Strain identifier

BacDive ID: 5437

Type strain: Yes

Species: Eubacterium nodatum

Strain Designation: D6A-5

Strain history: CIP <- 1994, ATCC <- L.V. Holdeman, VPI: strain D6A-5

NCBI tax ID(s): 1161902 (strain), 35518 (species)

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General

@ref: 1563

BacDive-ID: 5437

DSM-Number: 3993

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Eubacterium nodatum D6A-5 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from subgingival region of mouth.

NCBI tax id

NCBI tax idMatching level
1161902strain
35518species

strain history

@refhistory
1563<- ATCC <- L.V. Holdeman, VPI D6 A-5
67770CCUG 15996 <-- VPI D6A-5.
121321CIP <- 1994, ATCC <- L.V. Holdeman, VPI: strain D6A-5

doi: 10.13145/bacdive5437.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Eubacteriaceae
  • genus: Eubacterium
  • species: Eubacterium nodatum
  • full scientific name: Eubacterium nodatum Holdeman et al. 1980

@ref: 1563

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Eubacteriaceae

genus: Eubacterium

species: Eubacterium nodatum

full scientific name: Eubacterium nodatum Holdeman et al. 1980

strain designation: D6A-5

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

  • @ref: 46403
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1563PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
1563CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
34564MEDIUM 187 - for anaerobic bacteriayesDistilled water make up to (1000.000 ml);Glucose (5.000 g);Yeast extract(20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);Hemin solution - M00149(25.000 ml)
1563COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
121321CIP Medium 187yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187

culture temp

@refgrowthtypetemperaturerange
34564positivegrowth37mesophilic
46403positivegrowth37mesophilic
1563positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1563anaerobe
46403anaerobe
69480anaerobe99.167

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.963

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose+builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan+builds acid from
6838117306maltose+builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
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
68380urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46403C14:08.114
    46403C16:037.516
    46403C18:01.618
    46403C16:1 ω7c2.915.819
    46403C16:1 ω9c1.515.774
    46403C16:1 ω9c DMA1.316.242
    46403C17:0 anteiso1.716.722
    46403C17:1 ISO I/C16:0 DMA6.716.481
    46403C17:1 ω7c1.916.818
    46403C18:1 ω7c /12t/9t5.817.824
    46403C18:1 ω7c DMA9.118.282
    46403C18:1 ω9c2.617.769
    46403C18:1 ω9c DMA3.318.226
    46403C18:2 ω6,9c/C18:0 ANTE6.817.724
    46403Unidentified2.216.29
    46403unknown 18.1777.118.177
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1563-+---------------------------
1563-----------------------------
1563-+-------------------+/--------
46403-+---------------------------

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
46403--+--+---+--+----+---+--++------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
1563subgingival region of mouth
46403Human subgingival region
67770Subgingival area associated with periodontitis
121321Human, Subgingival region of mouth1978

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Mouth
#Host Body-Site#Oral cavity and airways#Gingiva

taxonmaps

  • @ref: 69479
  • File name: preview.99_598.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15810;96_381;97_429;98_489;99_598&stattab=map
  • Last taxonomy: [Eubacterium] nodatum subclade
  • 16S sequence: NR_118781
  • Sequence Identity:
  • Total samples: 17403
  • soil counts: 328
  • aquatic counts: 950
  • animal counts: 15984
  • plant counts: 141

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
15632Risk group (German classification)
1213211Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Eubacterium nodatum 16S ribosomal RNA subunit, partial sequenceU130411351ena1161902
20218E.nodatum (ATCC 33099) gene for ribosomal RNAZ362741406ena1161902
1563Eubacterium nodatum ATCC 33099 16S ribosomal RNA, partial sequenceNR_1187811351nuccore1161902

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Eubacterium nodatum ATCC 330991161902.3wgspatric1161902
66792Eubacterium nodatum ATCC 330992558860175draftimg1161902
67770Eubacterium nodatum ATCC 33099GCA_000510425contigncbi1161902

GC content

@refGC-contentmethod
156338.0
6777038thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno74no
motileno92.079no
gram-positiveyes59.124no
anaerobicyes99.324yes
aerobicno98.776no
halophileno70.173no
spore-formingno84.981no
flagellatedno98.361no
thermophileno92.076yes
glucose-utilyes84.424no
glucose-fermentyes57.278no

External links

@ref: 1563

culture collection no.: DSM 3993, ATCC 33099, CCUG 15996, JCM 14550, VPI D6 A-5, CIP 104213, JCM 9977, VPI D6A-5

straininfo link

  • @ref: 74925
  • straininfo: 40331

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1563Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3993)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3993
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
34564Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16097
46403Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15996)https://www.ccug.se/strain?id=15996
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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)
74925Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40331.1StrainInfo: A central database for resolving microbial strain identifiers
121321Curators of the CIPCollection of Institut Pasteur (CIP 104213)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104213