''Faecalibacterium'' is a genus of bacteria. The genus contains several species including ''Faecalibacterium prausnitzii'', ''Faecalibacterium butyricigenerans'', ''Faecalibacterium longum'', ''Faecalibacterium duncaniae'', ''Faecalibacterium hattorii'', and ''Faecalibacterium gallinarum''. Its first known species, ''Faecalibacterium prausnitzii'' (renamed as Faecalibacterium ''duncaniae'') is gram-positive, mesophilic, rod-shaped, and anaerobic, and is one of the most abundant and important commensal bacteria of the human

gut microbiota Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the g ...

. It is non-spore forming and non-motile. These bacteria produce

butyrate The conjugate acids are in :Carboxylic acids. {{Commons category, Carboxylate ions, Carboxylate anions Carbon compounds Anions ...

and other short-chain fatty acids through the fermentation of

dietary fiber Dietary fiber (fibre in English in the Commonwealth of Nations, Commonwealth English) or roughage is the portion of plant-derived food that cannot be completely broken down by human digestive enzymes. Dietary fibers are diverse in chemical co ...

. The production of

butyrate The conjugate acids are in :Carboxylic acids. {{Commons category, Carboxylate ions, Carboxylate anions Carbon compounds Anions ...

makes them an important member of the gut microbiota, fighting against

inflammation Inflammation (from ) is part of the biological response of body tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. The five cardinal signs are heat, pain, redness, swelling, and loss of function (Latin ''calor'', '' ...

History

Formerly assigned to the genus ''

Fusobacterium ''Fusobacterium'' is a genus of obligate anaerobic, Gram-negative, non-sporeforming bacteria belonging to Gracilicutes. Individual cells are slender, rod-shaped bacilli with pointed ends. ''Fusobacterium'' was discovered in 1900 by Courmont an ...

'' in the

phylum In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead ...

Fusobacteriota Fusobacteriota are obligately anaerobic non-sporeforming Gram-negative bacilli. Since the first reports in the late nineteenth century, various names have been applied to these organisms, sometimes with the same name being applied to different s ...

, ''Faecalibacterium prausnitzii'' was re-assigned to its own genus when phylogenetic analysis of isolates showed it to be a member of the phylum

Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have Gram-positive cell wall structure. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as '' Megasphaera'', ...

. It now is regarded as a member of the

Oscillospiraceae Oscillospiraceae, also commonly called Ruminococcaceae, is a family of bacteria in the class Clostridia. All Oscillospiraceae are obligate anaerobes. However, members of the family have diverse shapes, with some rod-shaped and others cocci. With ...

in Clostridium cluster IV. Although the Oscillospiraceae are largely

gram-negative bacteria Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the Crystal violet, crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelo ...

, ''Faecalibacterium prausnitzii'' resembles a

gram-positive bacterium In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. The Gram stain is ...

in its staining. 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 List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

(NCBI) 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 In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of ...

of 56.9%. The bacterium has been found to have 2,707 coding sequences, including 77 RNAs encoding genes. 128 metabolic pathways have been reconstructed, as well as 27 protein complexes and 64 tRNAs. 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. A protein produced by this bacterium has been linked to anti-inflammatory effects.

''Faecalibacterium prausnitzii'' in laboratory conditions

Faecalibacterium prausnitzii is strictly

anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: *Adhesive#Anaerobic, Anaerobic ad ...

, 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 ''In vitro'' (meaning ''in glass'', or ''in the glass'') Research, studies are performed with Cell (biology), cells or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in ...

. The rich medium YCFA is very suitable for the growth of this bacterium in anaerobic conditions. Another media suitable for the growth of F. prausnitzii is YBHI. 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. The anti-inflammatory properties of its

metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

s may alleviate imbalances between intestinal bacterial populations that lead to

dysbiosis Dysbiosis (also called dysbacteriosis) is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For e ...

. It is one of the main producers of butyrate in the intestine. Since

butyrate The conjugate acids are in :Carboxylic acids. {{Commons category, Carboxylate ions, Carboxylate anions Carbon compounds Anions ...

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. By blocking the NF-kB pathway, ''F. prausnitzii'' indirectly inhibts the production of the pro-inflammatory IL-8, secreted by the

intestinal epithelial cells The intestinal epithelium is the single cell layer that forms the luminal surface (lining) of both the small and large intestine (colon) of the gastrointestinal tract. Composed of simple columnar epithelium its main functions are absorptio ...

. Other research has shown that there is a correlation between high populations of ''Faecalibacterium prausnitzii'', low IL-12 abundance, and higher IL-10 production. The upregulated IL-10 inhibts the secretion of IFN-y,

TNF-alpha Tumor necrosis factor (TNF), formerly known as TNF-α, is a chemical messenger produced by the immune system that induces inflammation. TNF is produced primarily by activated macrophages, and induces inflammation by binding to its receptors o ...

, IL-6, and IL-12, which are all pro-inflammatory cytokines. Apart from butyrate, ''F. prausnitzii'' produce

formate Formate (IUPAC name: methanoate) is the conjugate base of formic acid. Formate is an anion () or its derivatives such as ester of formic acid. The salts and esters are generally colorless. Fundamentals When dissolved in water, formic acid co ...

and D-lactate as byproducts of fermentation of glucose and acetate. Lower than usual levels of ''F. prausnitzii'' in the intestines have been associated with

Crohn's disease Crohn's disease is a type of inflammatory bowel disease (IBD) that may affect any segment of the gastrointestinal tract. Symptoms often include abdominal pain, diarrhea, fever, abdominal distension, and weight loss. Complications outside of the ...

obesity Obesity is a medical condition, considered by multiple organizations to be a disease, in which excess Adipose tissue, body fat has accumulated to such an extent that it can potentially have negative effects on health. People are classifi ...

asthma Asthma is a common long-term inflammatory disease of the airways of the lungs. It is characterized by variable and recurring symptoms, reversible airflow obstruction, and easily triggered bronchospasms. Symptoms include episodes of wh ...

and

major depressive disorder Major depressive disorder (MDD), also known as clinical depression, is a mental disorder characterized by at least two weeks of pervasive depression (mood), low mood, low self-esteem, and anhedonia, loss of interest or pleasure in normally ...

. Higher than usual levels of the F06

clade In biology, a clade (), also known as a Monophyly, monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach t ...

of ''F. prausnitzii'' have been associated with

atopic dermatitis Atopic dermatitis (AD), also known as atopic eczema, is a long-term type of inflammation of the skin. Atopic dermatitis is also often called simply eczema but the same term is also used to refer to dermatitis, the larger group of skin conditi ...

. ''Faecalibacterium prausnitzii'' can improve gut barrier function. Supernatant of ''F. prausnitzii'' has been shown to improve the gut barrier by affecting the permeability of epithelial cells. Another way that ''F. prausnitzii'' improves the gut barrier is by improving the permeability and the expression of tightly bound proteins -

e-cadherin Cadherin-1 or Epithelial cadherin (E-cadherin), is a protein that in humans is encoded by the ''CDH1'' gene (not to be confused with the APC/C activator protein CDH1). Mutations are correlated with Hereditary diffuse gastric cancer, gastric, Here ...

and

occludin Occludin is a transmembrane protein that regulates the permeability of epithelial and endothelial barriers. It was first identified in epithelial cells as a 65 kDa integral plasma-membrane protein localized at the tight junctions. Together with ...

. Both of them increase the

tight junction Tight junctions, also known as occluding junctions or ''zonulae occludentes'' (singular, ''zonula occludens''), are multiprotein Cell junction, junctional complexes between epithelial cells, sealing and preventing leakage of solutes and water. Th ...

s between cells, strengthen the gut barrier and alleviate inflammation.

''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, ''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 ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...

'' are needed to create a suitable environment for ''F. prausnitzii'' by reducing the redox potential and alter the composition of the nutrients.

Inflammatory bowel disease

In Crohn's disease, as of 2015 most studies (with one exception) found reduced levels of ''F. prausnitzii''; this has been found in both fecal and mucosal samples. 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. However, it is a

fastidious organism A fastidious organism is any organism that has complex or particular nutritional requirements. In other words, a fastidious organism will only grow when specific nutrients are included in its medium. The more restrictive term fastidious microorga ...

sensitive to oxygen and difficult to deliver to the intestine. Exclusive

enteral nutrition Enteral administration is food or pharmaceutical drug#Administration, drug administration via the human gastrointestinal tract. This contrasts with parenteral nutrition or drug administration (Greek ''para'', "besides" + ''enteros''), which occu ...

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

Biomarker relevance

''F. prausnitzii'' can also serve as a biomarker discriminating between different intestinal inflammatory conditions. It is a good biomarker to differentiate between

and

colorectal cancer Colorectal cancer (CRC), also known as bowel cancer, colon cancer, or rectal cancer, is the development of cancer from the Colon (anatomy), colon or rectum (parts of the large intestine). Signs and symptoms may include Lower gastrointestinal ...

. 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 Ulcerative colitis (UC) is one of the two types of inflammatory bowel disease (IBD), with the other type being Crohn's disease. It is a long-term condition that results in inflammation and ulcers of the colon and rectum. The primary sympto ...

. 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 White blood cells (scientific name leukocytes), also called immune cells or immunocytes, are cells of the immune system that are involved in protecting the body against both infectious disease and foreign entities. White blood cells are genera ...

count.

References

{{Taxonbar, from1=Q3738294, from2=Q3738296 Eubacteriales Monotypic bacteria genera

History

Phylogeny

Genetics

''Faecalibacterium prausnitzii'' in laboratory conditions

Clinical relevance

''Faecalibacterium prausnitzii'' and other bacteria

Inflammatory bowel disease

Biomarker relevance

See also

References