Strain identifier

BacDive ID: 13262

Type strain: Yes

Species: Amycolatopsis jejuensis

Strain Designation: N7-3

Strain history: S. D. Lee N7-3.

NCBI tax ID(s): 330084 (species)

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General

@ref: 12269

BacDive-ID: 13262

DSM-Number: 45042

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

description: Amycolatopsis jejuensis N7-3 is an aerobe, spore-forming, mesophilic bacterium that was isolated from dried bat dung in natural cave.

NCBI tax id

  • NCBI tax id: 330084
  • Matching level: species

strain history

@refhistory
12269<- S. D. Lee; N7-3
67770S. D. Lee N7-3.

doi: 10.13145/bacdive13262.20230509.8.1

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 jejuensis
  • full scientific name: Amycolatopsis jejuensis Lee 2006

@ref: 12269

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis jejuensis

full scientific name: Amycolatopsis jejuensis Lee 2006 emend. Nouioui et al. 2018

strain designation: N7-3

type strain: yes

Morphology

cell morphology

  • @ref: 31605
  • gram stain: positive
  • cell shape: rod-shaped

pigmentation

  • @ref: 31605
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 12269
  • 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

@refgrowthtypetemperaturerange
12269positivegrowth28mesophilic
31605positivegrowth10-30
31605positiveoptimum10-30
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31605
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31605
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31605NaClpositivegrowth2 %
31605NaClpositiveoptimum2 %

observation

@refobservation
31605aggregates in chains
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3160515963ribitol+carbon source
3160522599arabinose+carbon source
3160528757fructose+carbon source
3160528260galactose+carbon source
3160529864mannitol+carbon source
3160537684mannose+carbon source
3160517632nitrate+reduction
6836925115malate+assimilation
6836917128adipate+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
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3160516136hydrogen sulfideyes
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31605catalase+1.11.1.6
31605urease+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
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
12269-++/-+/--++/-+/---++/----+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12269-----+--+-++++/-+-++++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12269dried bat dung in natural caveJejuRepublic of KoreaKORAsia
67770Dried bat dung inside a natural caveJeju IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial
#Host#Mammals
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3441.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_2153;98_2642;99_3441&stattab=map
  • Last taxonomy: Amycolatopsis jejuensis subclade
  • 16S sequence: DQ000200
  • Sequence Identity:
  • Total samples: 352
  • soil counts: 232
  • aquatic counts: 18
  • animal counts: 61
  • plant counts: 41

Safety information

risk assessment

  • @ref: 12269
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12269
  • description: Amycolatopsis jejuensis strain N7-3 16S ribosomal RNA gene, partial sequence
  • accession: DQ000200
  • length: 1514
  • database: ena
  • NCBI tax ID: 330084

Genome sequences

  • @ref: 67770
  • description: Amycolatopsis jejuensis NRRL B-24427
  • accession: GCA_000717335
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 330084

GC content

@refGC-contentmethod
1226971.7
6777071.7high performance liquid chromatography (HPLC)
6777068.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.056no
flagellatedno98.039no
gram-positiveyes88.083yes
anaerobicno99.112yes
halophileno90.293no
spore-formingyes90.764yes
glucose-utilyes88.978no
aerobicyes90.92yes
thermophileno97.365yes
glucose-fermentno92.309yes

External links

@ref: 12269

culture collection no.: DSM 45042, JCM 13280, NRRL B-24427, CIP 109183, NCIMB 14306

straininfo link

  • @ref: 82466
  • straininfo: 290957

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514025Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.63881-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, Animals, Chiroptera/microbiology, DNA, Ribosomal/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny23053697Amycolatopsis jiangsuensis sp. nov., a novel endophytic actinomycete isolated from a coastal plant in Jiangsu, China.Xing K, Liu W, Zhang YJ, Bian GK, Zhang WD, Tamura T, Lee JS, Qin S, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9823-y2012Actinomycetales/*classification/*isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, China, Chrysanthemum/*microbiology, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Endophytes/*classification/*isolation & purification, Fatty Acids/analysis, Microscopy, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisEnzymology
Phylogeny30605074Amycolatopsis panacis sp. nov., isolated from Panax notoginseng rhizospheric soil.Peng G, Xiong DS, Li LC, Hu JY, Bao S, Chen YW, Li YQ, Xu LH, Miao CP, Zhao LXInt J Syst Evol Microbiol10.1099/ijsem.0.0032022019Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax notoginseng/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12269Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45042)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45042
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
31605Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2789328776041
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
82466Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290957.1StrainInfo: A central database for resolving microbial strain identifiers