Faecalibacterium prausnitzii – A Superhero Bug

Faecalibacterium prausnitzii gut health digestive health byron bay australia herbalist naturopath

Faecalibacterium prausnitzii is a member of the Firmicutes phylum and is the most numerous single bacteria found in the large intestine. Some estimates have it at over 5% of the microbial population. Big numbers. 

There have been a number of different papers exploring the link between dysbiosis (imbalanced gut microbiota) and a range of different disease. A decrease in Faecalibacterium prausnitzii has been implicated in these findings and can be linked to different diseases. Some researchers consider F. prausnitzii a general marker for intestinal health, particularly inflammatory bowel disease (1).

‘The data reveal that the relative abundance of F. prausnitzii can serve as an indicator or biomarker of intestinal health in adults (1)’

This article will explore the role that Faecalibacterium prausnitzii plays in the human body, some gut illnesses that are marked by lower counts of this helpful bacteria and some ideas on how to feed your microbiome.


What Role Does Faecalibacterium prausnitzii Play?

Even though F. prausnitzii may be considered relatively new on the block (being extremely sensitive to oxygen culturing the bacteria is incredibly difficult) it has been getting a fair amount of interest from the science community. One recently published review covered a range of benefits that Faecalibacterium prausnitzii may contribute to health and homeostasis (2).


Anti-inflammatory Mechanisms

As a fermenter F. prausnitzii produces short chain fatty acids (SCFA) in the gut mainly in the form of butyrate. Butyrate, as I have written about previously, plays a number of important and beneficial roles including being:

  • A main energy source for the cells in the colon
  • Reducing mucosa inflammation
  • Protective against colorectal cancer
  • Protective against inflammatory bowel disease
  • F. prausnitzii has also been shown to block NF-κB activation and block IL-8 production, a pro-inflammatory cytokine messenger.

Improving Intestinal Permeability

Along with the anti-inflammatory properties F. prausnitzii  works on the tight junctions in the small intestine, reducing intestinal permeability. It is thought that the metabolites secreted by this friendly bacteria helps with the expression of particular tight junction proteins.


Lowered Amounts In Inflammatory Bowel Disease

As this particular bacteria is such a prolific producer of the beneficial butyrate, and in a healthy adult it comprises up to 5% of the microbiota it stands to reason that a decrease in the population would have some noticeable impacts.

An altered gut microbiome has been implicated in a range of different diseases. Inflammatory bowel disease, including Crohn’s disease and ulcerative colitis, is marked by a reduction in Faecalibacterium prausnitzii. One systematic review with meta analysis, which included 11 studies, found significant reduction in F. prausnitzii in patients with IBD compared to the controls (3).

They conclude that there is ‘a possible protective benefit of F. prausnitzii against the development of IBD.’ but, as with many meta-analysis conclusions recommend caution in jumping to conclusions.

This finding is echoed throughout the literature (4, 5).  


T-regulatory Cell Upregulation

Another incredible finding that relates to the immune dysregulation in IBD revolves around a certain white blood cell known as a T-regulatory cell or a T-reg. These immune cells help to moderate the immune system so that it doesn’t become overactive. A state of over-reactivity is a common hallmark in inflammatory bowel disease (6).

Test tube and animal studies have shown that F. prausnitzii can increase T-reg cells, help to regulate the immune system and improve inflammatory bowel disease markers (7).


How To Boost Faecalibacterium prausnitzii Levels

We’ve covered what this particular bacteria is and some of the beneficial effects it can play in the body, now lets talk about methods of improving the numbers.

But first, before we get into the prebiotic boosting approaches.

While we do have good evidence that F. prausnitzii is a beneficial bug in our gut microbiome we still are only just scratching the surface of this incredibly complex ecosystem. With this in mind the following points are best to keep in mind.

  1. Start low and go slow
  2. If you experience any negative side effects then stop for a few days and start again remembering rule number one above.
  3. For one reason or another some people just don’t do well on prebiotics. This may be an indication of a deeper imbalance or it may simply be how your gut microbiome is built. Don’t push it. If it feels wrong then stop the trial and seek help from a microbiome savvy clinician.

Ok now onto the studies showing Faecalibacterium prausnitzii boosting interventions. 

One interesting study looked at the effects of lactulose in hepatic encephalopathy.

From MSD manuals ‘Hepatic encephalopathy is deterioration of brain function that occurs in people with severe liver disease because toxic substances normally removed by the liver build up in the blood and reach the brain.’

They took seven men (true a small number) suffering from cirrhosis. Each of these men were already consuming the prebiotic lactulose to treat their hepatic encephalopathy. They removed the lactulose to determine the effects on the patients. 3 out of 7 people had spontaneous recurrence of their hepatic encephalopathy. One was so severe that it required a trip to the hospital.

So what is happening here. Along with changes in different cytokines (messenger molecules in the blood) they found that Faecalibacterium prausnitzii levels had dropped from 6% on the lactulose to 1% after stopping.

Another study found the prebiotic galactooligosaccharide, or GOS, to boost Faecalibacterium prausnitzii levels. Interestingly, as the table shows below, 2.5 grams of GOS boosted the bacterial levels slightly, 5 grams of GOS boosted it considerably but 10 grams of GOS per day reduced the numbers of F. prausnitzii to below baseline. Our friendly gut bug, Bifidobacterium, continued to increase in numbers with the increase in GOS. There may be some selective feeding at the 10 gram dose, limiting some bacteria like F. prausnitzii in favour of others like Bifidobacterium spp.

Faecalibacterium prausnitzii gut health IBD anti inflammatory herbal medicine IBS digestive health

Table taken from: Barcoded Pyrosequencing Reveals That Consumption of Galactooligosaccharides Results in a Highly Specific Bifidogenic Response in Humans

Yet another study looked at the influence of the prebiotic inulin, a fructo-oligosaccharide, on the the gut microbiome composition of 6 healthy volunteers. They consumed 5g of inulin twice daily. Their gut microbiome status was compared at baseline and day 16 of the trial using quantitative real-time PCR (DNA technology). Compared to the placebo arm both Faecalibacterium prausnitzii levels and Bifidobacterium levels increased dramatically. The inulin supplementation also showed a decrease in the gram negative, and less beneficial bugs belonging to the Bacteroides genus.

Faecalibacterium prausnitzii prebiotic gut health probiotic IBD IBS digestive health byron bay herbalist australia Graph taken from: Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii.


A Superhero Bug

I will be the first to admit that we are in the early days of understanding the gut microbiome. As we are still just getting a grip on the landscape it can be hard to point to certain microbes as being the key to health and disease. This includes Faecalibacterium prausnitzii. With that said I still think we need to push forward and experiment with different, low risk, concepts like prebiotic and probiotic supplementation. While we have all these amazing high tech testing options available one excellent barometer is taking a moment to assess how you feel. All the scientific trials in the world or testing won’t make up for that personal insight we can all tap into.

Now I want to hear from you. Have you had any experiences with any of the prebiotics above? What were the results? Share your thoughts in the comments below.


References and Resources

  1. Faecalibacterium prausnitzii and human intestinal health
  2. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics
  3. Association between Faecalibacterium prausnitzii Reduction and Inflammatory Bowel Disease: A Meta-Analysis and Systematic Review of the Literature
  4. The microbiota in inflammatory bowel disease: friend, bystander, and sometime-villain
  5. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
  6. Regulatory T Cells
  7. Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis
  8. A longitudinal systems biology analysis of lactulose withdrawal in hepatic encephalopathy
  9. Barcoded Pyrosequencing Reveals That Consumption of Galactooligosaccharides Results in a Highly Specific Bifidogenic Response in Humans
  10. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii
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  1. Hallo,
    I tried both inulin and GOS (Bimuno). Inulin, at 2.5 grams per day, caused bloating. GOS, at 4 grams per day, caused no sides.
    In your opinion, should I continue on inulin or should I suppose it’s bad for me?

    1. Hey Amedeo. Well done for testing out the prebiotics and noting your symptoms! I would say go for the prebiotic that does not cause bloating. Inulin isn’t tolerated by everyone and in some people (like you) can cause bloating. Great to know that the GOS was better tolerated.

  2. Hey Todd, I am a melanoma patient 10 yrs now. currently doing immunotherapy treatments(Optivo+Yervoy) thru infusion monthly at the John Wayne Cancer Center ,Santa Monica,Calif. My disease has been stable and progression free but I have noticed that’s in many cases its a matter of time until the melanoma progresses. I found a study conducted at MD Anderson university of Texas. Research ties the diversity of bacteria tract to the impact of cancer immunotherapy.Increased abundance of the Ruminococcaceae family of bacteria within the Clostridales in responders of treatment. I like to be a pro-active patient. Any suggestion on how I may help my gut respond best to immunotheraphy.

    1. Hello John,

      Great work being so proactive! I have not had a chance to do a deep dive on the cancer gut connection as it is such a big topic. I do know that there is a TON of research just starting to emerge and that it is being actively researched. When I do get a moment to dig into it I will post up a link here for you.

      Sorry I couldn’t be more helpful!


  3. Hi Todd, your website is a wealth of knowledge.
    Just wondering, since your website is the only one from australia to discuss FAECALIBACTERIUM PRAUSNITZII.

    This bacteria has come up on my PCR vaginal test, and i am wondering if it is causing the ant like smell im experiencing there, whenever i consume sugar.

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