Strain identifier

BacDive ID: 191

Type strain: Yes

Species: Actinomyces oris

Strain Designation: W1053

Strain history: CCUG 34288 <-- ATCC 27044 <-- L. K. Georg CDC W1053 <-- New York City Dept. Health, USA; WVU 474.

NCBI tax ID(s): 544580 (species)

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General

@ref: 16679

BacDive-ID: 191

DSM-Number: 23056

keywords: genome sequence, 16S sequence, Bacteria, human pathogen

description: Actinomyces oris W1053 is a human pathogen that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 544580
  • Matching level: species

strain history

@refhistory
16679<- CCUG <- P. Pienta, ATCC <- L. K. Georg, CDC; W1053 <- New York City Dept. Hlth.; WVU 474
67770CCUG 34288 <-- ATCC 27044 <-- L. K. Georg CDC W1053 <-- New York City Dept. Health, USA; WVU 474.

doi: 10.13145/bacdive191.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinomyces
  • species: Actinomyces oris
  • full scientific name: Actinomyces oris Henssge et al. 2009

@ref: 16679

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces oris

full scientific name: Actinomyces oris Henssge et al. 2009

strain designation: W1053

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive91.697
6948092.875no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16679COLUMBIA 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
16679PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) 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 4.0 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
16679positivegrowth37
67770positivegrowth37

Physiology and metabolism

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
16679---+-++---++--+---+-++-+-----

Isolation, sampling and environmental information

isolation

@refsample type
16679human sputum
67770Human sputum

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

  • @ref: 16679
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomyces viscosus 16S rRNA gene, strain CCUG 34288AJ2340531371nuccore1656
20218Actinomyces oris strain ATCC 27044 16S ribosomal RNA gene, partial sequenceGQ4213081475nuccore544580
20218Actinomyces oris partial 16S rRNA gene, strain WVU 474HF5583791494nuccore544580
16679Actinomyces oris strain ATCC 27044 16S ribosomal RNA gene, partial sequenceEU667403481nuccore544580
67770Actinomyces oris gene for 16S ribosomal RNA, partial sequenceAB5459351517nuccore544580

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces oris strain CCUG 34288544580.476wgspatric544580
66792Actinomyces oris strain FDAARGOS_1051544580.571completepatric544580
67770Actinomyces oris CCUG 34288GCA_006546825scaffoldncbi544580

GC content

@refGC-content
1667966.0
6777066

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.697no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no78.467no
69480spore-formingspore-formingAbility to form endo- or exosporesno81.945no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no76.517no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.583yes
69480flagellatedmotile2+Ability to perform flagellated movementno92.875no

External links

@ref: 16679

culture collection no.: DSM 23056, ATCC 27044, CCUG 34288, WVU 474, JCM 16131

straininfo link

  • @ref: 69873
  • straininfo: 38771

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244431Emended description of Actinomyces naeslundii and descriptions of Actinomyces oris sp. nov. and Actinomyces johnsonii sp. nov., previously identified as Actinomyces naeslundii genospecies 1, 2 and WVA 963.Henssge U, Do T, Radford DR, Gilbert SC, Clark D, Beighton DInt J Syst Evol Microbiol10.1099/ijs.0.000950-02009Actinomyces/*classification/genetics/isolation & purification/physiology, Actinomycosis/*microbiology, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Blood/microbiology, Cerebrospinal Fluid/microbiology, DNA, Bacterial/analysis, Humans, Molecular Sequence Data, Mouth/*microbiology, Phenotype, Plague/microbiology, Sequence Analysis, DNA, Species SpecificityPathogenicity
Phylogeny22900599Pathogenicity of exopolysaccharide-producing Actinomyces oris isolated from an apical abscess lesion.Yamane K, Nambu T, Yamanaka T, Ishihara K, Tatami T, Mashimo C, Walker CB, Leung KP, Fukushima HInt Endod J10.1111/j.1365-2591.2012.02099.x2012Actinomyces/classification/isolation & purification/*pathogenicity, Actinomycetales Infections/*microbiology, Animals, Biofilms, Culture Media, Male, Mice, Mice, Inbred BALB C, Periapical Abscess/*microbiology, Phylogeny, *Polysaccharides, Bacterial, Species Specificity, Virulence, ViscosityCultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16679Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23056)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23056
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
69873Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38771.1StrainInfo: A central database for resolving microbial strain identifiers