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/bacdive6355.20250331.9.3

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

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

@refgrowthtypetemperature
5171positivegrowth37
56709positivegrowth37
67770positivegrowth37

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5171anaerobe
56709anaerobe
125438anaerobe90.787
125439anaerobe99.8

murein

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

metabolite utilization

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

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-
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380glutamate decarboxylase-4.1.1.15
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
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 geneAJ1328421345nuccore88431
67770Dorea longicatena gene for 16S ribosomal RNA, partial sequence, strain: JCM 11232LC0372281493nuccore88431

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes81.063no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes90.787no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.254yes
125438spore-formingspore-formingAbility to form endo- or exosporesno61.991no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.564no
125438motile2+flagellatedAbility to perform flagellated movementno86.971no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes58.7
125439BacteriaNetmotilityAbility to perform movementyes75.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive67.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe99.8

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1