Strain identifier
BacDive ID: 7779
Type strain:
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)
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 id | Matching level |
---|---|
762948 | strain |
2047 | species |
strain history
@ref | history |
---|---|
11181 | <- K. P. Schaal, HIK; <- ATCC; ATCC 17931 <- CDC, Atlanta; CDC X599 <- G.D. Roth; XDIA |
67770 | KCC A-0067 <-- L. K. Georg W858 <-- G. D. Roth XDIA. |
118914 | CIP <- 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
@ref synonym 20215 Actinomyces dentocariosus 20215 Rothia 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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 96.841 | |
69480 | 100 | positive |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19951 | Cream (9001) | 10-14 days | 5006 |
19951 | Cream (9001) | 10-14 days | 5425 |
19951 | Cream (9001) | 10-14 days | 5530 |
19951 | Cream (9001) | 10-14 days | ISP 2 |
19951 | Cream (9001) | 10-14 days | ISP 5 |
52727 | 2 days |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19951 | no | ISP 2 |
19951 | no | 5006 |
19951 | no | 5245 |
19951 | no | 5530 |
19951 | no | ISP 5 |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
19951 | ISP 2 | yes | Name: 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 | |
19951 | 5006 | yes | Medium: 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 | |
19951 | 5425 | yes | Name: 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 | |
19951 | 5530 | yes | ||
19951 | ISP 5 | yes | Name: 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 | |
38801 | MEDIUM 4 - Columbia agar with 20 % sterile defibrinated horse serum | yes | Horse serum (200.000 ml);Columbia agar (39.000 g);Distilled water make up to (1000.000 ml) | |
11181 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf | |
11181 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base | https://mediadive.dsmz.de/medium/693 |
118914 | CIP Medium 4 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=4 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19951 | positive | optimum | 37 | mesophilic |
11181 | positive | growth | 37 | mesophilic |
38801 | positive | growth | 37 | mesophilic |
52727 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
11181 | aerobe |
52727 | microaerophile |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | + | fermentation |
68379 | 28087 | glycogen | - | fermentation |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | + | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68380 | 35581 | indole | - | |
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | + | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | + | |
68380 | glycin arylamidase | + | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | + | |
68380 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | + | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68379 | catalase | + | 1.11.1.6 |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG | Control | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19951 | + | - | + | - | - | - | + | - | + | - | - | + | - | - | - | + | - | + | - | ||
11181 | + | + | + | - | - | - | + | - | + | - | + | + | - | - | - | + | - | + | - | - | + |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19951 | - | - | + | - | + | + | + | + | + | + | + | - | - | + | + | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19951 | - | - | - | - | - | - | - | - | - | + | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
52727 | - | - | - | - | - | + | + | - | - | - | - | - | - | - | + | - | - | + | + | + | + | + | + | + | + | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
11181 | carious teeth |
52727 | Human caries lesion |
67770 | Carious teeth |
118914 | Carious 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
@ref | biosafety level | biosafety level comment |
---|---|---|
11181 | 2 | Risk group (German classification) |
19951 | 2 | German classification |
118914 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rothia dentocariosa ATCC 17931 16S ribosomal RNA gene, partial sequence | M59055 | 1475 | ena | 762948 |
20218 | Staphylococcus lentus strain DSM 20352 16S ribosomal RNA gene, partial sequence | AY688073 | 465 | ena | 42858 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rothia dentocariosa ATCC 17931 | GCA_000164695 | complete | ncbi | 762948 |
66792 | Rothia dentocariosa ATCC 17931 | 762948.4 | complete | patric | 762948 |
66792 | Rothia dentocariosa strain NCTC10917 | 2047.138 | wgs | patric | 2047 |
66792 | Rothia dentocariosa ATCC 17931 | 649633093 | complete | img | 762948 |
66792 | Rothia dentocariosa NCTC 10917 | 2844142769 | draft | img | 2047 |
67770 | Rothia dentocariosa NCTC10917 | GCA_900455895 | contig | ncbi | 2047 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 53.7 | genome sequence analysis |
67770 | 68.0-69.7 | thermal denaturation, midpoint method (Tm) |
67770 | 54.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 94.11 | no |
flagellated | no | 96.681 | no |
gram-positive | yes | 95.868 | no |
anaerobic | no | 98.897 | yes |
aerobic | no | 68.478 | no |
halophile | yes | 56.457 | no |
spore-forming | no | 92.509 | no |
thermophile | no | 97.644 | yes |
glucose-util | yes | 82.242 | no |
glucose-ferment | no | 56.847 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 4990847 | Isolation and serological characterization of a cell wall antigen of Rothia dentocariosa. | Hammond BF | J Bacteriol | 10.1128/jb.103.3.634-640.1970 | 1970 | Actinomycetales/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 Specificity | Enzymology |
Phylogeny | 9060153 | An investigation of the intra-generic structure of Rothia by pyrolysis mass spectrometry. | Sutcliffe IC, Manfio GP, Schaal KP, Goodfellow M | Zentralbl Bakteriol | 10.1016/s0934-8840(97)80028-x | 1997 | Actinomycetales/*classification, Fatty Acids/analysis, Mass Spectrometry |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11181 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43762) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43762 | |||
19951 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43762.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
38801 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11249 | ||||
52727 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 35437) | https://www.ccug.se/strain?id=35437 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68379 | Automatically annotated from API Coryne | |||||
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
77222 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39345.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118914 | Curators of the CIP | Collection of Institut Pasteur (CIP 81.83) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.83 |