Faecalibacterium spp.

Faecalibacterium spp. are a group of beneficial, butyrate-producing bacteria important in maintaining gut health and immune balance.

 Recent research reveals that this genus is more diverse than previously recognized, highlighting its potential as both a biomarker and therapeutic target for various gut and systemic diseases.

What is Faecalibacterium spp.?

Faecalibacterium is a genus of beneficial bacteria that live in the human gut. It belongs to the Firmicutes phylum, specifically within the Ruminococcaceae family. 

These bacteria are Gram-positive, rod-shaped, non-motile, and strictly anaerobic, meaning they can only survive in environments without oxygen.

The most well-known species is Faecalibacterium prausnitzii, which can comprise around 5% of the total bacteria in a healthy person's stool. It has gained attention for supporting gut health and reducing inflammation, and it is now considered one of the most promising next-generation probiotics (NGPs).

Role in the Gut Microbiota

In a balanced microbiome, Faecalibacterium spp. are abundant and serve critical roles. They help break down complex plant fibers into short-chain fatty acids (SCFAs), especially butyrate, which supports gut barrier function and helps regulate the immune system. 

New research shows this genus is more diverse than previously thought, including at least 22 species-level clades, some with unique functions and health benefits. 

The diversity of Faecalibacterium is now seen as a more accurate marker of gut health than just the total abundance alone.

The Importance of Faecalibacterium spp. in Gut Health

Faecalibacterium spp. are foundational to overall gut health in humans for many reasons, especially due to their:

Butyrate Production

One of the key contributions of Faecalibacterium spp. is its ability to produce butyrate, a SCFA that serves as the primary energy source for colonocytes (the cells lining the colon). 

Butyrate supports gut barrier integrity, reduces oxidative stress, and helps maintain the mucosal lining. It also has systemic anti-inflammatory effects, supporting gut and whole-body health.

Anti-Inflammatory Mechanisms

Faecalibacterium spp. produce metabolites—such as microbial anti-inflammatory molecules (MAMs) and salicylic acid—that calm immune responses. 

These molecules can block inflammatory pathways like NF-κB and promote regulatory T cells, which help keep inflammation in check. The result is a more balanced immune response in the gut and throughout the body.

Faecalibacterium prausnitzii: A Key Gut Health Biomarker

Faecalibacterium prausnitzii is one member of the Faecalibacterium spp. genus, and one of the most abundant and beneficial bacteria in the human gut due to its role in maintaining intestinal health. 

F. prausnitzii produces butyrate, a short-chain fatty acid essential for colonocyte energy, gut barrier integrity, and inflammation control. Additionally, F. prausnitzii secretes anti-inflammatory molecules that inhibit NF-κB activation, promote IL-10 production, and support regulatory T-cell responses, contributing to mucosal immune homeostasis.

Clinically, F. prausnitzii is consistently depleted in patients with IBD (Crohn's disease and ulcerative colitis), colorectal cancer, and, in some cases, IBS. Its reduction is associated with disease activity and mucosal inflammation in IBD. 

Two main phylogroups (I and II) show different depletion patterns, with phylogroup I more broadly affected across gut disorders, making it a promising diagnostic and prognostic biomarker.

Its abundance is sensitive to gut environmental factors (pH, oxygen, bile salts) and nutritional substrates (e.g., pectin, inulin), suggesting potential for targeted microbiota-modulating therapies. 

Given its consistent association with gut health, F. prausnitzii represents a clinically relevant biomarker that should be included in microbiome-based diagnostic strategies.

Who Should Get Faecalibacterium spp. Levels Assessed?

The following groups of people may benefit from Faecalibacterium spp. testing:

Individuals with Suspected Gut Dysbiosis

Low levels of Faecalibacterium spp. are commonly seen in people with disrupted gut microbiomes.

Inflammatory Bowel Disease (IBD)

Conditions like Crohn’s disease and ulcerative colitis show consistent reductions in Faecalibacterium, particularly F. prausnitzii, along with increased inflammation and impaired gut barrier function.

Irritable Bowel Syndrome (IBS)

Although the data are less consistent, individuals with IBS—especially IBS-M (mixed IBS, fluctuating between constipation and diarrhea)—often show reduced diversity of beneficial microbes, including Faecalibacterium.

Individuals with Other Related Health Conditions

People with other chronic health conditions may consider Faecalibacterium spp. testing:

Metabolic Disorders

Lower Faecalibacterium levels have been linked to obesity, insulin resistance, and type 2 diabetes. These individuals often have less microbial diversity overall, contributing to systemic inflammation.

Allergic and Autoimmune Conditions

Reduced Faecalibacterium diversity is also observed in atopic dermatitis and asthma, and may be associated with autoimmune diseases like rheumatoid arthritis, suggesting a connection between gut health and immune function.

Chronic Infections

Individuals struggling with chronic infections such as COVID-19 or HIV may consider Faecalibacterium spp. testing due to the connection between gut health and immune function.

People with HIV or severe COVID-19 often have low levels of this bacteria, which may contribute to worse immune function and increased inflammation.

What Do Low Levels of Faecalibacterium spp. Mean?

Low levels of butyrate producers like Faecalibacterium spp. can weaken the gut barrier, allowing toxins and bacteria to pass into the bloodstream—a process known as leaky gut. This increases the risk of chronic inflammation, contributing to gut and systemic diseases. 

Studies show that lower Faecalibacterium diversity is often linked to more severe disease symptoms in IBD and other conditions.

Factors Contributing to Low Levels

The following factors may affect Faecalibacterium spp. levels:

Diet

Low fiber intake and high consumption of processed foods reduce the nutrients needed to support Faecalibacterium growth.

Antibiotic Use

Antibiotics can wipe out beneficial microbes, including Faecalibacterium, and it can take weeks or months to recover.

Other Factors

Stress, poor sleep, certain medications (e.g., NSAIDs, proton pump inhibitors), and environmental toxins can also affect microbial balance.

Taking The Test: Sample Collection

Faecalibacterium is typically tested using stool samples, which can be conveniently collected at home. 

Patients are advised to avoid medications and supplements, including probiotics, before collection. Always follow the lab company's recommendations regarding preparation and sample collection.

What Do High Levels of Faecalibacterium spp. Mean?

A good presence of Faecalibacterium spp.—especially with diverse clades—is a sign of a healthy gut. High levels are often seen in people who eat fiber-rich, plant-based diets and maintain healthy lifestyles.

Overgrowth Considerations (Rare)

There's little evidence that Faecalibacterium overgrowth causes harm. However, balance matters—an overabundance of one microbe, even a beneficial one, might indicate reduced overall diversity. The key is microbial harmony, not just high numbers of one species.

Maintaining Optimal Faecalibacterium spp. Levels

The following dietary and lifestyle factors may support a healthy gut microbiome: 

Dietary Habits

To support Faecalibacterium, eat more:

• Soluble fiber (e.g., oats, legumes, vegetables)
• Resistant starch (e.g., cooked and cooled potatoes)
• Prebiotics (e.g., inulin, chicory root)
• Fermented foods and high-fiber diets like the Mediterranean diet

Lifestyle Modifications

Regular exercise, stress reduction, and adequate sleep all promote gut health and help maintain healthy microbial diversity. 

Avoid unnecessary antibiotic use and support recovery after illness with targeted probiotics and diet changes.

Faecalibacterium spp.—especially F. prausnitzii—are essential for gut and immune health. Testing and supporting their presence can provide insight into disease risk, inflammation levels, and treatment strategies for patients with chronic health concerns.

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