Strain identifier

BacDive ID: 6355

Type strain: Yes

Species: Dorea longicatena

Strain Designation: 111-35

Strain history: D. Taras 111-35.

NCBI tax ID(s): 411462 (strain), 88431 (species)

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General

@ref: 5171

BacDive-ID: 6355

DSM-Number: 13814

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Dorea longicatena 111-35 is an anaerobe, mesophilic bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
88431species
411462strain

strain history

@refhistory
5171<- D. Taras; 111-35
67770D. Taras 111-35.

doi: 10.13145/bacdive6355.20230509.8.1

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 longicatena
  • full scientific name: Dorea longicatena Taras et al. 2002

@ref: 5171

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Dorea

species: Dorea longicatena

full scientific name: Dorea longicatena Taras et al. 2002

strain designation: 111-35

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.039
69480100positive

Culture and growth conditions

culture medium

  • @ref: 5171
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
5171positivegrowth37mesophilic
56709positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

  • @ref: 56709
  • ability: positive
  • type: growth
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5171anaerobe
56709anaerobe
69480anaerobe99.998

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.823

murein

  • @ref: 5171
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

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
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
5171---+-+/-++----------+----------
5171---+-+/-++----------+----------
5171---+--++----------+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
5171human fecesGermanyDEUEurope
56709Human feces,healthy German individualGermanyDEUEurope1998-07-01Rehbrücke
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2993.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_1187;97_1878;98_2306;99_2993&stattab=map
  • Last taxonomy: Dorea longicatena subclade
  • 16S sequence: LC037228
  • Sequence Identity:
  • Total samples: 103953
  • soil counts: 510
  • aquatic counts: 3696
  • animal counts: 99499
  • plant counts: 248

Safety information

risk assessment

  • @ref: 5171
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5171Eubacterium sp. III-35 16S rRNA geneAJ1328421345ena88431
67770Dorea longicatena gene for 16S ribosomal RNA, partial sequence, strain: JCM 11232LC0372281493ena88431

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dorea longicatena DSM 13814411462.6wgspatric411462
66792Dorea longicatena DSM 13814640963046draftimg411462
66792Dorea longicatena DSM 13814GCA_000154065scaffoldncbi411462
66792Dorea longicatena DSM 13814GCA_025150085completencbi88431
66792Dorea longicatena strain DSM 1381488431.1235completepatric88431

GC content

  • @ref: 5171
  • GC-content: 45.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
motileno92.625no
flagellatedno96.507no
gram-positiveyes93.421no
anaerobicyes99.64yes
aerobicno99.233yes
halophileno62.404no
spore-formingno77.705no
glucose-fermentyes80.109no
thermophileno96.87yes
glucose-utilyes91.407no

External links

@ref: 5171

culture collection no.: DSM 13814, CCUG 45247, JCM 11232

straininfo link

  • @ref: 75828
  • straininfo: 100631

literature

  • topic: Phylogeny
  • Pubmed-ID: 11931151
  • title: Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces.
  • authors: Taras D, Simmering R, Collins MD, Lawson PA, Blaut M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-2-423
  • year: 2002
  • mesh: Eubacterium/*classification/genetics/isolation & purification, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Bacterial/chemistry, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitle
5171Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13814)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13814
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
56709Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45247)https://www.ccug.se/strain?id=45247
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
75828Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100631.1StrainInfo: A central database for resolving microbial strain identifiers