Database Authors
Ron Caspi1, Anamika Kothari1
1SRI International
Summary Faecalibacterium prausnitzii (previously known incorrectly as Fusobacterium prauznitzii) accounts for around 8% of the total colonic microbiota. It is a Gram-positive, non-motile, non-spore-forming, anaerobic bacterium. It has been proposed as a potential probiotic for treatment of gut inflammation since it stimulates the expression of the anti-inflammatory cytokine interleukin 10 (IL-10) in peripheral blood mononuclear cells.

Faecalibacterium prausnitzii is known to utilize a variety of carbohydrates, including glucose, acetate, inulin, apple pectin, and some host-derived carbon sources, such as D-glucosamine and N-acetyl-D-glucosamine [LopezSiles12]. The major end products of glucose fermentation are butanoate, formate, and (R)-lactate [Duncan02]. Even though the organism is sensitive to oxygen, it can grow in the presence of low concentrations of oxygen, utilizing it as as an electron acceptor for an extracellular electron shuttle that involves thiols (such as cysteine or glutathione) and riboflavin [Khan12]. Faecalibacterium prausnitzii does not biosynthesize either ubiquinone or menaquinone [Fenn17].

A genome-based analysis of the metabolic network of Faecalibacterium prausnitzii was published in 2014 [Heinken14].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 25.0 and MetaCyc [Caspi18] version 25.0 on 23-Feb-2021. The database has been improved by some manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP022479.13,0022,797851203,110,044RefSeq:NZ_CP022479.1
Ortholog data available?Yes
Database Contents
Genes3,002
Pathways144
Enzymatic Reactions806
Transport Reactions60
Polypeptides2,799
Protein Complexes65
Enzymes506
Transporters272
Compounds956
Transcription Units1,789
tRNAs63
Protein Features8,505
GO Terms15,830
Database Version29.0
Sequence SourceGCF_002734145.1
Synonyms Faecalibacterium prausnitzii A2-165GCF_002734145.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Oscillospiraceae
Faecalibacterium
Faecalibacterium prausnitzii
Faecalibacterium prausnitzii A2-165
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07362387
NCBI BioProjectPRJNA224116
NCBI-Taxonomy411483
Environmenthuman fecal sample
Geographic LocationFrance
Collection Date2016-02-9
Relationship to Oxygenanaerobe
Trophic Levelheterotroph
Biotic Relationshipmutualistic
HostHomo sapiens
Health/Disease Statehealthy
Human Microbiome Body Sitegastrointestinal-tract
Annotation ProviderNCBI RefSeq
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Duncan02: Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ (2002). "Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov." Int J Syst Evol Microbiol 52(Pt 6);2141-2146. PMID: 12508881

Fenn17: Fenn K, Strandwitz P, Stewart EJ, Dimise E, Rubin S, Gurubacharya S, Clardy J, Lewis K (2017). "Quinones are growth factors for the human gut microbiota." Microbiome 5(1);161. PMID: 29262868

Heinken14: Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I (2014). "Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe." J Bacteriol 196(18);3289-302. PMID: 25002542

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Khan12: Khan MT, Duncan SH, Stams AJ, van Dijl JM, Flint HJ, Harmsen HJ (2012). "The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases." ISME J 6(8);1578-85. PMID: 22357539

LopezSiles12: Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ (2012). "Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth." Appl Environ Microbiol 78(2);420-8. PMID: 22101049

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