Strain identifier
BacDive ID: 11102
Type strain:
Species: Nocardioides luteus
Strain Designation: 939-9
Strain history: CIP <- 1986, NCIMB <- H. Prauser, IMET
NCBI tax ID(s): 1844 (species)
General
@ref: 10986
BacDive-ID: 11102
DSM-Number: 43366
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Nocardioides luteus 939-9 is an aerobe, mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1844
- Matching level: species
strain history
@ref | history |
---|---|
10986 | <- IMET <- H. Prauser, 939-9 |
67770 | IMET 7830 <-- H. Prauser 939-9. |
120707 | CIP <- 1986, NCIMB <- H. Prauser, IMET |
doi: 10.13145/bacdive11102.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides luteus
- full scientific name: Nocardioides luteus Prauser 1985
@ref: 10986
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides luteus
full scientific name: Nocardioides luteus Prauser 1985
strain designation: 939-9
type strain: yes
Morphology
colony morphology
- @ref: 54000
- incubation period: >3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
10986 | 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 |
40646 | MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g) | |
10986 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf | |
120707 | CIP Medium 57 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57 | |
120707 | CIP Medium 236 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18488 | positive | optimum | 30 | mesophilic |
10986 | positive | growth | 28 | mesophilic |
40646 | positive | growth | 25 | mesophilic |
54000 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 54000
- oxygen tolerance: aerobe
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18488 | 17234 | glucose | + | |
18488 | 22599 | arabinose | + | |
18488 | 17992 | sucrose | + | |
18488 | 18222 | xylose | - | |
18488 | 17268 | myo-inositol | - | |
18488 | 29864 | mannitol | + | |
18488 | 28757 | fructose | + | |
18488 | 26546 | rhamnose | - | |
18488 | 16634 | raffinose | - | |
18488 | 62968 | cellulose | - | |
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 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
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 | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18488 | + | + | + | + | + | - | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
10986 | soil | Khartoum | Sudan | SDN | Africa |
54000 | Soil under Ficus | Khartoum | Sudan | SDN | Africa |
67770 | Soil | ||||
120707 | Environment, Soil under Ficus | Khartoum | Sudan | SDN | Africa |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_7662.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_3563;97_4377;98_5605;99_7662&stattab=map
- Last taxonomy: Nocardioides
- 16S sequence: AF005007
- Sequence Identity:
- Total samples: 15718
- soil counts: 9755
- aquatic counts: 920
- animal counts: 2174
- plant counts: 2869
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
10986 | 1 | Risk group (German classification) |
18488 | 1 | |
120707 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Nocardioides luteus 16S ribosomal RNA gene, partial sequence | AF005007 | 1469 | ena | 1844 |
20218 | Nocardioides luteus strain KCTC 9575 16S-23S internal transcribed spacer, complete sequence | AF017492 | 473 | ena | 1844 |
20218 | Nocardioides luteus partial 16S rRNA | X53212 | 1447 | ena | 1844 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardioides luteus JCM 3358 | GCA_014648595 | scaffold | ncbi | 1844 |
66792 | Nocardioides luteus strain JCM 3358 | 1844.5 | wgs | patric | 1844 |
66792 | Nocardioides luteus DSM 43366 | 2923421364 | draft | img | 1844 |
GC content
- @ref: 67770
- GC-content: 67.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 97.633 | no |
gram-positive | yes | 90.605 | no |
anaerobic | no | 99.167 | yes |
aerobic | yes | 93.978 | yes |
halophile | no | 81.352 | no |
spore-forming | no | 56.782 | no |
thermophile | no | 97.642 | yes |
glucose-util | yes | 89.14 | no |
motile | no | 97.348 | no |
glucose-ferment | no | 91.807 | no |
External links
@ref: 10986
culture collection no.: DSM 43366, ATCC 43052, DSM 43811, IFO 14491, IMET 7830, JCM 3358, NBRC 14491, NCIB 11455, CCUG 37986, CIP 103450, IMSNU 22020, KCTC 9575, LMG 16209, NCIMB 11455, VKM Ac-1246
straininfo link
- @ref: 80351
- straininfo: 13982
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9542088 | Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. | Yoon JH, Lee ST, Park YH | Int J Syst Bacteriol | 10.1099/00207713-48-1-187 | 1998 | DNA, Bacterial/analysis, Molecular Sequence Data, Nocardiaceae/*classification/*genetics, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/*analysis | Genetics |
Genetics | 10810191 | Structure of a teichoic acid from Nocardioides luteus VKM Ac-1246T cell wall. | Shashkov AS, Tul'skaya EM, Evtushenko LI, Gratchev AA, Naumova IB | Biochemistry (Mosc) | BCM65040598 | 2000 | Actinomycetales/*chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Cell Wall/*chemistry, Chromatography, Gel, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Pyruvic Acid/chemistry, Teichoic Acids/*chemistry | |
Phylogeny | 15545450 | Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. | Yi H, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63192-0 | 2004 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis/isolation & purification | Enzymology |
Phylogeny | 22552630 | Nocardioides panzhihuaensis sp. nov., a novel endophytic actinomycete isolated from medicinal plant Jatropha curcas L. | Qin S, Yuan B, Zhang YJ, Bian GK, Tamura T, Sun BZ, Li WJ, Jiang JH | Antonie Van Leeuwenhoek | 10.1007/s10482-012-9745-8 | 2012 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Base Composition, Endophytes/classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Jatropha/*microbiology, Molecular Sequence Data, Phylogeny, Plants, Medicinal/*microbiology | Metabolism |
Phylogeny | 22798645 | Nocardioides albertanoniae sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Miller AZ, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.043885-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
10986 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43366) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43366 | |||
18488 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43366.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 | |
40646 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15249 | ||||
54000 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 37986) | https://www.ccug.se/strain?id=37986 | |||
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
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 | |||
80351 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13982.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120707 | Curators of the CIP | Collection of Institut Pasteur (CIP 103450) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103450 |