Strain identifier

BacDive ID: 13239

Type strain: Yes

Species: Amycolatopsis thermoflava

Strain Designation: N-1165, T526

Strain history: <- M. Goodfellow <- IFO

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11871

BacDive-ID: 13239

DSM-Number: 44574

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

description: Amycolatopsis thermoflava N-1165 is an aerobe, thermophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
84480species
1068979strain

strain history

doi: 10.13145/bacdive13239.20220920.7

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 thermoflava
  • full scientific name: Amycolatopsis thermoflava Chun et al. 1999
  • synonyms

    • @ref: 20215
    • synonym: Amycolatopsis eurytherma

@ref: 11871

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis thermoflava

full scientific name: Amycolatopsis thermoflava Chun et al. 1999 emend. Nouioui et al. 2018

strain designation: N-1165, T526

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
21424Honey yellow (1005)10-14 daysISP 2
21424Ivory (1014)10-14 daysISP 3
21424Ivory (1014)10-14 daysISP 4
21424Broom yellow (1032)10-14 daysISP 5
21424Broom yellow (1032)10-14 daysISP 7
21424Sand yellow (1002)10-14 daysSuter with tyrosine
21424Ochre yellow10-14 daysSuter without tyrosine

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11871GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://bacmedia.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 12.0 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
21424ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21424ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21424ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21424ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21424ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21424Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21424Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
39583MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)

culture temp

@refgrowthtypetemperaturerange
11871positivegrowth45thermophilic
39583positivegrowth45thermophilic
67770positivegrowth45thermophilic
67771positivegrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

  • @ref: 21424
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H_4_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2142417234glucose+
2142422599arabinose+
2142417992sucrose+
2142418222xylose+
2142417268myo-inositol-
2142437684mannose+
2142428757fructose+
2142426546rhamnose+
2142416634raffinose-
2142462968cellulose+
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction

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
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21424---+/----+-----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21424++/-+-++/----++/-----++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11871soilHainan IslandChinaCHNAsia
67771From soilHainan IslandChinaCHNAsia
67770SoilHainan IslandChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118711Risk group (German classification)
21424L1German classification

Sequence information

16S sequences

  • @ref: 20218
  • description: Amycolatopsis thermoflava 16S ribosomal RNA gene, partial sequence
  • accession: AF052390
  • length: 1495
  • database: ena
  • NCBI tax ID: 1068979

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis thermoflava N1165, DSM 445742512564010draftimg1068979
67770Amycolatopsis thermoflava N1165, whole genome shotgun sequencing projectAXBH00000000ncbi1068979

GC content

@refGC-contentmethod
6777075thermal denaturation, midpoint method (Tm)
6777071.6genome sequence analysis
6777175.0thermal denaturation, midpoint method (Tm)

External links

@ref: 11871

culture collection no.: DSM 44574, CIP 106795, IFO 14333, JCM 10669, KCTC 9833, NBRC 14333, IMSNU 21194, NRRL B-24140, BCRC 16371, IFO (now NBRC) 14333

straininfo link

@refpassport
20218http://www.straininfo.net/strains/169818
20218http://www.straininfo.net/strains/148551
20218http://www.straininfo.net/strains/148553
20218http://www.straininfo.net/strains/148552
20218http://www.straininfo.net/strains/148554
20218http://www.straininfo.net/strains/336533

literature

  • topic: Phylogeny
  • Pubmed-ID: 10555314
  • title: Amycolatopsis thermoflava sp. nov., a novel soil actinomycete from Hainan Island, China.
  • authors: Chun J, Kim SB, Oh YK, Seong CN, Lee DH, Bae KS, Lee KJ, Kang SO, Hah YC, Goodfellow M
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-4-1369
  • year: 1999
  • mesh: Actinomycetales/*classification/*genetics/physiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/*genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11871Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44574)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44574
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
21424Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44574.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
39583Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18964
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym