Strain identifier

BacDive ID: 13266

Type strain: Yes

Species: Amycolatopsis niigatensis

Strain Designation: LC11

Strain history: IAM 15388 <-- L. Ding LC11.

NCBI tax ID(s): 369932 (species)

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General

@ref: 15470

BacDive-ID: 13266

DSM-Number: 45165

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

description: Amycolatopsis niigatensis LC11 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from filtration substrate made from volcanic soil.

NCBI tax id

  • NCBI tax id: 369932
  • Matching level: species

strain history

@refhistory
15470<- JCM/RIKEN <- IAM <- L. Ding; LC11
67770IAM 15388 <-- L. Ding LC11.

doi: 10.13145/bacdive13266.20240916.9.1

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 niigatensis
  • full scientific name: Amycolatopsis niigatensis Ding et al. 2007

@ref: 15470

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis niigatensis

full scientific name: Amycolatopsis niigatensis Ding et al. 2007 emend. Nouioui et al. 2018

strain designation: LC11

type strain: yes

Morphology

cell morphology

  • @ref: 32003
  • gram stain: positive
  • motility: no

multimedia

  • @ref: 15470
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45165.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 15470
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

@refgrowthtypetemperature
15470positivegrowth28
32003positivegrowth5.0-45
32003positiveoptimum30
67770positivegrowth28

culture pH

@refabilitytypepHPH range
32003positivegrowth6.0-11alkaliphile
32003positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 32003
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
32003NaClpositivegrowth3.0-7.0 %
32003NaClpositiveoptimum5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3200315963ribitol+carbon source
3200328260galactose+carbon source
3200317234glucose+carbon source
3200326546rhamnose+carbon source
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
32003acid phosphatase+3.1.3.2
32003alkaline phosphatase+3.1.3.1
32003catalase+1.11.1.6
32003gelatinase+
32003pyrazinamidase+3.5.1.B15
32003urease+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 (C 4)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
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
15470-+-+/--+----+/-+/-----+/-++-

API 20NE

@refTRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
15470----+-+/-++++++/-+-+/-+++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15470filtration substrate made from volcanic soilNiigataJapanJPNAsia
67770Filtration substrate made from volcanic soilNiigataJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Volcanic

taxonmaps

  • @ref: 69479
  • File name: preview.99_760.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_606;99_760&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AB248537
  • Sequence Identity:
  • Total samples: 74
  • soil counts: 53
  • aquatic counts: 1
  • animal counts: 16
  • plant counts: 4

Safety information

risk assessment

  • @ref: 15470
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15470
  • description: Amycolatopsis niigatensis gene for 16S rRNA, partial sequence
  • accession: AB248537
  • length: 1472
  • database: nuccore
  • NCBI tax ID: 369932

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis niigatensis strain DSM 45165369932.4wgspatric369932
66792Amycolatopsis niigatensis DSM 451652627854290draftimg369932
67770Amycolatopsis niigatensis DSM 45165GCA_002846615contigncbi369932

GC content

@refGC-contentmethod
1547072.4
6777072.4high performance liquid chromatography (HPLC)
6777069.5genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes86.803yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.921yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes77.897no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.97yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97yes
69480flagellatedmotile2+Ability to perform flagellated movementno89.1yes

External links

@ref: 15470

culture collection no.: DSM 45165, CCTCC AB 206020, CIP 109735, IAM 15388, JCM 21832

straininfo link

  • @ref: 82470
  • straininfo: 309426

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684249
  • title: Amycolatopsis echigonensis sp. nov. and Amycolatopsis niigatensis sp. nov., novel actinomycetes isolated from a filtration substrate.
  • authors: Ding L, Hirose T, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64791-0
  • year: 2007
  • mesh: Actinobacteria/*classification/cytology/genetics/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15470Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45165)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45165
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
32003Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2825728776041
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)
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
82470Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309426.1StrainInfo: A central database for resolving microbial strain identifiers