Faecalibacterium

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.{{cite journal | vauthors = Duncan SH, Hold GL, Harmsen HJ, Stewart CS, Flint HJ | title = Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 52 | issue = Pt 6 | pages = 2141–2146 | date = November 2002 | pmid = 12508881 | doi = 10.1099/00207713-52-6-2141 | doi-access = free }} Although the Oscillospiraceae are largely gram-negative bacteria, Faecalibacterium prausnitzii resembles a gram-positive bacterium in its staining.{{cite journal | vauthors = Miquel S, Martín R, Rossi O, Bermúdez-Humarán LG, Chatel JM, Sokol H, Thomas M, Wells JM, Langella P | display-authors = 6 | title = Faecalibacterium prausnitzii and human intestinal health | journal = Current Opinion in Microbiology | volume = 16 | issue = 3 | pages = 255–261 | date = June 2013 | pmid = 23831042 | doi = 10.1016/j.mib.2013.06.003 }} 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.

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN){{cite web |author=A.C. Parte |url=https://lpsn.dsmz.de/genus/faecalibacterium |title=Faecalibacterium |access-date=2023-09-09 |publisher=List of Prokaryotic names with Standing in Nomenclature (LPSN) |display-authors=et al.}} and National Center for Biotechnology Information (NCBI){{cite web |author=Sayers |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=216851&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Faecalibacterium |access-date=2023-09-09 |publisher=National Center for Biotechnology Information (NCBI) taxonomy database |display-authors=et al.}}

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

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. 128 metabolic pathways have been reconstructed, as well as 27 protein complexes and 64 tRNAs.{{Cite web|url=https://biocyc.org/FAECPRAU/organism-summary|title=Summary of Faecalibacterium prausnitzii, Strain A2-165, version 21.5|website=BioCyc}} 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.{{cite journal | vauthors = Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ | title = Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth | journal = Applied and Environmental Microbiology | volume = 78 | issue = 2 | pages = 420–428 | date = January 2012 | pmid = 22101049 | pmc = 3255724 | doi = 10.1128/AEM.06858-11 | bibcode = 2012ApEnM..78..420L }} A protein produced by this bacterium has been linked to anti-inflammatory effects.{{cite journal | vauthors = Quévrain E, Maubert MA, Michon C, Chain F, Marquant R, Tailhades J, Miquel S, Carlier L, Bermúdez-Humarán LG, Pigneur B, Lequin O, Kharrat P, Thomas G, Rainteau D, Aubry C, Breyner N, Afonso C, Lavielle S, Grill JP, Chassaing G, Chatel JM, Trugnan G, Xavier R, Langella P, Sokol H, Seksik P | display-authors = 6 | title = Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease | journal = Gut | volume = 65 | issue = 3 | pages = 415–425 | date = March 2016 | pmid = 26045134 | pmc = 5136800 | doi = 10.1136/gutjnl-2014-307649 }}

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.{{cite journal | vauthors = Wrzosek L, Miquel S, Noordine ML, Bouet S, Joncquel Chevalier-Curt M, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, Langella P, Thomas M | display-authors = 6 | title = Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent | journal = BMC Biology | volume = 11 | issue = 1 | page = 61 | date = May 2013 | pmid = 23692866 | pmc = 3673873 | doi = 10.1186/1741-7007-11-61 | doi-access = free }} 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.

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 metabolites may alleviate imbalances between intestinal bacterial populations that lead to dysbiosis. 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.{{Cite journal | vauthors = He X, Zhao S, Li Y |date=2021-03-05 |title=Faecalibacterium prausnitzii: A Next-Generation Probiotic in Gut Disease Improvement |journal=Canadian Journal of Infectious Diseases and Medical Microbiology |language=en |volume=2021 |pages=e6666114 |doi=10.1155/2021/6666114 |issn=1712-9532 |doi-access=free }}{{cite journal | vauthors = Inan MS, Rasoulpour RJ, Yin L, Hubbard AK, Rosenberg DW, Giardina C | title = The luminal short-chain fatty acid butyrate modulates NF-kappaB activity in a human colonic epithelial cell line | journal = Gastroenterology | volume = 118 | issue = 4 | pages = 724–734 | date = April 2000 | pmid = 10734024 | doi = 10.1016/s0016-5085(00)70142-9 }}{{Cite journal |last1=Zhang |first1=Jianbo |last2=Huang |first2=Yu-Ja |last3=Yoon |first3=Jun Young |last4=Kemmitt |first4=John |last5=Wright |first5=Charles |last6=Schneider |first6=Kirsten |last7=Sphabmixay |first7=Pierre |last8=Hernandez-Gordillo |first8=Victor |last9=Holcomb |first9=Steven J. |last10=Bhushan |first10=Brij |last11=Rohatgi |first11=Gar |last12=Benton |first12=Kyle |last13=Carpenter |first13=David |last14=Kester |first14=Jemila C. |last15=Eng |first15=George |date=January 2021 |title=Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture |journal=Med |volume=2 |issue=1 |pages=74–98.e9 |doi=10.1016/j.medj.2020.07.001 |issn=2666-6340 |pmc=7839961 |pmid=33511375}} By blocking the NF-kB pathway, F. prausnitzii indirectly inhibts the production of the pro-inflammatory IL-8, secreted by the intestinal epithelial cells.{{cite journal | vauthors = Miquel S, Leclerc M, Martin R, Chain F, Lenoir M, Raguideau S, Hudault S, Bridonneau C, Northen T, Bowen B, Bermúdez-Humarán LG, Sokol H, Thomas M, Langella P | display-authors = 6 | title = Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii | journal = mBio | volume = 6 | issue = 2 | date = April 2015 | pmid = 25900655 | pmc = 4453580 | doi = 10.1128/mBio.00300-15 | veditors = Blaser MJ }} Other research has shown that there is a correlation between high populations of Faecalibacterium prausnitzii, low IL-12 abundance, and higher IL-10 production.{{cite journal | vauthors = Qiu X, Zhang M, Yang X, Hong N, Yu C | title = Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis | journal = Journal of Crohn's & Colitis | volume = 7 | issue = 11 | pages = e558–e568 | date = December 2013 | pmid = 23643066 | doi = 10.1016/j.crohns.2013.04.002 | doi-access = free }}{{cite journal | vauthors = Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottière HM, Doré J, Marteau P, Seksik P, Langella P | display-authors = 6 | title = Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 43 | pages = 16731–16736 | date = October 2008 | pmid = 18936492 | pmc = 2575488 | doi = 10.1073/pnas.0804812105 | doi-access = free }} The upregulated IL-10 inhibts the secretion of IFN-y, TNF-alpha, IL-6, and IL-12, which are all pro-inflammatory cytokines. Apart from butyrate, F. prausnitzii produce formate 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, obesity, asthma and major depressive disorder.{{cite web |url= http://news.bbc.co.uk/1/hi/health/7679347.stm |title= Bacterium 'to blame for Crohn's' |publisher=BBC News |date=2008-10-21 |access-date= 2008-10-21}}{{cite journal | vauthors = Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, Sogin ML | title = Sewage reflects the microbiomes of human populations | journal = mBio | volume = 6 | issue = 2 | pages = e02574 | date = February 2015 | pmid = 25714718 | pmc = 4358014 | doi = 10.1128/mBio.02574-14 | author-link6 = A. Murat Eren }}{{cite journal | vauthors = Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L, Ruan B | display-authors = 6 | title = Altered fecal microbiota composition in patients with major depressive disorder | journal = Brain, Behavior, and Immunity | volume = 48 | pages = 186–194 | date = August 2015 | pmid = 25882912 | doi = 10.1016/j.bbi.2015.03.016 | doi-access = free }} Higher than usual levels of the F06 clade of F. prausnitzii have been associated with atopic dermatitis.{{Cite journal |last=Song |first=Han |last2=Yoo |first2=Young |last3=Hwang |first3=Junghyun |last4=Na |first4=Yun-Cheol |last5=Kim |first5=Heenam Stanley |date=March 2016 |title=Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis |url=https://pubmed.ncbi.nlm.nih.gov/26431583/ |journal=The Journal of Allergy and Clinical Immunology |volume=137 |issue=3 |pages=852–860 |doi=10.1016/j.jaci.2015.08.021 |issn=1097-6825 |pmid=26431583|doi-access=free }} Faecalibacterium prausnitzii can improve gut barrier function.{{cite journal | vauthors = Stenman LK, Burcelin R, Lahtinen S | title = Establishing a causal link between gut microbes, body weight gain and glucose metabolism in humans - towards treatment with probiotics | journal = Beneficial Microbes | volume = 7 | issue = 1 | pages = 11–22 | date = February 2016 | pmid = 26565087 | doi = 10.3920/BM2015.0069 | doi-access = free }} Supernatant of F. prausnitzii has been shown to improve the gut barrier by affecting the permeability of epithelial cells.{{cite journal | vauthors = Rossi O, van Berkel LA, Chain F, Tanweer Khan M, Taverne N, Sokol H, Duncan SH, Flint HJ, Harmsen HJ, Langella P, Samsom JN, Wells JM | display-authors = 6 | title = Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses | journal = Scientific Reports | volume = 6 | issue = 1 | page = 18507 | date = January 2016 | pmid = 26725514 | pmc = 4698756 | doi = 10.1038/srep18507 | bibcode = 2016NatSR...618507R }} 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.{{cite journal | vauthors = Laval L, Martin R, Natividad JN, Chain F, Miquel S, Desclée de Maredsous C, Capronnier S, Sokol H, Verdu EF, van Hylckama Vlieg JE, Bermúdez-Humarán LG, Smokvina T, Langella P | display-authors = 6 | title = Lactobacillus rhamnosus CNCM I-3690 and the commensal bacterium Faecalibacterium prausnitzii A2-165 exhibit similar protective effects to induced barrier hyper-permeability in mice | journal = Gut Microbes | volume = 6 | issue = 1 | pages = 1–9 | date = 2015-01-02 | pmid = 25517879 | pmc = 4615674 | doi = 10.4161/19490976.2014.990784 }}

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,{{cite journal | vauthors = Licht TR, Hansen M, Bergström A, Poulsen M, Krath BN, Markowski J, Dragsted LO, Wilcks A | display-authors = 6 | title = Effects of apples and specific apple components on the cecal environment of conventional rats: role of apple pectin | journal = BMC Microbiology | volume = 10 | issue = 1 | page = 13 | date = January 2010 | pmid = 20089145 | pmc = 2822772 | doi = 10.1186/1471-2180-10-13 | doi-access = free }} 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.{{cite journal | vauthors = Cheng L, Kiewiet MB, Logtenberg MJ, Groeneveld A, Nauta A, Schols HA, Walvoort MT, Harmsen HJ, de Vos P | display-authors = 6 | title = Effects of Different Human Milk Oligosaccharides on Growth of Bifidobacteria in Monoculture and Co-culture With Faecalibacterium prausnitzii | journal = Frontiers in Microbiology | volume = 11 | page = 569700 | date = 2020 | pmid = 33193162 | pmc = 7662573 | doi = 10.3389/fmicb.2020.569700 | doi-access = free }}

In Crohn's disease, as of 2015 most studies (with one exception) found reduced levels of F. prausnitzii;{{cite journal | vauthors = Wright EK, Kamm MA, Teo SM, Inouye M, Wagner J, Kirkwood CD | title = Recent advances in characterizing the gastrointestinal microbiome in Crohn's disease: a systematic review | journal = Inflammatory Bowel Diseases | volume = 21 | issue = 6 | pages = 1219–1228 | date = June 2015 | pmid = 25844959 | pmc = 4450900 | doi = 10.1097/MIB.0000000000000382 }} this has been found in both fecal and mucosal samples.{{cite journal | vauthors = El Hage R, Hernandez-Sanabria E, Van de Wiele T | title = Emerging Trends in "Smart Probiotics": Functional Consideration for the Development of Novel Health and Industrial Applications | journal = Frontiers in Microbiology | volume = 8 | page = 1889 | date = 2017-09-29 | pmid = 29033923 | pmc = 5626839 | doi = 10.3389/fmicb.2017.01889 | doi-access = free }} 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 sensitive to oxygen and difficult to deliver to the intestine.

Exclusive enteral nutrition, which is known to induce remission in Crohn's, has been found to reduce F. prausnitzii in responders.{{cite journal | vauthors = Gerasimidis K, Russell R, Hansen R, Quince C, Loman N, Bertz M, Hanske L, Blaut M, McGrogan P, Edwards CA | display-authors = 6 | title = Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter? | journal = Inflammatory Bowel Diseases | volume = 20 | issue = 7 | pages = E18–E19 | date = July 2014 | pmid = 24859302 | doi = 10.1097/MIB.0000000000000079 | doi-access = free }} This could be due to the lack of specific nutrients, that the bacteria need to survive.{{cite journal | vauthors = Diederen K, Li JV, Donachie GE, de Meij TG, de Waart DR, Hakvoort TB, Kindermann A, Wagner J, Auyeung V, Te Velde AA, Heinsbroek SE, Benninga MA, Kinross J, Walker AW, de Jonge WJ, Seppen J | display-authors = 6 | title = Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn's disease | journal = Scientific Reports | volume = 10 | issue = 1 | page = 18879 | date = November 2020 | pmid = 33144591 | pmc = 7609694 | doi = 10.1038/s41598-020-75306-z | bibcode = 2020NatSR..1018879D }}

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.{{cite journal | vauthors = Lopez-Siles M, Martinez-Medina M, Abellà C, Busquets D, Sabat-Mir M, Duncan SH, Aldeguer X, Flint HJ, Garcia-Gil LJ | display-authors = 6 | title = Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease | journal = Applied and Environmental Microbiology | volume = 81 | issue = 21 | pages = 7582–7592 | date = November 2015 | pmid = 26296733 | pmc = 4592880 | doi = 10.1128/AEM.02006-15 | bibcode = 2015ApEnM..81.7582L | veditors = Elkins CA }} 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.

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.{{cite journal | vauthors = Swidsinski A, Loening-Baucke V, Vaneechoutte M, Doerffel Y | title = Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora | journal = Inflammatory Bowel Diseases | volume = 14 | issue = 2 | pages = 147–161 | date = February 2008 | pmid = 18050295 | doi = 10.1002/ibd.20330 | s2cid = 46449782 | doi-access = free }}

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

{{Reflist}}

{{Bacteria classification}}

{{Taxonbar|from1=Q3738294|from2=Q3738296}}

Category:Eubacteriales

Category:Monotypic bacteria genera