Strain identifier

BacDive ID: 24116

Type strain: Yes

Species: Oribacterium asaccharolyticum

Strain Designation: ACB7, HM-482

Strain history: <- DSM <- M. Sizova, Northeastern Univ., Boston, USA

NCBI tax ID(s): 1501332 (species)

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

@ref: 20700

BacDive-ID: 24116

DSM-Number: 24638

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

description: Oribacterium asaccharolyticum ACB7 is an anaerobe, mesophilic, motile bacterium that was isolated from subgingival plaque, healthy 25-year-old African American female.

NCBI tax id

  • NCBI tax id: 1501332
  • Matching level: species

strain history

@refhistory
20700<- M. Sizova, Northeastern Univ., Boston, USA
67771<- DSM <- M. Sizova, Northeastern Univ., Boston, USA

doi: 10.13145/bacdive24116.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Oribacterium
  • species: Oribacterium asaccharolyticum
  • full scientific name: Oribacterium asaccharolyticum Sizova et al. 2014

@ref: 20700

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Oribacterium

species: Oribacterium asaccharolyticum

full scientific name: Oribacterium asaccharolyticum Sizova et al. 2014

strain designation: ACB7, HM-482

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771rod-shapedyes
67771variable

Culture and growth conditions

culture medium

  • @ref: 20700
  • name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/339
  • composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20700positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
20700anaerobe
67771anaerobe

spore formation

  • @ref: 67771
  • spore formation: no

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-
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
20700-+-+-++----------++--+---+/----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20700subgingival plaque, healthy 25-year-old African American femaleMA, BostonUSAUSANorth America
67771From subgingival plaque, healthy 25-year-old African American femaleBostonUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Subgingival plaque
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_4525.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_112;96_314;97_350;98_3401;99_4525&stattab=map
  • Last taxonomy: Oribacterium
  • 16S sequence: HM120211
  • Sequence Identity:
  • Total samples: 8583
  • soil counts: 59
  • aquatic counts: 56
  • animal counts: 8384
  • plant counts: 84

Safety information

risk assessment

  • @ref: 20700
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20700
  • description: Oribacterium asaccharolyticum ACB7 16S ribosomal RNA gene, partial sequence
  • accession: HM120211
  • length: 1436
  • database: ena
  • NCBI tax ID: 796944

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oribacterium asaccharolyticum ACB7GCA_000238075scaffoldncbi796944
66792Oribacterium asaccharolyticum ACB72513237306draftimg796944

GC content

@refGC-contentmethod
2070043.3sequence analysis
6777143.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes79.736yes
flagellatedno75.343no
gram-positiveyes64.456yes
anaerobicyes99.05yes
aerobicno98.769yes
halophileno70.65no
spore-formingno85.187yes
thermophileno98.218yes
glucose-utilyes83.935no
glucose-fermentyes75.068no

External links

@ref: 20700

culture collection no.: DSM 24638, ATCC BAA 2639, KCTC 15511

straininfo link

  • @ref: 88076
  • straininfo: 399846

literature

  • topic: Phylogeny
  • Pubmed-ID: 24824639
  • title: Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.
  • authors: Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, Hohmann T, Doerfert SN, Fowle W, Earl AM, Nelson KE, Epstein SS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.060988-0
  • year: 2014
  • mesh: Adult, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dental Plaque/*microbiology, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Female, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification, Humans, Molecular Sequence Data, Mouth/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20700Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24638Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24638)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88076Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399846.1