Strain identifier

BacDive ID: 13287

Type strain: Yes

Species: Amycolatopsis dongchuanensis

Variant: Isotype of BacDive ID 13286

Strain history: S.-K. Tang YIM 75904.

NCBI tax ID(s): 1070866 (species)

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General

@ref: 18041

BacDive-ID: 13287

DSM-Number: 45675

keywords: 16S sequence, Bacteria, mesophilic

description: Amycolatopsis dongchuanensis DSM 45675 is a mesophilic bacterium that was isolated from soil from a dry and hot river valley.

NCBI tax id

  • NCBI tax id: 1070866
  • Matching level: species

strain history

@refhistory
18041<- S.-K. Tang, YIM; YIM 75904 <- J. Zhang
67770S.-K. Tang YIM 75904.

doi: 10.13145/bacdive13287.20230509.8.1

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 dongchuanensis
  • full scientific name: Amycolatopsis dongchuanensis Nie et al. 2012

@ref: 18041

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis dongchuanensis

full scientific name: Amycolatopsis dongchuanensis Nie et al. 2012

variant: Isotype of BacDive ID 13286

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69420Broom yellow (1032)ISP 5
69420Ivory (1014)suter with tyrosine
69420Ivory (1014)suter without tyrosine
69420Sand yellow (1002)ISP 4
69420Sand yellow (1002)ISP 6
69420Sand yellow (1002), broom yellow (1032)ISP 2
69420Sand yellow (1002), ivory (1014)ISP 7
69420Zinc yellow (1018)ISP 3

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69420noAerial myceliumISP 2
69420noAerial myceliumISP 3
69420noAerial myceliumISP 4
69420noAerial myceliumISP 5
69420noAerial myceliumISP 6
69420noAerial myceliumISP 7
69420noAerial myceliumsuter with tyrosine
69420noAerial myceliumsuter without tyrosine

pigmentation

  • @ref: 69420
  • production: no
  • name: soluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
18041https://www.dsmz.de/microorganisms/photos/DSM_45675.jpgMedium 65 28°C© Leibniz-Institut DSMZ
69420DSM_45675_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69420DSM_45675_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 18041
  • 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
18041positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 69420
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6942022599arabinose+/-growth
6942062968cellulose-growth
6942028757fructose+growth
6942017234glucose+growth
6942017268inositol+growth
6942037684mannose+growth
6942016634raffinose-growth
6942026546rhamnose+growth
6942017992sucrose+growth
6942018222xylose+growth
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
68382lipase (C 14)-
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69420---+---++-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69420++/-+/--+++/-++++---++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18041soil from a dry and hot river valleyYunnan province, Dongchuan countyChinaCHNAsia
67770Soil from a dry and hot river valleyDongchuan District, Yunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Soil
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 18041
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Amycolatopsis dongchuanensis strain YIM 75904 16S ribosomal RNA gene, partial sequenceJN1889361488ena1070866
18041Amycolatopsis dongchuanensis strain YIM 75904 16S ribosomal RNA gene, partial sequenceJN6567101488ena1070866

GC content

  • @ref: 18041
  • GC-content: 68.5
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 18041

culture collection no.: DSM 45675, CCTCC AA 2011016, JCM 18054, YIM 75904

straininfo link

  • @ref: 82488
  • straininfo: 402143

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22199220Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil.Nie GX, Ming H, Li S, Zhou EM, Cheng J, Tang X, Feng HG, Tang SK, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.038125-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny22771685Amycolatopsis magusensis sp. nov., isolated from soil.Camas M, Sahin N, Sazak A, Sproer C, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.042770-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cyprus, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny23645018Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine.Tatar D, Sazak A, Guven K, Cetin D, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.050963-02013Actinomycetales/*classification/genetics/isolation & purification, Arabinose/analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Galactose/analysis, *Mining, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Turkey, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny29537361Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil.Thawai CInt J Syst Evol Microbiol10.1099/ijsem.0.0027042018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18041Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45675)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45675
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69420Wink, J.https://cdn.dsmz.de/wink/DSM%2045675.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
82488Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402143.1StrainInfo: A central database for resolving microbial strain identifiers