Strain identifier

BacDive ID: 13516

Type strain: Yes

Species: Amycolatopsis arida

Strain Designation: RA45

Strain history: L.-X. Zhang RA45.

NCBI tax ID(s): 587909 (species)

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General

@ref: 17971

BacDive-ID: 13516

DSM-Number: 45648

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Amycolatopsis arida RA45 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil from a desert region.

NCBI tax id

  • NCBI tax id: 587909
  • Matching level: species

strain history

@refhistory
17971<- JCM; JCM 16584 <- L.-X. Zhang; RA45
67770L.-X. Zhang RA45.

doi: 10.13145/bacdive13516.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis arida
  • full scientific name: Amycolatopsis arida Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Yuhushiella deserti

@ref: 17971

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis arida

full scientific name: Amycolatopsis arida Nouioui et al. 2018

strain designation: RA45

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29726positiverod-shapedno
69480no91.69
69480positive100

pigmentation

  • @ref: 29726
  • production: yes

multimedia

  • @ref: 17971
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45648.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17971GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
17971GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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

culture temp

@refgrowthtypetemperaturerange
17971positivegrowth28mesophilic
29726positiveoptimum37-45
67770positivegrowth28mesophilic

culture pH

  • @ref: 29726
  • ability: positive
  • type: optimum
  • pH: 9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 29726
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29726no
69481no92
69480yes100

halophily

  • @ref: 29726
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 3.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9, MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29726urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
17971-++/-++/-+++/--+-----+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
17971-------+/-+/-+/-+/-+/-+++-+/-+/-+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17971soil from a desert regionXinjiang Uigur Autonomous RegionChinaCHNAsia
67770Soil from a desert regionXinjiang Uigur Autonomous Region, north-western ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_105015.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_42288;97_54069;98_71475;99_105015&stattab=map
  • Last taxonomy: Amycolatopsis arida subclade
  • 16S sequence: FJ526746
  • Sequence Identity:
  • Total samples: 442
  • soil counts: 127
  • aquatic counts: 10
  • animal counts: 286
  • plant counts: 19

Safety information

risk assessment

  • @ref: 17971
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17971
  • description: Yuhushiella deserti strain RA45 16S ribosomal RNA gene, partial sequence
  • accession: FJ526746
  • length: 1493
  • database: ena
  • NCBI tax ID: 587909

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yuhushiella deserti strain CGMCC 4.5579587909.3wgspatric587909
66792Yuhushiella deserti strain DSM 45648587909.9wgspatric587909
66792Amycolatopsis arida DSM 456482731639259draftimg587909
66792Amycolatopsis arida CGMCC 4.55792675903051draftimg587909
67770Amycolatopsis arida CGMCC 4.5579GCA_900115565scaffoldncbi587909
67770Amycolatopsis arida DSM 45648GCA_004365925contigncbi587909

GC content

@refGC-contentmethod
1797169.9
6777072.7genome sequence analysis
6777069.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
gram-positiveyes90.614yes
anaerobicno99.265yes
halophileno51.32no
spore-formingyes73.215yes
glucose-utilyes89.24no
thermophileno89.708yes
flagellatedno97.167no
aerobicyes92.22no
motileno93.508yes
glucose-fermentno93.281yes

External links

@ref: 17971

culture collection no.: DSM 45648, CGMCC 4.5579, JCM 16584

straininfo link

  • @ref: 82707
  • straininfo: 399473

literature

  • topic: Phylogeny
  • Pubmed-ID: 20400669
  • title: Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae.
  • authors: Mao J, Wang J, Dai HQ, Zhang ZD, Tang QY, Ren B, Yang N, Goodfellow M, Zhang LX, Liu ZH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.019588-0
  • year: 2010
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Molecular Sequence Data, Muramic Acids/analysis, Mycolic Acids/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17971Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45648)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45648
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
29726Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2610928776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82707Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399473.1StrainInfo: A central database for resolving microbial strain identifiers