Strain identifier

BacDive ID: 13272

Type strain: Yes

Species: Amycolatopsis helveola

Strain Designation: TT00-43

Strain history: <- T Tamura & Y Ishida, NBRC <- T Tamura, IFO

NCBI tax ID(s): 450800 (species)

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General

@ref: 18018

BacDive-ID: 13272

DSM-Number: 45661

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

description: Amycolatopsis helveola TT00-43 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 450800
  • Matching level: species

strain history

@refhistory
18018<- NBRC; NBRC 103394 <- T. Tamura; TT00-43
67771<- T Tamura & Y Ishida, NBRC <- T Tamura, IFO

doi: 10.13145/bacdive13272.20230509.8.1

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 helveola
  • full scientific name: Amycolatopsis helveola Tamura et al. 2010

@ref: 18018

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis helveola

full scientific name: Amycolatopsis helveola Tamura et al. 2010

strain designation: TT00-43

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29650positive1.5 µm0.7 µmrod-shapedno
67771positive

pigmentation

  • @ref: 29650
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18018
  • name: GPHF-MEDIUM (DSMZ Medium 553)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/553
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
18018positivegrowth28mesophilic
29650positivegrowth20-37
29650positivegrowth25-37mesophilic
29650positiveoptimum20-37
29650positiveoptimum25-37mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
29650positivegrowth7
29650positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationtype of spore
29650yes
67771yesspore

halophily

@refsaltgrowthtested relationconcentration
29650NaClpositivegrowth0-3 %
29650NaClpositivegrowth0-5 %
29650NaClpositiveoptimum0-3 %
29650NaClpositiveoptimum0-5 %

observation

@refobservation
29650aggregates in chains
67771quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2965015963ribitol+carbon source
2965028053melibiose+carbon source
2965033942ribose+carbon source
2965017992sucrose+carbon source
2965022599arabinose+carbon source
2965018403L-arabitol+carbon source
2965017057cellobiose+carbon source
2965028757fructose+carbon source
2965028260galactose+carbon source
2965024265gluconate+carbon source
2965017234glucose+carbon source
2965017754glycerol+carbon source
2965029864mannitol+carbon source
2965037684mannose+carbon source
29650506227N-acetylglucosamine+carbon source
2965026546rhamnose+carbon source
2965027082trehalose+carbon source
2965018222xylose+carbon source
2965017632nitrate+reduction

enzymes

  • @ref: 29650
  • value: acid phosphatase
  • activity: +
  • ec: 3.1.3.2

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18018forest soilAmami Oshima,KagoshimaJapanJPNAsia
67771From forest soilAmami Oshima, KagoshimaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_28136.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_13900;97_16938;98_21042;99_28136&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AB327253
  • Sequence Identity:
  • Total samples: 693
  • soil counts: 505
  • aquatic counts: 27
  • animal counts: 73
  • plant counts: 88

Safety information

risk assessment

  • @ref: 18018
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 29650
  • description: Amycolatopsis helveola gene for 16S rRNA, partial sequence, strain: TT 00-43 (= NBRC 103394)
  • accession: AB327253
  • length: 1477
  • database: nuccore
  • NCBI tax ID: 450800

GC content

@refGC-content
1801868.9
2965067.2
6777167.0-69.0

External links

@ref: 18018

culture collection no.: DSM 45661, KCTC 19329, NBRC 103394

straininfo link

  • @ref: 82476
  • straininfo: 398035

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20023060Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil.Tamura T, Ishida Y, Otoguro M, Suzuki KIInt J Syst Evol Microbiol10.1099/ijs.0.017871-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny31913343Amycolatopsis pithecelloba sp. nov., a novel actinomycete isolated from roots of Pithecellobium dulce in Thailand.Mingma R, Inahashi Y, Matsumoto A, Takahashi Y, Duangmal KJ Antibiot (Tokyo)10.1038/s41429-019-0271-z2020Actinobacteria/classification/genetics/*isolation & purification, Fabaceae/*microbiology, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S, ThailandEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18018Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45661)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45661
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
29650Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2603928776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
82476Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398035.1StrainInfo: A central database for resolving microbial strain identifiers