Strain identifier
BacDive ID: 10998
Type strain:
Species: Rhodococcus opacus
Strain Designation: 1b, 18
Strain history: CIP <- 1995, DSM <- D. Claus, DSM 427 <- IMG: strain 1b <- D. Siebert: strain 18
NCBI tax ID(s): 37919 (species)
General
@ref: 10865
BacDive-ID: 10998
DSM-Number: 43205
keywords: genome sequence, 16S sequence, obligate aerobe, mesophilic, Gram-positive
description: Rhodococcus opacus 1b is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.
NCBI tax id
- NCBI tax id: 37919
- Matching level: species
strain history
@ref | history |
---|---|
10865 | <- IMG, 1b (Nocardia opaca) <- D. Siebert, 1B |
41630 | 2015, J. Kreit, Mohammed V Univ. Rabat, Morocco: strain GK3 |
67770 | DSM 43205 <-- IMG, 1b <-- D. Siebert 1B. |
121422 | CIP <- 1995, DSM <- D. Claus, DSM 427 <- IMG: strain 1b <- D. Siebert: strain 18 |
doi: 10.13145/bacdive10998.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- genus: Rhodococcus
- species: Rhodococcus opacus
- full scientific name: Rhodococcus opacus Klatte et al. 1995
synonyms
@ref synonym 20215 Rhodococcus imtechensis 20215 Rhodococcus percolatus
@ref: 10865
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Rhodococcus
species: Rhodococcus opacus
full scientific name: Rhodococcus opacus Klatte et al. 1995
strain designation: 1b, 18
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
121422 | positive | rod-shaped | no |
multimedia
- @ref: 10865
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43205.jpg
- caption: Medium 535 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
10865 | 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 |
10865 | 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 |
35692 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
41630 | MEDIUM 29- Brain heart agar | yes | Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g) | |
121422 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
10865 | positive | growth | 28 | mesophilic |
35692 | positive | growth | 30 | mesophilic |
41630 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
121422 | positive | growth | 10-37 | |
121422 | no | growth | 41 | thermophilic |
121422 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 121422
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.368
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
18483 | NaCl | positive | maximum | 7.5 % |
121422 | NaCl | positive | growth | 0-6 % |
121422 | NaCl | no | growth | 8 % |
121422 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H2)
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 |
121422 | 4853 | esculin | - | hydrolysis |
121422 | 606565 | hippurate | - | hydrolysis |
121422 | 17632 | nitrate | + | reduction |
121422 | 16301 | nitrite | - | reduction |
121422 | 17632 | nitrate | - | respiration |
68379 | 4853 | esculin | - | 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 | 28087 | glycogen | - | fermentation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - | |
121422 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | - | |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
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 |
121422 | oxidase | - | |
121422 | beta-galactosidase | + | 3.2.1.23 |
121422 | alcohol dehydrogenase | - | 1.1.1.1 |
121422 | gelatinase | - | |
121422 | amylase | + | |
121422 | DNase | - | |
121422 | catalase | + | 1.11.1.6 |
121422 | tween esterase | - | |
121422 | lecithinase | - | |
121422 | lysine decarboxylase | - | 4.1.1.18 |
121422 | ornithine decarboxylase | - | 4.1.1.17 |
121422 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18483 | - | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | - | + | - | |
10865 | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18483 | - | - | - | - | + | + | + | + | - | - | + | + | + | - | + | + | - | - | - | |
10865 | + | - | - | - | + | +/- | - | - | - | +/- | - | - | + | - | +/- | - | - | - | - | - |
121422 | - | + | + | - | + | + | - | - | - | + | - | + | + | - | + | - | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18483 | + | + | - | + | + | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121422 | + | + | + | - | - | - | + | + | + | + | - | + | + | + | + | - | - | - | + | - | - | - | + | - | - | + | + | - | - | - | - | - | + | + | + | + | + | - | - | - | - | + | - | + | - | + | + | - | - | + | + | + | - | + | - | - | + | + | - | + | + | + | + | + | + | + | + | + | + | + | - | + | + | + | + | + | - | - | - | + | + | + | - | - | + | - | - | - | + | + | - | - | + | + | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
10865 | soil |
67770 | Soil from the surroundings of a defective town gas pipe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18483 | 1 | German classification |
10865 | 1 | Risk group (German classification) |
121422 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rhodococcus opacus strain DSM 43205 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF536493 | 301 | ena | 37919 |
20218 | Rhodococcus opacus strain DSM 43205 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF536494 | 308 | ena | 37919 |
20218 | Rhodococcus opacus strain DSM 43205 note copy 3 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF536495 | 302 | ena | 37919 |
20218 | Rhodococcus opacus strain DSM 43205 16S ribosomal RNA gene, partial sequence | KF410349 | 1481 | ena | 37919 |
20218 | Rhodococcus opacus 16S rRNA gene, strain DSM43205T | X80630 | 1481 | ena | 37919 |
67770 | Rhodococcus opacus partial 16S rRNA gene, strain DSM 43205, isolate Clone 1 | LN827918 | 1510 | ena | 37919 |
67770 | Rhodococcus opacus partial 16S rRNA gene, strain DSM 43205, isolate Clone 2 | LN827919 | 1510 | ena | 37919 |
67770 | Rhodococcus opacus partial 16S rRNA gene, strain DSM 43205, isolate Clone 3 | LN827920 | 1509 | ena | 37919 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodococcus opacus strain ATCC 51881 | 37919.38 | wgs | patric | 37919 |
66792 | Rhodococcus opacus strain DSM 43205 | 37919.12 | wgs | patric | 37919 |
66792 | Rhodococcus opacus DSM 43205 | 2744054613 | draft | img | 37919 |
67770 | Rhodococcus opacus ATCC 51881 | GCA_012396235 | contig | ncbi | 37919 |
67770 | Rhodococcus opacus DSM 43205 | GCA_001646735 | contig | ncbi | 37919 |
66792 | Rhodococcus opacus DSM 43205 | GCA_910591545 | contig | ncbi | 37919 |
GC content
- @ref: 67770
- GC-content: 67.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 83 | no |
gram-positive | yes | 81.053 | no |
anaerobic | no | 98.956 | no |
halophile | no | 85.91 | no |
spore-forming | no | 62.956 | no |
glucose-util | yes | 89.686 | no |
aerobic | yes | 88.47 | no |
motile | no | 92.333 | no |
flagellated | no | 97.941 | no |
thermophile | no | 99.488 | yes |
glucose-ferment | no | 89.538 | no |
External links
@ref: 10865
culture collection no.: DSM 43205, ATCC 51881, CIP 104549, DSM 427, JCM 9703, CGMCC 4.1820, IFO 16217, KCTC 9811, LMG 18000, NBRC 100624, NBRC 16217, NCIMB 10810, NCIMB 13353
straininfo link
- @ref: 80252
- straininfo: 10716
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16902038 | Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete. | Ghosh A, Paul D, Prakash D, Mayilraj S, Jain RK | Int J Syst Evol Microbiol | 10.1099/ijs.0.63939-0 | 2006 | Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, India, Molecular Sequence Data, Nitrophenols/*metabolism, Pesticides, Phylogeny, Rhodococcus/chemistry/*classification/genetics/metabolism, Sequence Homology, Nucleic Acid, Soil Pollutants, Species Specificity | Genetics |
Biotechnology | 36281430 | Production of biopolymer precursors beta-alanine and L-lactic acid from CO(2) with metabolically versatile Rhodococcus opacus DSM 43205. | Salusjarvi L, Ojala L, Peddinti G, Lienemann M, Jouhten P, Pitkanen JP, Toivari M | Front Bioeng Biotechnol | 10.3389/fbioe.2022.989481 | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
10865 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43205) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43205 | |||
18483 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43205.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 | |
35692 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16470 | ||||
41630 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/34481 | ||||
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/ | ||||
68368 | Automatically annotated from API 20E | |||||
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) | |||
80252 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10716.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121422 | Curators of the CIP | Collection of Institut Pasteur (CIP 104549) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104549 |