Strain identifier

BacDive ID: 6354

Type strain: Yes

Species: Dorea formicigenerans

Strain history: <- DSM <- ATCC <- LV Holdeman, VPI C8-13

NCBI tax ID(s): 411461 (strain), 39486 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1562

BacDive-ID: 6354

DSM-Number: 3992

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped

description: Dorea formicigenerans DSM 3992 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
39486species
411461strain

strain history

@refhistory
1562<- ATCC <- L.V. Holdeman, VPI C8-13
67771<- DSM <- ATCC <- LV Holdeman, VPI C8-13

doi: 10.13145/bacdive6354.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Dorea
  • species: Dorea formicigenerans
  • full scientific name: Dorea formicigenerans (Holdeman and Moore 1974) Taras et al. 2002
  • synonyms

    • @ref: 20215
    • synonym: Eubacterium formicigenerans

@ref: 1562

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Dorea

species: Dorea formicigenerans

full scientific name: Dorea formicigenerans (Holdeman and Moore 1974) Taras et al. 2002

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771positive
69480no91.049
69480positive100

Culture and growth conditions

culture medium

  • @ref: 1562
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Glucose 10.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
1562positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1562anaerobe
67771anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
67771no
69480no99.964

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1562---+-+-----------------------

Isolation, sampling and environmental information

isolation

@refsample type
1562human faeces
67771From human faeces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 1562
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Dorea formicigenerans strain ATCC 27755 16S ribosomal RNA gene, partial sequence
  • accession: L34619
  • length: 1479
  • database: ena
  • NCBI tax ID: 39486

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dorea formicigenerans ATCC 27755GCA_000169235contigncbi411461
66792Dorea formicigenerans ATCC 27755411461.4wgspatric411461
66792Dorea formicigenerans ATCC 27755411461.20wgspatric411461
66792Dorea formicigenerans ATCC 27755641736133draftimg411461
66792Dorea formicigenerans ATCC 27755GCA_025150245completencbi39486
66792Dorea formicigenerans strain ATCC 2775539486.544completepatric39486

GC content

  • @ref: 67771
  • GC-content: 40-44

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes51no
motileno89.912no
flagellatedno96.441yes
gram-positiveyes91.743yes
anaerobicyes99.999yes
aerobicno98.691yes
halophileno77.584no
spore-formingno70.244no
glucose-fermentyes71.474no
thermophileno98.068yes
glucose-utilyes82.336no

External links

@ref: 1562

culture collection no.: DSM 3992, ATCC 27755, JCM 10342, KCTC 15690, VPI C8-13

straininfo link

  • @ref: 75827
  • straininfo: 39158

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny33512312Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse.Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, Vogensen FKInt J Syst Evol Microbiol10.1099/ijsem.0.0046732021
Transcriptome34252073Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects.Verma S, Dutta SK, Firnberg E, Phillips L, Vinayek R, Nair PPPLoS One10.1371/journal.pone.02515902021Adult, Clostridioides/*physiology, *Fecal Microbiota Transplantation, Gastrointestinal Microbiome/genetics, *Healthy Volunteers, Humans, Male, *Metagenome, Middle Aged, Sequence AnalysisPathogenicity
Pathogenicity35578355Golden bifid might improve diarrhea-predominant irritable bowel syndrome via microbiota modulation.Luo M, Liu Q, Xiao L, Xiong LSJ Health Popul Nutr10.1186/s41043-022-00302-02022*Bacterial Infections, Diarrhea/etiology/therapy, Feces/microbiology, *Gastrointestinal Microbiome, Humans, *Irritable Bowel Syndrome/complications/diagnosis/therapy

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1562Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3992)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3992
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75827Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39158.1StrainInfo: A central database for resolving microbial strain identifiers