Strain identifier
BacDive ID: 10610
Type strain:
Species: Gordonia otitidis
Strain history: Y. Mikami IFM 10032.
NCBI tax ID(s): 1108044 (strain), 249058 (species)
General
@ref: 12094
BacDive-ID: 10610
DSM-Number: 44809
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Gordonia otitidis DSM 44809 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human.
NCBI tax id
NCBI tax id | Matching level |
---|---|
249058 | species |
1108044 | strain |
strain history
@ref | history |
---|---|
12094 | <- Y. Mikami, IFM |
67770 | Y. Mikami IFM 10032. |
doi: 10.13145/bacdive10610.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Gordoniaceae
- genus: Gordonia
- species: Gordonia otitidis
- full scientific name: Gordonia otitidis Iida et al. 2005
@ref: 12094
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Gordoniaceae
genus: Gordonia
species: Gordonia otitidis
full scientific name: Gordonia otitidis Iida et al. 2005
type strain: yes
Morphology
cell morphology
- @ref: 31314
- gram stain: positive
- cell length: 2.5-3.1 µm
- cell width: 0.6-0.8 µm
- cell shape: coccus-shaped
- motility: no
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20124 | Pure orange (2004) | 10-14 days | ISP 2 |
20124 | Beige (1001) | 10-14 days | ISP 3 |
20124 | 10-14 days | ISP 4 | |
20124 | Pure orange (2004) | 10-14 days | ISP 5 |
20124 | Beige (1001) | 10-14 days | ISP 6 |
20124 | Pure orange (2004) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20124 | no | ISP 2 |
20124 | no | ISP 3 |
20124 | no | ISP 4 |
20124 | no | ISP 5 |
20124 | no | ISP 6 |
20124 | no | ISP 7 |
pigmentation
- @ref: 31314
- production: yes
multimedia
- @ref: 12094
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44809.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12094 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
12094 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
20124 | 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 | |
20124 | ISP 3 | yes | Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms: | |
20124 | ISP 4 | yes | Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml | |
20124 | 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 | |
20124 | ISP 6 | yes | Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
20124 | ISP 7 | yes | Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12094 | positive | growth | 28 | mesophilic |
20124 | positive | optimum | 28 | mesophilic |
59484 | positive | growth | 30-37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31314 | aerobe |
59484 | aerobe |
observation
@ref | observation |
---|---|
31314 | aggregates in clumps |
67770 | quinones: MK-9(H2), MK-8(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
20124 | 17234 | glucose | + | |
20124 | 22599 | arabinose | - | |
20124 | 17992 | sucrose | + | |
20124 | 18222 | xylose | - | |
20124 | 17268 | myo-inositol | - | |
20124 | 29864 | mannitol | + | |
20124 | 28757 | fructose | + | |
20124 | 26546 | rhamnose | - | |
20124 | 16634 | raffinose | - | |
20124 | 62968 | cellulose | - | |
31314 | 17879 | 4-hydroxybenzoate | + | carbon source |
31314 | 16449 | alanine | + | carbon source |
31314 | 22599 | arabinose | + | carbon source |
31314 | 18403 | L-arabitol | + | carbon source |
31314 | 28260 | galactose | + | carbon source |
31314 | 25017 | leucine | + | carbon source |
31314 | 506227 | N-acetylglucosamine | + | carbon source |
31314 | 18401 | phenylacetate | + | carbon source |
31314 | 26271 | proline | + | carbon source |
31314 | 17148 | putrescine | + | carbon source |
31314 | 26490 | quinate | + | carbon source |
31314 | 17822 | serine | + | carbon source |
31314 | 17992 | sucrose | + | carbon source |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17992 | sucrose | + | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | - | |
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 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
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 | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | SAC |
---|---|---|---|---|---|---|---|---|---|---|---|
20124 | - | - | - | - | - | + | - | - | - | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20124 | - | - | + | + | + | - | - | - | - | + | + | - | - | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
12094 | human | Japan | JPN | Asia |
59484 | Human | Japan | JPN | Asia |
67770 | Ear discharge of a Japanese patient with external otitis |
isolation source categories
- Cat1: #Host
- Cat2: #Human
taxonmaps
- @ref: 69479
- File name: preview.99_3430.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_2147;98_2632;99_3430&stattab=map
- Last taxonomy: Gordonia
- 16S sequence: AB122026
- Sequence Identity:
- Total samples: 5392
- soil counts: 169
- aquatic counts: 1283
- animal counts: 3862
- plant counts: 78
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12094 | 2 | Risk group (German classification) |
20124 | 2 | German classification |
Sequence information
16S sequences
- @ref: 31314
- description: Gordonia otitidis gene for 16S rRNA, partial sequence, strain:IFM 10032
- accession: AB122026
- length: 1471
- database: nuccore
- NCBI tax ID: 1108044
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Gordonia otitidis NBRC 100426 | 1108044.3 | wgs | patric | 1108044 |
66792 | Gordonia otitidis NBRC 100426 | 2514885045 | draft | img | 1108044 |
67770 | Gordonia otitidis NBRC 100426 | GCA_000248075 | contig | ncbi | 1108044 |
GC content
@ref | GC-content | method |
---|---|---|
31314 | 64.9 | |
67770 | 64.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.557 | yes |
flagellated | no | 98.433 | yes |
gram-positive | yes | 90.492 | no |
anaerobic | no | 99.224 | yes |
aerobic | yes | 88.696 | yes |
halophile | no | 82.181 | no |
spore-forming | no | 81.697 | no |
thermophile | no | 99.157 | yes |
glucose-util | yes | 89.026 | yes |
glucose-ferment | no | 88.108 | no |
External links
@ref: 12094
culture collection no.: DSM 44809, IFM 10032, JCM 12355, NBRC 100426, CCUG 52243, CIP 109016
straininfo link
- @ref: 79883
- straininfo: 127244
literature
- topic: Phylogeny
- Pubmed-ID: 16166681
- title: Gordonia otitidis sp. nov., isolated from a patient with external otitis.
- authors: Iida S, Taniguchi H, Kageyama A, Yazawa K, Chibana H, Murata S, Nomura F, Kroppenstedt RM, Mikami Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63282-0
- year: 2005
- mesh: Actinomycetales Infections/*microbiology, Adult, Bronchitis/*microbiology, DNA, Bacterial, Female, Genes, rRNA, Genotype, Gordonia Bacterium/chemistry/*classification/genetics/isolation & purification, Humans, Male, Middle Aged, Molecular Sequence Data, Nucleic Acid Hybridization, Otitis Externa/*microbiology, Phenotype, Phylogeny, Pleural Effusion/*microbiology, RNA, Ribosomal, 16S
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
12094 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44809) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44809 | |||
20124 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44809.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 | |||
31314 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27629 | 28776041 | |
59484 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 52243) | https://www.ccug.se/strain?id=52243 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68379 | Automatically annotated from API Coryne | |||||
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 | |||
79883 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127244.1 | StrainInfo: A central database for resolving microbial strain identifiers |