Strain identifier
BacDive ID: 10794
Type strain:
Species: Nocardia thailandica
Strain history: CIP <- 2005, JCM <- 2004, IFM
NCBI tax ID(s): 1206740 (strain), 257275 (species)
General
@ref: 12093
BacDive-ID: 10794
DSM-Number: 44808
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, human pathogen
description: Nocardia thailandica DSM 44808 is an obligate aerobe, spore-forming, mesophilic human pathogen that was isolated from human.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1206740 | strain |
257275 | species |
strain history
@ref | history |
---|---|
12093 | <- Y. Mikami, IFM |
67770 | Y. Mikami IFM 10145. |
123497 | CIP <- 2005, JCM <- 2004, IFM |
doi: 10.13145/bacdive10794.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Nocardiaceae
- genus: Nocardia
- species: Nocardia thailandica
- full scientific name: Nocardia thailandica Kageyama et al. 2005
@ref: 12093
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Nocardia
species: Nocardia thailandica
full scientific name: Nocardia thailandica Kageyama et al. 2005
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 95.388 | ||
69480 | 100 | positive | ||
123497 | no | positive | rod-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20123 | Rose (3017) | 10-14 days | ISP 2 |
20123 | 10-14 days | ISP 3 | |
20123 | 10-14 days | ISP 4 | |
20123 | Saffron yellow (1017) | 10-14 days | ISP 5 |
20123 | Saffron yellow (1017) | 10-14 days | ISP 6 |
20123 | Saffron yellow (1017) | 10-14 days | ISP 7 |
123497 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20123 | no | ISP 2 |
20123 | no | ISP 3 |
20123 | no | ISP 4 |
20123 | no | ISP 5 |
20123 | no | ISP 6 |
20123 | no | ISP 7 |
multimedia
- @ref: 12093
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44808.jpg
- caption: Medium 535 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12093 | 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 |
20123 | 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 | |
20123 | 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: | |
20123 | 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 | |
20123 | 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 | |
20123 | 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 | |
20123 | 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 | |
38301 | 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) | |
123497 | CIP Medium 116 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12093 | positive | growth | 28 | mesophilic |
20123 | positive | optimum | 28 | mesophilic |
38301 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
123497 | positive | growth | 25-41 | |
123497 | no | growth | 10 | psychrophilic |
123497 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 123497
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 95 |
69480 | no | 99.355 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123497 | NaCl | positive | growth | 0-4 % |
123497 | NaCl | no | growth | 6 % |
123497 | NaCl | no | growth | 8 % |
123497 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H4, ω-cycl)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
20123 | 17234 | glucose | + | |
20123 | 22599 | arabinose | - | |
20123 | 17992 | sucrose | - | |
20123 | 18222 | xylose | + | |
20123 | 17268 | myo-inositol | - | |
20123 | 29864 | mannitol | - | |
20123 | 28757 | fructose | + | |
20123 | 26546 | rhamnose | - | |
20123 | 16634 | raffinose | - | |
20123 | 62968 | cellulose | - | |
123497 | 16947 | citrate | - | carbon source |
123497 | 4853 | esculin | + | hydrolysis |
123497 | 606565 | hippurate | - | hydrolysis |
123497 | 17632 | nitrate | + | reduction |
123497 | 16301 | nitrite | - | reduction |
123497 | 17632 | nitrate | - | respiration |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17992 | sucrose | - | fermentation |
metabolite production
- @ref: 123497
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
123497 | 15688 | acetoin | - | |
123497 | 17234 | glucose | - |
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 |
123497 | oxidase | - | |
123497 | beta-galactosidase | - | 3.2.1.23 |
123497 | alcohol dehydrogenase | - | 1.1.1.1 |
123497 | gelatinase | - | |
123497 | amylase | - | |
123497 | DNase | - | |
123497 | caseinase | - | 3.4.21.50 |
123497 | catalase | + | 1.11.1.6 |
123497 | tween esterase | - | |
123497 | gamma-glutamyltransferase | + | 2.3.2.2 |
123497 | lecithinase | - | |
123497 | lipase | - | |
123497 | lysine decarboxylase | - | 4.1.1.18 |
123497 | ornithine decarboxylase | - | 4.1.1.17 |
123497 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123497 | tryptophan deaminase | - | |
123497 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
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-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 |
---|---|---|---|---|---|---|---|---|---|---|---|
20123 | - | - | + | - | - | + | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20123 | + | + | + | + | + | + | - | - | - | + | + | - | - | - | + | + | - | - | - | |
123497 | + | + | + | - | + | + | - | + | - | + | + | - | + | - | + | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123497 | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
12093 | human | Thailand | THA | Asia |
67770 | Pus of a patient | Thailand | THA | Asia |
123497 | Human, Pus | Thailand | THA | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Human
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
12093 | yes, in single cases | 1 | Risk group (German classification) |
123497 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Nocardia thailandica strain DSM 44808 16S ribosomal RNA gene, partial sequence | JF797320 | 1412 | ena | 257275 |
20218 | Nocardia thailandica strain DSM 44808 16S ribosomal RNA gene, partial sequence | JN041449 | 462 | ena | 257275 |
20218 | Nocardia thailandica gene for 16S rRNA, partial sequence | AB126874 | 1440 | ena | 257275 |
20218 | Nocardia thailandica 16S ribosomal RNA gene, partial sequence | GQ376186 | 1439 | ena | 257275 |
20218 | Nocardia testacea strain W9870 16S ribosomal RNA gene, partial sequence | GQ853070 | 1439 | ena | 248551 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardia thailandica NBRC 100428 | 1206740.4 | wgs | patric | 1206740 |
66792 | Nocardia thailandica NBRC 100428 | 2551306162 | draft | img | 1206740 |
67770 | Nocardia thailandica NBRC 100428 | GCA_000308795 | contig | ncbi | 1206740 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 71.7 | genome sequence analysis |
67770 | 72 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 95 | no |
motile | no | 92.704 | no |
gram-positive | yes | 89.599 | no |
anaerobic | no | 99.628 | no |
halophile | no | 93.375 | no |
spore-forming | yes | 72.216 | no |
thermophile | no | 99.392 | no |
glucose-util | yes | 88.654 | yes |
flagellated | no | 97.859 | no |
aerobic | yes | 93.22 | no |
glucose-ferment | no | 93.116 | no |
External links
@ref: 12093
culture collection no.: DSM 44808, IFM 10145, JCM 12356, CIP 108722, NBRC 100428
straininfo link
- @ref: 80059
- straininfo: 138030
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
12093 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44808) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44808 | |||
20123 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44808.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 | |
38301 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6382 | ||||
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 | |||||
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 | |||
80059 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID138030.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123497 | Curators of the CIP | Collection of Institut Pasteur (CIP 108722) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108722 |