Strain identifier
BacDive ID: 11199
Type strain:
Species: Nocardiopsis kunsanensis
Strain Designation: HA-9
Strain history: CIP <- 2003, KCTC <- JCM <- S.J. Kim: strain HA-9
NCBI tax ID(s): 1246445 (strain), 141693 (species)
General
@ref: 11731
BacDive-ID: 11199
DSM-Number: 44524
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Nocardiopsis kunsanensis HA-9 is an aerobe, spore-forming, mesophilic bacterium that was isolated from saltern.
NCBI tax id
NCBI tax id | Matching level |
---|---|
141693 | species |
1246445 | strain |
strain history
@ref | history |
---|---|
11731 | <- JCM <- KCTC <- S.-J. Kim; HA-9 |
67770 | KCTC 9831 <-- S.-J. Kim HA-9. |
67771 | <- S-J Kim HA-9 |
120513 | CIP <- 2003, KCTC <- JCM <- S.J. Kim: strain HA-9 |
doi: 10.13145/bacdive11199.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Nocardiopsidaceae
- genus: Nocardiopsis
- species: Nocardiopsis kunsanensis
- full scientific name: Nocardiopsis kunsanensis Chun et al. 2000
synonyms
- @ref: 20215
- synonym: Nocardiopsis litoralis
@ref: 11731
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiopsaceae
genus: Nocardiopsis
species: Nocardiopsis kunsanensis
full scientific name: Nocardiopsis kunsanensis Chun et al. 2000 emend. Nouioui et al. 2018
strain designation: HA-9
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence | cell shape |
---|---|---|---|---|
67771 | positive | |||
69480 | no | 92.115 | ||
69480 | positive | 100 | ||
120513 | positive | no | rod-shaped |
colony morphology
- @ref: 120513
multimedia
@ref | multimedia content | intellectual property rights | caption |
---|---|---|---|
11731 | https://www.dsmz.de/microorganisms/photos/DSM_44524-1.jpg | © Leibniz-Institut DSMZ | |
11731 | https://www.dsmz.de/microorganisms/photos/DSM_44524.jpg | © Leibniz-Institut DSMZ | Medium 1159 37°C |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11731 | GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) | yes | https://mediadive.dsmz.de/medium/1159 | Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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 |
37398 | MEDIUM 493 - for Nocardiopsis kunsanensis | yes | Distilled water make up to (1000.000 ml);Sodium chloride (100.000 g);Potassium chloride (2.000 g);Magnesium sulphate heptahydrate (10.000 g);Agar (15.000 g);Yeast extract (10.000 g);Casein hydrolysate acid hydrolysed vitamine-free (1.500 g);sodium citrate | |
11731 | MODIFIED CM+YE MEDIUM (B) (DSMZ Medium 910) | yes | https://mediadive.dsmz.de/medium/910 | Name: MODIFIED CM+YE MEDIUM (B) (DSMZ Medium 910) Composition: NaCl 100.0 g/l Agar 15.0 g/l MgSO4 x 7 H2O 10.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Trisodium citrate x 2 H2O 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.0498 g/l Distilled water |
120513 | CIP Medium 493 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=493 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
11731 | positive | growth | 37 | mesophilic |
37398 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
120513 | positive | growth | 25-37 | mesophilic |
120513 | no | growth | 10 | psychrophilic |
120513 | no | growth | 41 | thermophilic |
120513 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 92 |
69480 | yes | 98.946 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120513 | NaCl | positive | growth | 8-10 % |
120513 | NaCl | no | growth | 0 % |
120513 | NaCl | no | growth | 2 % |
120513 | NaCl | no | growth | 4 % |
120513 | NaCl | no | growth | 6 % |
observation
@ref | observation |
---|---|
67770 | quinones: MK-10(H8), MK-10(H6), MK-9(H8), MK-9(H6) |
67771 | quinones: MK-8 (H_6_), MK-8 (H_8_) |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
120513 | citrate | - | carbon source | 16947 |
120513 | esculin | - | hydrolysis | 4853 |
120513 | hippurate | + | hydrolysis | 606565 |
120513 | nitrate | - | reduction | 17632 |
120513 | nitrite | - | reduction | 16301 |
antibiotic resistance
- @ref: 120513
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 120513
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120513 | 15688 | acetoin | - | |
120513 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
120513 | oxidase | + | |
120513 | beta-galactosidase | - | 3.2.1.23 |
120513 | alcohol dehydrogenase | - | 1.1.1.1 |
120513 | gelatinase | + | |
120513 | catalase | + | 1.11.1.6 |
120513 | gamma-glutamyltransferase | + | 2.3.2.2 |
120513 | lysine decarboxylase | - | 4.1.1.18 |
120513 | ornithine decarboxylase | - | 4.1.1.17 |
120513 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
120513 | tryptophan deaminase | - | |
120513 | urease | - | 3.5.1.5 |
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 zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120513 | - | - | + | + | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120513 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120513 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11731 | saltern | Kunsan | Korea (north), Democratic People's Republic of | PRK | Asia |
67770 | Saltern | Kunsan | Republic of Korea | KOR | Asia |
67771 | From saltern at kunsan | Republic of Korea | KOR | Asia | |
120513 | Environment, Saltern | Kunsan | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Condition | #Saline | |
#Environmental | #Aquatic | #Non-marine Saline and Alkaline |
#Environmental | #Terrestrial |
taxonmaps
- @ref: 69479
- File name: preview.99_6051.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_1154;98_1377;99_6051&stattab=map
- Last taxonomy: Nocardiopsis
- 16S sequence: AB368716
- Sequence Identity:
- Total samples: 497
- soil counts: 82
- aquatic counts: 28
- animal counts: 376
- plant counts: 11
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11731 | 1 | Risk group (German classification) |
120513 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Nocardiopsis kunsanensis gene for 16S rRNA, partial sequence | AB368716 | 1459 | ena | 141693 |
11731 | Nocardiopsis kunsanensis HA-9T 16S ribosomal RNA gene, partial sequence | AF195412 | 1449 | ena | 141693 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardiopsis kunsanensis DSM 44524 | 1246445.3 | wgs | patric | 1246445 |
66792 | Nocardiopsis kunsanensis DSM 44524 | 2551306680 | draft | img | 1246445 |
67770 | Nocardiopsis kunsanensis DSM 44524 | GCA_000340965 | contig | ncbi | 1246445 |
GC content
@ref | GC-content | method |
---|---|---|
11731 | 71 | |
67770 | 69.6 | genome sequence analysis |
67770 | 71 | thermal denaturation, midpoint method (Tm) |
67771 | 71.0 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 92 | no |
motile | no | 93.692 | no |
gram-positive | yes | 91.178 | no |
anaerobic | no | 99.492 | no |
halophile | yes | 79.063 | no |
spore-forming | yes | 92.265 | no |
thermophile | no | 96.631 | no |
glucose-util | yes | 90.972 | no |
flagellated | no | 97.888 | no |
aerobic | yes | 93.205 | no |
glucose-ferment | no | 92.276 | no |
External links
@ref: 11731
culture collection no.: DSM 44524, JCM 10721, KCTC 9831, BCRC 16383, CGMCC 4.2083, CIP 108008, NBRC 100348
straininfo link
- @ref: 80446
- straininfo: 50671
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11034504 | Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern. | Chun J, Bae KS, Moon EY, Jung SO, Lee HK, Kim SJ | Int J Syst Evol Microbiol | 10.1099/00207713-50-5-1909 | 2000 | Actinomycetales/*classification/*genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA | Genetics |
Phylogeny | 19625431 | Nocardiopsis litoralis sp. nov., a halophilic marine actinomycete isolated from a sea anemone. | Chen YG, Wang YX, Zhang YQ, Tang SK, Liu ZX, Xiao HD, Xu LH, Cui XL, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.009704-0 | 2009 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Animals, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Anemones/*microbiology, Sodium Chloride/*metabolism | Metabolism |
Phylogeny | 20118291 | Nocardiopsis nikkonensis sp. nov., isolated from a compost sample. | Yamamura H, Ohkubo SY, Ishida Y, Otoguro M, Tamura T, Hayakawa M | Int J Syst Evol Microbiol | 10.1099/ijs.0.016956-0 | 2010 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Genetics |
Phylogeny | 34128783 | Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata. | Li F, Xie Q, Zhou S, Kong F, Xu Y, Ma Q, Wu W, Huang D, Zhao Y, Huang X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004817 | 2021 | Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardiopsis/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11731 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44524) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44524 | |||
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 | |
37398 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5583 | ||||
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/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
80446 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID50671.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120513 | Curators of the CIP | Collection of Institut Pasteur (CIP 108008) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108008 |