Strain identifier

BacDive ID: 13274

Type strain: Yes

Species: Amycolatopsis thailandensis

Strain Designation: CMU-PLA07

Strain history: A. Siazar and S. Lumyong CMU-PLA07.

NCBI tax ID(s): 589330 (species)

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General

@ref: 17975

BacDive-ID: 13274

DSM-Number: 45650

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Amycolatopsis thailandensis CMU-PLA07 is a mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 589330
  • Matching level: species

strain history

@refhistory
17975<- C Suriyachadkun, BCC; BCC 38279 <- A. Chomchoei
67770A. Siazar and S. Lumyong CMU-PLA07.

doi: 10.13145/bacdive13274.20230509.8.1

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 thailandensis
  • full scientific name: Amycolatopsis thailandensis Chomchoei et al. 2011

@ref: 17975

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis thailandensis

full scientific name: Amycolatopsis thailandensis Chomchoei et al. 2011

strain designation: CMU-PLA07

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69416Ivory (1014)ISP 4
69416Ivory (1014)suter with tyrosine
69416Ivory (1014), Rape yellow (1021)ISP 3
69416Lemon yellow (1012)ISP 6
69416Oyster white (1013), Lemon yellow (1012)ISP 5
69416Sand yellow (1002)ISP 2
69416Sulfur yellow (1016)ISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
69416noAerial myceliumISP 2
69416noAerial myceliumISP 3
69416noAerial myceliumISP 4
69416noAerial myceliumISP 5
69416noAerial myceliumISP 6
69416noAerial myceliumISP 7
69416yesAerial myceliumsuter with tyrosineRape yellow (1021)

pigmentation

@refproductionname
69416noMelanin
69416nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69416DSM_45650_image3.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69416DSM_45650_image4.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 17975
  • 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
17975positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 69416
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6941622599arabinose-growth
6941662968cellulose-growth
6941628757fructose+/-growth
6941617234glucose+growth
6941617268inositol-growth
6941637684mannose+/-growth
6941616634raffinose+/-growth
6941626546rhamnose-growth
6941617992sucrose+growth
6941618222xylose-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
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase-3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
69416--++------+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69416++++-+/----+/-++-----+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17975soilThailandTHAAsia
67770Soil in a natural parkThailandTHAAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2224.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_1734;99_2224&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: FJ581021
  • Sequence Identity:
  • Total samples: 106
  • soil counts: 92
  • aquatic counts: 3
  • animal counts: 11

Safety information

risk assessment

  • @ref: 17975
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17975
  • description: Amycolatopsis thailandensis strain CMU-PLA07 16S ribosomal RNA gene, partial sequence
  • accession: FJ581021
  • length: 1446
  • database: ena
  • NCBI tax ID: 589330

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis thailandensis strain JCM 16380589330.4wgspatric589330
66792Amycolatopsis thailandensis JCM 163802854973814draftimg589330
67770Amycolatopsis thailandensis JCM 16380GCA_002234405contigncbi589330

GC content

@refGC-contentmethod
1797567
6777067high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes84.847no
anaerobicno99.427no
halophileno89.346no
spore-formingyes90.543no
glucose-utilyes89.131yes
thermophileno98.614yes
flagellatedno96.761no
aerobicyes93.953no
motileno92.51no
glucose-fermentno93.966no

External links

@ref: 17975

culture collection no.: DSM 45650, BCC 38279, JCM 16380, NBRC 112719

straininfo link

  • @ref: 82478
  • straininfo: 398867

literature

  • topic: Phylogeny
  • Pubmed-ID: 20495035
  • title: Amycolatopsis thailandensis sp. nov., a poly(L-lactic acid)-degrading actinomycete, isolated from soil.
  • authors: Chomchoei A, Pathom-Aree W, Yokota A, Kanongnuch C, Lumyong S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.023564-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Lactic Acid/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polyesters, Polymers/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
17975Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45650)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45650
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
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69416Wink, J.https://cdn.dsmz.de/wink/DSM%2045650.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
82478Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398867.1StrainInfo: A central database for resolving microbial strain identifiers