Strain identifier

BacDive ID: 7779

Type strain: Yes

Species: Rothia dentocariosa

Strain Designation: XDIA, X599

Strain history: CIP <- 1981, ATCC <- CDC: strain X599 <- G.D. Roth: strain XDIA

NCBI tax ID(s): 762948 (strain), 2047 (species)

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

@ref: 11181

BacDive-ID: 7779

DSM-Number: 43762

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

description: Rothia dentocariosa XDIA is an aerobe, mesophilic bacterium that was isolated from carious teeth.

NCBI tax id

NCBI tax idMatching level
762948strain
2047species

strain history

@refhistory
11181<- K. P. Schaal, HIK; <- ATCC; ATCC 17931 <- CDC, Atlanta; CDC X599 <- G.D. Roth; XDIA
67770KCC A-0067 <-- L. K. Georg W858 <-- G. D. Roth XDIA.
118914CIP <- 1981, ATCC <- CDC: strain X599 <- G.D. Roth: strain XDIA

doi: 10.13145/bacdive7779.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Rothia
  • species: Rothia dentocariosa
  • full scientific name: Rothia dentocariosa corrig. (Onishi 1949) Georg and Brown 1967 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Actinomyces dentocariosus
    20215Rothia dentocariosus

@ref: 11181

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Rothia

species: Rothia dentocariosa

full scientific name: Rothia dentocariosa (Onishi 1949) Georg and Brown 1967 emend. Nouioui et al. 2018

strain designation: XDIA, X599

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no96.841
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19951Cream (9001)10-14 days5006
19951Cream (9001)10-14 days5425
19951Cream (9001)10-14 days5530
19951Cream (9001)10-14 daysISP 2
19951Cream (9001)10-14 daysISP 5
527272 days

multicellular morphology

@refforms multicellular complexmedium name
19951noISP 2
19951no5006
19951no5245
19951no5530
19951noISP 5

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19951ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
199515006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
199515425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
199515530yes
19951ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
38801MEDIUM 4 - Columbia agar with 20 % sterile defibrinated horse serumyesHorse serum (200.000 ml);Columbia agar (39.000 g);Distilled water make up to (1000.000 ml)
11181TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
11181COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
118914CIP Medium 4yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=4

culture temp

@refgrowthtypetemperaturerange
19951positiveoptimum37mesophilic
11181positivegrowth37mesophilic
38801positivegrowth37mesophilic
52727positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
11181aerobe
52727microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.998

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
6836815688acetoin+
6836835581indole-

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
68379catalase+1.11.1.6
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
19951+-+---+-+--+---+-+-
11181+++---+-+-++---+-+--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19951--+-+++++++--+++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19951---------+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
52727-----++-------+--++++++++++-+

Isolation, sampling and environmental information

isolation

@refsample type
11181carious teeth
52727Human caries lesion
67770Carious teeth
118914Carious teeth

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_754.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_13;97_13;98_15;99_754&stattab=map
  • Last taxonomy: Rothia dentocariosa
  • 16S sequence: M59055
  • Sequence Identity:
  • Total samples: 8842
  • soil counts: 134
  • aquatic counts: 100
  • animal counts: 8553
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
111812Risk group (German classification)
199512German classification
1189141Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rothia dentocariosa ATCC 17931 16S ribosomal RNA gene, partial sequenceM590551475ena762948
20218Staphylococcus lentus strain DSM 20352 16S ribosomal RNA gene, partial sequenceAY688073465ena42858

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rothia dentocariosa ATCC 17931GCA_000164695completencbi762948
66792Rothia dentocariosa ATCC 17931762948.4completepatric762948
66792Rothia dentocariosa strain NCTC109172047.138wgspatric2047
66792Rothia dentocariosa ATCC 17931649633093completeimg762948
66792Rothia dentocariosa NCTC 109172844142769draftimg2047
67770Rothia dentocariosa NCTC10917GCA_900455895contigncbi2047

GC content

@refGC-contentmethod
6777053.7genome sequence analysis
6777068.0-69.7thermal denaturation, midpoint method (Tm)
6777054.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.11no
flagellatedno96.681no
gram-positiveyes95.868no
anaerobicno98.897yes
aerobicno68.478no
halophileyes56.457no
spore-formingno92.509no
thermophileno97.644yes
glucose-utilyes82.242no
glucose-fermentno56.847no

External links

@ref: 11181

culture collection no.: DSM 43762, ATCC 17931, DSM 46363, IFO 12531, JCM 3067, KCC A-0067, NBRC 12531, CCUG 35437, CIP 81.83, NCTC 10917, CDC X599, CCM 7007, IAM 14816, IFM 1284, IMET 11515, IMSNU 21309, KCTC 3204, NRRL B-8017, PCM 2349

straininfo link

  • @ref: 77222
  • straininfo: 39345

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny4990847Isolation and serological characterization of a cell wall antigen of Rothia dentocariosa.Hammond BFJ Bacteriol10.1128/jb.103.3.634-640.19701970Actinomycetales/classification/*immunology, Animals, Antigens/analysis/*isolation & purification, Cell Wall/*immunology, Chromatography, Gas, Chromatography, Paper, Fluorescent Antibody Technique, Fructose/analysis, Galactose/analysis, Glucose/analysis, Immune Sera, Immunodiffusion, Immunoelectrophoresis, Microscopy, Fluorescence, *Polysaccharides, Bacterial/analysis/isolation & purification, Rabbits, Ribose/analysis, Serotyping, Species SpecificityEnzymology
Phylogeny9060153An investigation of the intra-generic structure of Rothia by pyrolysis mass spectrometry.Sutcliffe IC, Manfio GP, Schaal KP, Goodfellow MZentralbl Bakteriol10.1016/s0934-8840(97)80028-x1997Actinomycetales/*classification, Fatty Acids/analysis, Mass Spectrometry

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11181Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43762)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43762
19951Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43762.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
38801Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11249
52727Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35437)https://www.ccug.se/strain?id=35437
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77222Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39345.1StrainInfo: A central database for resolving microbial strain identifiers
118914Curators of the CIPCollection of Institut Pasteur (CIP 81.83)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.83