Biology:Faecalibacterium

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Faecalibacterium is a genus of bacteria. The genus contains several species including Faecalibacterium prausnitzii, Faecalibacterium butyricigenerans, Faecalibacterium longum,[1] Faecalibacterium duncaniae, Faecalibacterium hattorii, and Faecalibacterium gallinarum.[2] Its first known species, Faecalibacterium prausnitzii is gram-positive,[3] mesophilic, rod-shaped,[3] and anaerobic,[4] and is one of the most abundant and important commensal bacteria of the human gut microbiota. It is non-spore forming and non-motile.[5] These bacteria produce butyrate and other short-chain fatty acids through the fermentation of dietary fiber. The production of butyrate makes them an important member of the gut microbiota, fighting against inflammation.[6]

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.[7] Although the Oscillospiraceae are largely gram-negative bacteria, Faecalibacterium prausnitzii resembles a gram-positive bacterium in its staining.[8] 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)[9] and National Center for Biotechnology Information (NCBI)[10]

16S rRNA based LTP_10_2024[11][12][13] 120 marker proteins based GTDB 09-RS220[14][15][16]
Faecalibacterium
 

F. gallinarum

 
 
 

F. hattorii

 
 
 

F. prausnitzii

 
 
 
 

F. butyricigenerans Zou et al. 2021

 
 

F. longum

 
 
 
 

F. duncaniae

 
 

F. hominis Liu et al. 2023 non Afrizal et al. 2022

 
 
 
 
 
 
Faecalibacterium
 
 

F. prausnitzii (Hauduroy et al. 1937) Duncan et al. 2002

 
 
 

F. longum Zou et al. 2021

 
 
 

F. duncaniae Sakamoto et al. 2022

 
 

F. hattorii Sakamoto et al. 2022

 
 
 
 
 
 
 

"Ca. F. intestinavium" Gilroy et al. 2021

 
 

F. gallinarum Sakamoto et al. 2022

 
 
 
 

"Ca. F. avium" Gilroy et al. 2021

 
 
 

"Ca. F. faecipullorum" Gilroy et al. 2021

 
 
 

"Ca. F. intestinigallinarum" Gilroy et al. 2021

 
 
 

"Ca. F. faecigallinarum" Gilroy et al. 2021

 
 

"Ca. F. gallistercoris" Gilroy et al. 2021

 
 
 
 
 
 
 

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.[5] 128 metabolic pathways have been reconstructed, as well as 27 protein complexes and 64 tRNAs.[17] 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.[18] A protein produced by this bacterium has been linked to anti-inflammatory effects.[19]

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.[20] Another media suitable for the growth of F. prausnitzii is YBHI.[20] 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 most common gut bacteria.[8] The anti-inflammatory properties of its metabolites may alleviate imbalances between intestinal bacterial populations that lead to dysbiosis.[8] 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.[21][22][23] By blocking the NF-kB pathway, F. prausnitzii indirectly inhibts the production of the pro-inflammatory IL-8, secreted by the intestinal epithelial cells.[24] Other research has shown that there is a correlation between high populations of Faecalibacterium prausnitzii, low IL-12 abundance, and higher IL-10 production.[25][26] The upregulated IL-10 inhibts the secretion of IFN-y, TNF-alpha, IL-6, and IL-12, which are all pro-inflammatory cytokines.[26] Apart from butyrate, F. prausnitzii produce formate and D-lactate as byproducts of fermentation of glucose and acetate.[21][7] Lower than usual levels of F. prausnitzii in the intestines have been associated with Crohn's disease, obesity, asthma and major depressive disorder.[26][27][28][29] Higher than usual levels of the F06 clade of F. prausnitzii have been associated with atopic dermatitis.[30] Faecalibacterium prausnitzii can improve gut barrier function.[31] Supernatant of F. prausnitzii has been shown to improve the gut barrier by affecting the permeability of epithelial cells.[32] 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.[33][21]

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,[34][20] 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.[35][20]

Inflammatory bowel disease

In Crohn's disease, as of 2015 most studies (with one exception) found reduced levels of F. prausnitzii;[36] this has been found in both fecal and mucosal samples.[37] 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.[26] However, it is a fastidious organism sensitive to oxygen and difficult to deliver to the intestine.[37]

Exclusive enteral nutrition, which is known to induce remission in Crohn's, has been found to reduce F. prausnitzii in responders.[38] This could be due to the lack of specific nutrients, that the bacteria need to survive.[39]

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.[40] 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.[40]

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.[41]

See also

References

  1. ↑ Zou, Yuanqiang; Lin, Xiaoqian; Xue, Wenbin; Tuo, Li; Chen, Ming-Sheng; Chen, Xiao-Hui; Sun, Cheng-hang; Li, Feina et al. (2021-05-31). "Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces" (in en). Scientific Reports 11 (1): 11340. doi:10.1038/s41598-021-90786-3. ISSN 2045-2322. PMID 34059761. Bibcode: 2021NatSR..1111340Z. 
  2. ↑ Sakamoto, Mitsuo; Sakurai, Naomi; Tanno, Hiroki; Iino, Takao; Ohkuma, Moriya; Endo, Akihito (2022). "Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov.". International Journal of Systematic and Evolutionary Microbiology 72 (4): 005379. doi:10.1099/ijsem.0.005379. ISSN 1466-5034. PMID 35416766. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005379. 
  3. ↑ 3.0 3.1 "Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic". Frontiers in Microbiology 8: 1226. 2017. doi:10.3389/fmicb.2017.01226. PMID 28713353. 
  4. ↑ "The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases". The ISME Journal 6 (8): 1578–1585. August 2012. doi:10.1038/ismej.2012.5. PMID 22357539. Bibcode: 2012ISMEJ...6.1578K. 
  5. ↑ 5.0 5.1 "Complete Genome Sequence of Faecalibacterium prausnitzii Isolated from the Gut of a Healthy Indian Adult". Genome Announcements 5 (46). November 2017. doi:10.1128/genomeA.01286-17. PMID 29146862. 
  6. ↑ "Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics". The ISME Journal 11 (4): 841–852. April 2017. doi:10.1038/ismej.2016.176. PMID 28045459. Bibcode: 2017ISMEJ..11..841L. 
  7. ↑ 7.0 7.1 "Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov". International Journal of Systematic and Evolutionary Microbiology 52 (Pt 6): 2141–2146. November 2002. doi:10.1099/00207713-52-6-2141. PMID 12508881. 
  8. ↑ 8.0 8.1 8.2 "Faecalibacterium prausnitzii and human intestinal health". Current Opinion in Microbiology 16 (3): 255–261. June 2013. doi:10.1016/j.mib.2013.06.003. PMID 23831042. 
  9. ↑ A.C. Parte. "Faecalibacterium". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/genus/faecalibacterium. 
  10. ↑ Sayers. "Faecalibacterium". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=216851&lvl=3&lin=f&keep=1&srchmode=1&unlock. 
  11. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  12. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_10_2024.ntree. 
  13. ↑ "LTP_10_2024 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_10_2024_release_notes.pdf. 
  14. ↑ "GTDB release 09-RS220". https://gtdb.ecogenomic.org/about#4%7C. 
  15. ↑ "bac120_r220.sp_labels". https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/bac120_r220.sp_labels.tree. 
  16. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  17. ↑ "Summary of Faecalibacterium prausnitzii, Strain A2-165, version 21.5". https://biocyc.org/FAECPRAU/organism-summary. 
  18. ↑ "Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth". Applied and Environmental Microbiology 78 (2): 420–428. January 2012. doi:10.1128/AEM.06858-11. PMID 22101049. Bibcode: 2012ApEnM..78..420L. 
  19. ↑ "Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease". Gut 65 (3): 415–425. March 2016. doi:10.1136/gutjnl-2014-307649. PMID 26045134. 
  20. ↑ 20.0 20.1 20.2 20.3 "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". BMC Biology 11 (1). May 2013. doi:10.1186/1741-7007-11-61. PMID 23692866. 
  21. ↑ 21.0 21.1 21.2 "Faecalibacterium prausnitzii: A Next-Generation Probiotic in Gut Disease Improvement" (in en). Canadian Journal of Infectious Diseases and Medical Microbiology 2021. 2021-03-05. doi:10.1155/2021/6666114. ISSN 1712-9532. 
  22. ↑ "The luminal short-chain fatty acid butyrate modulates NF-kappaB activity in a human colonic epithelial cell line". Gastroenterology 118 (4): 724–734. April 2000. doi:10.1016/s0016-5085(00)70142-9. PMID 10734024. 
  23. ↑ Zhang, Jianbo; Huang, Yu-Ja; Yoon, Jun Young; Kemmitt, John; Wright, Charles; Schneider, Kirsten; Sphabmixay, Pierre; Hernandez-Gordillo, Victor et al. (January 2021). "Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture". Med 2 (1): 74–98.e9. doi:10.1016/j.medj.2020.07.001. ISSN 2666-6340. PMID 33511375. 
  24. ↑ "Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii". mBio 6 (2). April 2015. doi:10.1128/mBio.00300-15. PMID 25900655. 
  25. ↑ "Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis". Journal of Crohn's & Colitis 7 (11): e558–e568. December 2013. doi:10.1016/j.crohns.2013.04.002. PMID 23643066. 
  26. ↑ 26.0 26.1 26.2 26.3 "Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients". Proceedings of the National Academy of Sciences of the United States of America 105 (43): 16731–16736. October 2008. doi:10.1073/pnas.0804812105. PMID 18936492. 
  27. ↑ "Bacterium 'to blame for Crohn's'". BBC News. 2008-10-21. https://news.bbc.co.uk/2/hi/health/7679347.stm. 
  28. ↑ "Sewage reflects the microbiomes of human populations". mBio 6 (2): e02574. February 2015. doi:10.1128/mBio.02574-14. PMID 25714718. 
  29. ↑ "Altered fecal microbiota composition in patients with major depressive disorder". Brain, Behavior, and Immunity 48: 186–194. August 2015. doi:10.1016/j.bbi.2015.03.016. PMID 25882912. 
  30. ↑ Song, Han; Yoo, Young; Hwang, Junghyun; Na, Yun-Cheol; Kim, Heenam Stanley (March 2016). "Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis". The Journal of Allergy and Clinical Immunology 137 (3): 852–860. doi:10.1016/j.jaci.2015.08.021. ISSN 1097-6825. PMID 26431583. 
  31. ↑ "Establishing a causal link between gut microbes, body weight gain and glucose metabolism in humans - towards treatment with probiotics". Beneficial Microbes 7 (1): 11–22. February 2016. doi:10.3920/BM2015.0069. PMID 26565087. 
  32. ↑ "Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses". Scientific Reports 6 (1). January 2016. doi:10.1038/srep18507. PMID 26725514. Bibcode: 2016NatSR...618507R. 
  33. ↑ "Lactobacillus rhamnosus CNCM I-3690 and the commensal bacterium Faecalibacterium prausnitzii A2-165 exhibit similar protective effects to induced barrier hyper-permeability in mice". Gut Microbes 6 (1): 1–9. 2015-01-02. doi:10.4161/19490976.2014.990784. PMID 25517879. 
  34. ↑ "Effects of apples and specific apple components on the cecal environment of conventional rats: role of apple pectin". BMC Microbiology 10 (1): 13. January 2010. doi:10.1186/1471-2180-10-13. PMID 20089145. 
  35. ↑ "Effects of Different Human Milk Oligosaccharides on Growth of Bifidobacteria in Monoculture and Co-culture With Faecalibacterium prausnitzii". Frontiers in Microbiology 11. 2020. doi:10.3389/fmicb.2020.569700. PMID 33193162. 
  36. ↑ "Recent advances in characterizing the gastrointestinal microbiome in Crohn's disease: a systematic review". Inflammatory Bowel Diseases 21 (6): 1219–1228. June 2015. doi:10.1097/MIB.0000000000000382. PMID 25844959. 
  37. ↑ 37.0 37.1 "Emerging Trends in "Smart Probiotics": Functional Consideration for the Development of Novel Health and Industrial Applications". Frontiers in Microbiology 8: 1889. 2017-09-29. doi:10.3389/fmicb.2017.01889. PMID 29033923. 
  38. ↑ "Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter?". Inflammatory Bowel Diseases 20 (7): E18–E19. July 2014. doi:10.1097/MIB.0000000000000079. PMID 24859302. 
  39. ↑ "Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn's disease". Scientific Reports 10 (1). November 2020. doi:10.1038/s41598-020-75306-z. PMID 33144591. Bibcode: 2020NatSR..1018879D. 
  40. ↑ 40.0 40.1 "Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease". Applied and Environmental Microbiology 81 (21): 7582–7592. November 2015. doi:10.1128/AEM.02006-15. PMID 26296733. Bibcode: 2015ApEnM..81.7582L. 
  41. ↑ "Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora". Inflammatory Bowel Diseases 14 (2): 147–161. February 2008. doi:10.1002/ibd.20330. PMID 18050295. 

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