Faecalibacterium prausnitzii and Ruminococcus gnavus: The Gut's Tug of War

In IBD, the microbiome often shifts in a very specific way. Helpful species that protect the gut lining can drop, while others that thrive in inflammation have more room to grow. Two microbes that often show this imbalance are Faecalibacterium prausnitzii (a key peacekeeper) and Ruminococcus gnavus (which can stir up trouble when it overgrows).

Faecalibacterium prausnitzii: the quiet defender

Faecalibacterium is one of the main producers of butyrate, the short-chain fatty acid that fuels the gut lining and keeps the barrier strong. When F. prausnitzii is abundant, the gut is better nourished and more resilient.

It also helps guide the immune system. Faecalibacterium supports T-reg cells, which tell the immune system when to dial things down, and it influences cytokines in a way that reduces inflammation.Higher levels have even been linked with better responses to anti-TNF medications such as infliximab.

Ruminococcus gnavus: the one to watch

R. gnavus is a normal resident of the gut, but in Crohn’s disease it often rises when protective species are low. Some strains produce molecules that the immune system reads as a threat, triggering inflammatory cytokines.

It can also release enzymes that thin the mucus layer, the protective gel that keeps microbes at a safe distance. When this layer weakens:

• the immune system is more easily provoked

• the gut lining becomes more permeable

• mucus-loving microbes like Akkermansia may struggle

This creates the kind of environment where R. gnavus continues to thrive and inflammation keeps looping.

What I see in testing

In many children with Crohn’s or colitis, stool tests show the same pattern: Faecalibacterium prausnitzii low, Ruminococcus gnavus higher than ideal.

The encouraging part is that this can shift back. As inflammation settles and the gut lining heals, Faecalibacterium often returns naturally, and R. gnavus becomes less dominant.

Supporting the balance through food

Faecalibacterium thrives on gentle fermentable fibres such as resistant starch and inulin, many of which also support Bifidobacteria and Akkermansia. Helpful everyday options include:

• oats

• lentils

• cooked then cooled potatoes or rice

• green bananas

• onions, garlic, leeks, chicory root

Polyphenol-rich foods (berries, apples) and omega-3 fats also support a more stable microbial balance.

If your child is in a flare

High-fibre foods may feel uncomfortable. Softer, easier options can still provide fuel:

• mashed potatoes

• blended soups

• smoothies

• ripe bananas

• small amounts of oats

Fibre can be increased slowly as symptoms improve.

If your child has a stoma

Fibre tolerance may vary day to day. Gentle foods like oats, root vegetables, potatoes and ripe bananas are often easiest. Soft, blended or slow-cooked meals and cooled starches can still help support Faecalibacterium. Introduce new fibres gradually and monitor comfort.

Faecalibacterium prausnitzii and Ruminococcus gnavus - the balance

Faecalibacterium helps strengthen the barrier and calm inflammation. R. gnavus tends to grow when the mucus layer is weakened and inflammation is already high.

By creating the conditions that let protective microbes thrive, we support a steadier, calmer gut environment - and help shift the tug of war back toward balance.

For more about microbes that live in your gut and how to support - visit the microbes hub.