Why it is called a keystone microbe

A landmark study identified F. prausnitzii as an anti-inflammatory commensal that was notably reduced in patients with Crohn disease, and showed its metabolites calmed inflammation in laboratory and animal models (PMID: 18936492).

A later meta-analysis of 11 studies confirmed that F. prausnitzii is significantly reduced in inflammatory bowel disease, with a greater reduction in Crohn disease than in ulcerative colitis (PMID: 24799893). Low levels are therefore often read as a marker of reduced anti-inflammatory capacity in the gut.

What a low level suggests

On a GI-MAP report, a low F. prausnitzii sits under the beneficial/commensal category and can point toward dysbiosis or reduced butyrate production. It is interpreted together with the rest of the microbiome profile; it is not a diagnosis of any disease.

The GI-MAP™ reports this and 85+ other markers from one at-home sample.

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References

Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA. 2008;105(43):16731–16736. PMID: 18936492.
Cao Y, Shen J, Ran ZH. Association between Faecalibacterium prausnitzii reduction and inflammatory bowel disease: a meta-analysis and systematic review of the literature. Gastroenterol Res Pract. 2014;2014:872725. PMID: 24799893.

Medically reviewed by

Madison Ordway, FDN-P

Functional Diagnostic Nutrition Practitioner specializing in gut health, hormone balance and mineral optimization. Madison uses GI-MAP testing in her work with clients and has been featured in US Insider, Women’s Journal and The Science Times. See press features →

Content reviewed against Diagnostic Solutions Laboratory documentation and peer-reviewed literature. Last reviewed 6 July 2026.

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