Strain identifier
BacDive ID: 17836
Type strain:
Species: Armatimonas rosea
Strain Designation: YO-36
Strain history: <- H. Tamaki, Natl. Inst. Advanced Industrial Sci. and Technol., Tsukuba, Japan; YO-36 <- Y. Tanaka, University of Yamanashi, Kofu, Japan
NCBI tax ID(s): 685828 (species)
General
@ref: 17284
BacDive-ID: 17836
DSM-Number: 23562
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Armatimonas rosea YO-36 is a mesophilic, Gram-negative bacterium that was isolated from rhizoplane of reed Phragmites australis inhabiting a mesophilic freshwater lake.
NCBI tax id
- NCBI tax id: 685828
- Matching level: species
strain history
- @ref: 17284
- history: <- H. Tamaki, Natl. Inst. Advanced Industrial Sci. and Technol., Tsukuba, Japan; YO-36 <- Y. Tanaka, University of Yamanashi, Kofu, Japan
doi: 10.13145/bacdive17836.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/armatimonadota
- domain: Bacteria
- phylum: Armatimonadota
- class: Armatimonadia
- order: Armatimonadales
- family: Armatimonadaceae
- genus: Armatimonas
- species: Armatimonas rosea
- full scientific name: Armatimonas rosea Tamaki et al. 2011
@ref: 17284
domain: Bacteria
phylum: Armatimonadetes
class: Armatimonadia
order: Armatimonadales
family: Armatimonadaceae
genus: Armatimonas
species: Armatimonas rosea
full scientific name: Armatimonas rosea Tamaki et al. 2011
strain designation: YO-36
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.933
colony morphology
- @ref: 17284
- incubation period: 3-7 days
pigmentation
@ref | production | name |
---|---|---|
69306 | no | Melanin |
69306 | no | soluble pigment |
Culture and growth conditions
culture medium
- @ref: 17284
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: 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: 17284
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.932
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
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 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
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 coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69306 | - | - | - | + | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69306 | + | +/- | +/- | +/- | + | +/- | +/- | - | - | +/- | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 17284
- sample type: rhizoplane of reed Phragmites australis inhabiting a mesophilic freshwater lake
- host species: Phragmites australis
- geographic location: Yamanashi Prefecture
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #Lake (large) |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Rhizoplane |
taxonmaps
- @ref: 69479
- File name: preview.99_77939.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1525;96_21359;97_26652;98_33898;99_77939&stattab=map
- Last taxonomy: Armatimonas rosea subclade
- 16S sequence: AB529679
- Sequence Identity:
- Total samples: 14
- aquatic counts: 11
- animal counts: 3
Safety information
risk assessment
- @ref: 17284
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17284
- description: Armatimonas rosea gene for 16S ribosomal RNA, partial sequence
- accession: AB529679
- length: 1438
- database: ena
- NCBI tax ID: 685828
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Armatimonas rosea DSM 23562 | GCA_014202505 | scaffold | ncbi | 685828 |
66792 | Armatimonas rosea strain DSM 23562 | 685828.3 | wgs | patric | 685828 |
66792 | Armatimonas rosea DSM 23562 | 2861551589 | draft | img | 685828 |
GC content
- @ref: 17284
- GC-content: 62.4
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 86 | no |
flagellated | no | 98.009 | no |
gram-positive | no | 86.219 | no |
anaerobic | no | 98.281 | no |
aerobic | yes | 88.164 | no |
halophile | no | 94.079 | no |
spore-forming | no | 89.597 | no |
glucose-util | yes | 78.818 | no |
thermophile | no | 93.74 | yes |
motile | no | 92.439 | no |
glucose-ferment | no | 86.43 | no |
External links
@ref: 17284
culture collection no.: DSM 23562, NBRC 105658
straininfo link
- @ref: 86827
- straininfo: 407100
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20622056 | Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. | Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng XY, Hanada S, Mori K, Kamagata Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.025643-0 | 2010 | Aerobiosis, Bacteria/*classification/*genetics/isolation & purification/metabolism, Bacterial Physiological Phenomena, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Phylogeny, Plant Leaves/microbiology, Poaceae/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Vitamin K 2/analysis | Genetics |
Phylogeny | 30475202 | Capsulimonas corticalis gen. nov., sp. nov., an aerobic capsulated bacterium, of a novel bacterial order, Capsulimonadales ord. nov., of the class Armatimonadia of the phylum Armatimonadetes. | Li J, Kudo C, Tonouchi A | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003135 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fagus/*microbiology, Fatty Acids/chemistry, Gram-Negative Aerobic Rods and Cocci/*classification/isolation & purification, Japan, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
17284 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23562) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23562 | |
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) | |
68379 | Automatically annotated from API Coryne | |||
68382 | Automatically annotated from API zym | |||
69306 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2023562.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
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) | |
86827 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407100.1 | StrainInfo: A central database for resolving microbial strain identifiers |