Strain identifier
BacDive ID: 10611
Type strain:
Species: Gordonia effusa
Strain history: CIP <- 2006, JCM <- 2003, IFM
NCBI tax ID(s): 1077974 (strain), 263908 (species)
General
@ref: 12095
BacDive-ID: 10611
DSM-Number: 44810
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, human pathogen
description: Gordonia effusa CCUG 53882 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from human sputum.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1077974 | strain |
263908 | species |
strain history
@ref | history |
---|---|
12095 | <- Y. Mikami, IFM |
67770 | Y. Mikami IFM 10200. |
118998 | CIP <- 2006, JCM <- 2003, IFM |
doi: 10.13145/bacdive10611.20230509.8.1
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 effusa
- full scientific name: Gordonia effusa Kageyama et al. 2006
@ref: 12095
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Gordoniaceae
genus: Gordonia
species: Gordonia effusa
full scientific name: Gordonia effusa Kageyama et al. 2006 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31693 | positive | 0.5-2.1 µm | 0.3-0.6 µm | rod-shaped | no | |
69480 | no | 95.48 | ||||
69480 | positive | 99.999 | ||||
118998 | positive | rod-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20125 | Pastel yellow (1034) | 10-14 days | ISP 2 |
20125 | Pastel yellow (1034) | 10-14 days | ISP 3 |
20125 | Pastel yellow (1034) | 10-14 days | ISP 4 |
20125 | Pastel yellow (1034) | 10-14 days | ISP 5 |
20125 | Pastel yellow (1034) | 10-14 days | ISP 6 |
20125 | Pastel yellow (1034) | 10-14 days | ISP 7 |
60051 | 2 days |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20125 | no | ISP 2 |
20125 | no | ISP 3 |
20125 | no | ISP 4 |
20125 | no | ISP 5 |
20125 | no | ISP 6 |
20125 | no | ISP 7 |
pigmentation
- @ref: 31693
- production: yes
multimedia
- @ref: 12095
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44810.jpg
- caption: Medium 535 28 °C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12095 | 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 |
20125 | 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 | |
20125 | 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: | |
20125 | 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 | |
20125 | 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 | |
20125 | 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 | |
20125 | 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 | |
37519 | MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum | yes | Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g) | |
118998 | CIP Medium 116 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12095 | positive | growth | 28 | mesophilic |
20125 | positive | optimum | 28 | mesophilic |
31693 | positive | growth | 30 | mesophilic |
31693 | positive | optimum | 30 | mesophilic |
37519 | positive | growth | 30 | mesophilic |
60051 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31693 | positive | growth | 7 |
31693 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31693 | aerobe |
60051 | microaerophile |
118998 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31693 | yes | |
69481 | yes | 100 |
69480 | no | 99.925 |
observation
@ref | observation |
---|---|
31693 | aggregates in chains |
67770 | quinones: MK-9(H8), MK-9(H6) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31693 | 16449 | alanine | + | carbon source |
31693 | 35391 | aspartate | + | carbon source |
31693 | 16947 | citrate | + | carbon source |
31693 | 506227 | N-acetylglucosamine | + | carbon source |
31693 | 30031 | succinate | + | carbon source |
31693 | 17992 | sucrose | + | carbon source |
118998 | 17632 | nitrate | - | reduction |
118998 | 16301 | nitrite | - | reduction |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | 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 |
metabolite production
- @ref: 118998
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31693 | cytochrome oxidase | + | 1.9.3.1 |
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 | pyrazinamidase | - | 3.5.1.B15 |
118998 | oxidase | - | |
118998 | catalase | + | 1.11.1.6 |
118998 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase lipase (C 8) | + | |
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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20125 | - | - | +/- | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20125 | + | + | + | + | + | - | - | - | - | + | + | - | + | - | + | + | - | - | - | |
118998 | + | - | + | - | - | - | - | - | - | + | + | - | + | - | + | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
12095 | human sputum | Japan | JPN | Asia |
60051 | Human sputum,74-yr-old man,kidney dysfunction | Japan | JPN | Asia |
67770 | Sputum of a 74-year-old Japanese male patient with kidney dysfunction | |||
118998 | Human, Sputum | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Fluids | #Sputum |
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
12095 | yes, in single cases | 1 | Risk group (German classification) |
20125 | 2 | ||
118998 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 12095
- description: Gordonia effusa gene for 16S rRNA, partial sequence, strain: IFM 10200
- accession: AB162799
- length: 1509
- database: ena
- NCBI tax ID: 263908
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Gordonia effusa NBRC 100432 | 1077974.3 | wgs | patric | 1077974 |
66792 | Gordonia effusa NBRC 100432 | 2523231038 | draft | img | 1077974 |
67770 | Gordonia effusa NBRC 100432 | GCA_000241305 | contig | ncbi | 1077974 |
GC content
- @ref: 67770
- GC-content: 62.5
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 95.481 | yes |
flagellated | no | 98.235 | yes |
gram-positive | yes | 91.208 | yes |
anaerobic | no | 99.479 | yes |
aerobic | yes | 89.367 | no |
halophile | no | 94.209 | no |
spore-forming | no | 76.593 | yes |
thermophile | no | 99.478 | no |
glucose-util | yes | 88.967 | no |
glucose-ferment | no | 92.311 | no |
External links
@ref: 12095
culture collection no.: CCUG 53882, CIP 109345, DSM 44810, IFM 10200, JCM 12130, NBRC 100432
straininfo link
- @ref: 79884
- straininfo: 297194
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16902014 | Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan. | Kageyama A, Iida S, Yazawa K, Kudo T, Suzuki SI, Koga T, Saito H, Inagawa H, Wada A, Kroppenstedt RM, Mikami Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64067-0 | 2006 | Aged, Base Composition, Corynebacterium/chemistry/*classification/physiology, Corynebacterium Infections/complications/microbiology, DNA, Bacterial/chemistry/genetics, Humans, Japan, Kidney Diseases/complications, Male, Middle Aged, Molecular Sequence Data, Phenotype, Pneumonia, Bacterial/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Sputum/microbiology | Pathogenicity |
Phylogeny | 33709899 | Gordonia asplenii sp. nov., isolated from humic soil on bird's nest fern (Asplenium nidus L.). | Suriyachadkun C, Ngaemthao W, Pujchakarn T, Chunhametha S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004746 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
12095 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44810) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44810 | ||||
20125 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44810.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 | ||||
31693 | 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 | 27970 | 28776041 | ||
37519 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7076 | |||||
60051 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53882) | https://www.ccug.se/strain?id=53882 | ||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
79884 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297194.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
118998 | Curators of the CIP | Collection of Institut Pasteur (CIP 109345) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109345 |