Strain identifier
BacDive ID: 7618
Type strain: 
Species: Arthrobacter oryzae
Strain Designation: KV-651
Strain history: NRRL B-24478 <-- S. ?mura KV-651.
NCBI tax ID(s): 409290 (species)
version 9.3 (current version)
General
@ref: 18052
BacDive-ID: 7618
DSM-Number: 25586
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Arthrobacter oryzae KV-651 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from paddy soil.
NCBI tax id
- NCBI tax id: 409290
- Matching level: species
strain history
| @ref | history |
|---|---|
| 18052 | <- NRRL; NRRL B-24478 |
| 67770 | NRRL B-24478 <-- S. ?mura KV-651. |
doi: 10.13145/bacdive7618.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Arthrobacter
- species: Arthrobacter oryzae
- full scientific name: Arthrobacter oryzae Kageyama et al. 2008
@ref: 18052
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Arthrobacter
species: Arthrobacter oryzae
full scientific name: Arthrobacter oryzae Kageyama et al. 2008
strain designation: KV-651
type strain: yes
Morphology
cell morphology
- @ref: 32047
- gram stain: positive
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 18052
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 18052 | positive | growth | 28 |
| 32047 | positive | growth | 04-34 |
| 67770 | positive | growth | 28 |
culture pH
- @ref: 32047
- ability: positive
- type: growth
- pH: 06-11
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 32047 | aerobe | |
| 125439 | obligate aerobe | 96.1 |
halophily
- @ref: 32047
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <2 %
observation
- @ref: 67770
- observation: quinones: MK-9(H2)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32047 | 17234 | glucose | + | carbon source |
| 32047 | 29864 | mannitol | + | carbon source |
| 32047 | 28053 | melibiose | + | carbon source |
| 32047 | 16634 | raffinose | + | carbon source |
| 32047 | 17992 | sucrose | + | carbon source |
| 32047 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32047 | acid phosphatase | + | 3.1.3.2 |
| 32047 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | geographic location |
|---|---|---|---|---|---|
| 18052 | paddy soil | Japan | JPN | Asia | |
| 67770 | Paddy soil | Japan | JPN | Asia | Saitama Pref. |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Engineered | #Agriculture | #Field |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Condition | #Anoxic (anaerobic) | |
| #Condition | #Humid |
taxonmaps
- @ref: 69479
- File name: preview.99_625.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_106;98_386;99_625&stattab=map
- Last taxonomy: Arthrobacter
- 16S sequence: AB279889
- Sequence Identity:
- Total samples: 5810
- soil counts: 2849
- aquatic counts: 364
- animal counts: 580
- plant counts: 2017
Safety information
risk assessment
- @ref: 18052
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18052
- description: Arthrobacter oryzae gene for 16S rRNA, partial sequence
- accession: AB279889
- length: 1465
- database: nuccore
- NCBI tax ID: 409290
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Arthrobacter oryzae strain DSM 25586 | 409290.3 | wgs | patric | 409290 |
| 66792 | Arthrobacter oryzae DSM 25586 | 2757320374 | draft | img | 409290 |
| 67770 | Arthrobacter oryzae DSM 25586 | GCA_003634095 | scaffold | ncbi | 409290 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 18052 | 67 | |
| 67770 | 67 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 88.806 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.323 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 65.861 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.859 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.967 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 74.5 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 79.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 52.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 87.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 96.1 |
External links
@ref: 18052
culture collection no.: DSM 25586, JCM 15922, NBRC 102055, NRRL B-24478
straininfo link
- @ref: 77062
- straininfo: 404081
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18175682 | Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov. | Kageyama A, Morisaki K, Omura S, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64875-0 | 2008 | Arthrobacter/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/analysis, Genes, rRNA, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 25525122 | Arthrobacter liuii sp. nov., resuscitated from Xinjiang desert soil. | Yu XY, Zhang L, Ren B, Yang N, Liu M, Liu XT, Zhang LX, Ding LX | Int J Syst Evol Microbiol | 10.1099/ijs.0.000037 | 2014 | Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Lysine/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 18052 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25586) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25586 | ||||
| 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 | ||||
| 32047 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28297 | 28776041 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 77062 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404081.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | ||||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |