Strain identifier
BacDive ID: 11129
Type strain:
Species: Nocardioides exalbidus
Strain Designation: RC825
Strain history: IAM 15416 <-- B. Li et al. RC825.
NCBI tax ID(s): 402596 (species)
General
@ref: 16105
BacDive-ID: 11129
DSM-Number: 22017
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Nocardioides exalbidus RC825 is a mesophilic, Gram-positive bacterium that was isolated from Lichen.
NCBI tax id
- NCBI tax id: 402596
- Matching level: species
strain history
@ref | history |
---|---|
16105 | <- JCM/RIKEN <- B. Li et al., Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan; RC825 |
67770 | IAM 15416 <-- B. Li et al. RC825. |
doi: 10.13145/bacdive11129.20230509.8.1
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 exalbidus
- full scientific name: Nocardioides exalbidus Li et al. 2007
@ref: 16105
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides exalbidus
full scientific name: Nocardioides exalbidus Li et al. 2007 emend. Nouioui et al. 2018
strain designation: RC825
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16105 | 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 |
16105 | 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 |
16105 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
67770 | positive | growth | 28 | mesophilic |
16105 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 91 |
69480 | no | 99.502 |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16105 | Lichen | Izu-Oshima Island | Japan | JPN | Asia |
67770 | Lichen | Izu-Oshima Island | Japan | JPN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Other
- Cat3: #Lichen
taxonmaps
- @ref: 69479
- File name: preview.99_17362.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2445;97_2980;98_13150;99_17362&stattab=map
- Last taxonomy: Nocardioides exalbidus
- 16S sequence: AB273624
- Sequence Identity:
- Total samples: 321
- soil counts: 163
- aquatic counts: 29
- animal counts: 82
- plant counts: 47
Safety information
risk assessment
- @ref: 16105
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16105
- description: Nocardioides exalbidus gene for 16S rRNA, partial sequence, strain: RC825
- accession: AB273624
- length: 1453
- database: ena
- NCBI tax ID: 402596
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardioides exalbidus strain DSM 22017 | 402596.4 | wgs | patric | 402596 |
66792 | Nocardioides exalbidus DSM 22017 | 2639762616 | draft | img | 402596 |
67770 | Nocardioides exalbidus DSM 22017 | GCA_900105585 | contig | ncbi | 402596 |
GC content
@ref | GC-content | method |
---|---|---|
16105 | 74.0 | high performance liquid chromatography (HPLC) |
67770 | 71.8 | genome sequence analysis |
67770 | 74 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 91 | no |
gram-positive | yes | 90.901 | no |
anaerobic | no | 98.941 | no |
halophile | no | 96.066 | no |
spore-forming | no | 82.042 | no |
glucose-util | yes | 89.506 | no |
aerobic | yes | 92.443 | no |
flagellated | no | 94.113 | no |
thermophile | no | 99.468 | yes |
motile | no | 78.558 | no |
glucose-ferment | no | 88.795 | no |
External links
@ref: 16105
culture collection no.: DSM 22017, CCTCC AA 206016, IAM 15416, JCM 23199
straininfo link
- @ref: 80378
- straininfo: 319384
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27654931 | Nocardioides flavus sp. nov., isolated from marine sediment. | Wang S, Zhou Y, Zhang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001507 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Enzymology |
Phylogeny | 27902315 | Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave. | Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001676 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 32141810 | Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil. | Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SB | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004095 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sand/microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 34542392 | Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula. | Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005012 | 2021 | *Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Tagetes | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16105 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22017) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22017 | |||
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 | |||
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/ | ||||
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 | |||
80378 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID319384.1 | StrainInfo: A central database for resolving microbial strain identifiers |