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History

Formerly assigned to the genus Fusobacterium in the phylum Fusobacteriota, Faecalibacterium prausnitzii was re-assigned to its own genus when phylogenetic analysis of isolates showed it to be a member of the phylum Bacillota. It now is regarded as a member of the Oscillospiraceae in Clostridium cluster IV.⁸ Although the Oscillospiraceae are largely gram-negative bacteria, Faecalibacterium prausnitzii resembles a gram-positive bacterium in its staining.⁹ This can be ascribed to the fact that it lacks lipopolysaccharides in its outer membrane, so that, in its staining, it more closely resembles gram-positive bacteria, than gram-negative.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)¹⁰ and National Center for Biotechnology Information (NCBI)¹¹

Species incertae sedis:

• "F. faecis" Hitch et al. 2024
• "F. hominis" Afrizal et al. 2022 non Liu et al. 2023
• "F. intestinale" Hitch et al. 2024
• "F. langellae" Plomp & Harmsen 2024
• F. taiwanense Liou et al. 2024
• "F. tardum" Hitch et al. 2024
• F. wellingii Plomp & Harmsen 2025

Genetics

Faecalibacterium prausnitzii has a genome 2,868,932 bp long and has a GC-content of 56.9%. The bacterium has been found to have 2,707 coding sequences, including 77 RNAs encoding genes.¹⁸ 128 metabolic pathways have been reconstructed, as well as 27 protein complexes and 64 tRNAs.¹⁹ Phylogenetically, the strains of F. prausnitzii compose phylogroups I and II. Most of the new isolates of this species isolated by Muhammad Tanweer Khan belong to phylogroup II.²⁰ A protein produced by this bacterium has been linked to anti-inflammatory effects.²¹

Faecalibacterium prausnitzii in laboratory conditions

Faecalibacterium prausnitzii is strictly anaerobic, and accordingly difficult to culture in the laboratory. However, with due attention to the requisite conditions and media, it is possible to culture the species in vitro. The rich medium YCFA is very suitable for the growth of this bacterium in anaerobic conditions.²² Another media suitable for the growth of F. prausnitzii is YBHI.²³ Any liquid media or agar plates should be pretreated beforehand for 24 hours in an anaerobic chamber, to ensure they are completely anaerobic.

Clinical relevance

In healthy adults, Faecalibacterium prausnitzii represent approximately 5% of the total fecal microbiota but this can increase to around 15% in some individuals, making it one of the commonest of the gut bacteria.²⁴ The anti-inflammatory properties of its metabolites may alleviate imbalances between intestinal bacterial populations that lead to dysbiosis.²⁵ It is one of the main producers of butyrate in the intestine. Since butyrate inhibits the production of NF-kB and IFN-y, both involved in the pro-inflammatory response, Faecalibacterium prausnitzii acts as an anti-inflammatory gut bacterium.²⁶²⁷²⁸ By blocking the NF-kB pathway, F. prausnitzii indirectly inhibts the production of the pro-inflammatory IL-8, secreted by the intestinal epithelial cells.²⁹ Other research has shown that there is a correlation between high populations of Faecalibacterium prausnitzii, low IL-12 abundance, and higher IL-10 production.³⁰³¹ The upregulated IL-10 inhibts the secretion of IFN-y, TNF-alpha, IL-6, and IL-12, which are all pro-inflammatory cytokines.³² Apart from butyrate, F. prausnitzii produce formate and D-lactate as byproducts of fermentation of glucose and acetate.³³³⁴ Lower than usual levels of F. prausnitzii in the intestines have been associated with Crohn's disease, obesity, asthma and major depressive disorder.^35363738 Higher than usual levels of the F06 clade of F. prausnitzii have been associated with atopic dermatitis.³⁹ Faecalibacterium prausnitzii can improve gut barrier function.⁴⁰ Supernatant of F. prausnitzii has been shown to improve the gut barrier by affecting the permeability of epithelial cells.⁴¹ Another way that F. prausnitzii improves the gut barrier is by improving the permeability and the expression of tightly bound proteins - e-cadherin and occludin. Both of them increase the tight junctions between cells, strengthen the gut barrier and alleviate inflammation.⁴²⁴³

Faecalibacterium prausnitzii and other bacteria

Studies show that F. prausnitzii interacts with other bacteria, which affects its butyrate production, and survival. When F. prausnitzii is cultured with Bacteroides thetaiotaomicron, it produces more butyric acid than standing alone,⁴⁴⁴⁵ F. prausnitzii also benefits from growing with certain other bacteria. For example, in order to survive in the gut environment, it requires certain bacteria to be preexisting. B. thetaiotaomicron and Escherichia coli are needed to create a suitable environment for F. prausnitzii by reducing the redox potential and alter the composition of the nutrients.⁴⁶⁴⁷

Inflammatory bowel disease

In Crohn's disease, as of 2015 most studies (with one exception) found reduced levels of F. prausnitzii;⁴⁸ this has been found in both fecal and mucosal samples.⁴⁹ The lower abundance of these bacteria is not only associated to the chance of developing IBD, but also to the chance of relapsing after a successful therapy. People with lower abundance are six times more likely to relapse in the future.⁵⁰ However, it is a fastidious organism sensitive to oxygen and difficult to deliver to the intestine.⁵¹

Exclusive enteral nutrition, which is known to induce remission in Crohn's, has been found to reduce F. prausnitzii in responders.⁵² This could be due to the lack of specific nutrients, that the bacteria need to survive.⁵³

Biomarker relevance

F. prausnitzii can also serve as a biomarker discriminating between different intestinal inflammatory conditions. It is a good biomarker to differentiate between Crohn's disease and colorectal cancer.⁵⁴ An even better biomarker is F. prausnitzii in comparison to E. coli as a complementary indicator (F-E index). This index serves really well in differentiating between colorectal cancer and ulcerative colitis.⁵⁵

Combining both the host serological data plus microbiological indicators could serve as good biomarker, since it has been reported that Crohn's disease and ulcerative colitis can be differentiated based on monitoring of F. prausnitzii in conjunction with leukocyte count.⁵⁶

See also

• IMPDH RNA motif, a transcription regulator in Faecalibacterium
• List of bacterial orders
• List of bacteria genera

f

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