Strain identifier

BacDive ID: 17836

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refproductionname
69306noMelanin
69306nosoluble 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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69306---+-+----+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- 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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Armatimonas rosea DSM 23562GCA_014202505scaffoldncbi685828
66792Armatimonas rosea strain DSM 23562685828.3wgspatric685828
66792Armatimonas rosea DSM 235622861551589draftimg685828

GC content

  • @ref: 17284
  • GC-content: 62.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
flagellatedno98.009no
gram-positiveno86.219no
anaerobicno98.281no
aerobicyes88.164no
halophileno94.079no
spore-formingno89.597no
glucose-utilyes78.818no
thermophileno93.74yes
motileno92.439no
glucose-fermentno86.43no

External links

@ref: 17284

culture collection no.: DSM 23562, NBRC 105658

straininfo link

  • @ref: 86827
  • straininfo: 407100

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20622056Armatimonas 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 YInt J Syst Evol Microbiol10.1099/ijs.0.025643-02010Aerobiosis, 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/analysisGenetics
Phylogeny30475202Capsulimonas 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 AInt J Syst Evol Microbiol10.1099/ijsem.0.0031352018Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
17284Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23562)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23562
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69306Wink, J.https://cdn.dsmz.de/wink/DSM%2023562.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
86827Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407100.1StrainInfo: A central database for resolving microbial strain identifiers