Strain identifier

BacDive ID: 13248

Type strain: Yes

Species: Amycolatopsis australiensis

Strain Designation: GY048

Strain history: CIP <- 2006, DSMZ <- M. Goodfellow <- G.Y.A. Tan, Newcastle Univ., Newcastle upon Tyne, UK: strain GY048

NCBI tax ID(s): 546364 (species)

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General

@ref: 11968

BacDive-ID: 13248

DSM-Number: 44671

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic

description: Amycolatopsis australiensis GY048 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from composite soil.

NCBI tax id

  • NCBI tax id: 546364
  • Matching level: species

strain history

@refhistory
11968<- M. Goodfellow; GY048 <- G. Y. A. Tan
67770NCIMB 14142 <-- A. L. Jones <-- G. Y. A. Tan GY048.
116647CIP <- 2006, DSMZ <- M. Goodfellow <- G.Y.A. Tan, Newcastle Univ., Newcastle upon Tyne, UK: strain GY048

doi: 10.13145/bacdive13248.20230509.8.1

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 australiensis
  • full scientific name: Amycolatopsis australiensis Tan et al. 2006

@ref: 11968

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis australiensis

full scientific name: Amycolatopsis australiensis Tan et al. 2006 emend. Nouioui et al. 2018

strain designation: GY048

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.406
69480100positive
116647positiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20092Sand yellow (1002)10-14 daysISP 2
20092Beige (1001)10-14 daysISP 3
20092Beige (1001)10-14 daysISP 4
20092Beige (1001)10-14 daysISP 5
20092Beige (1001)10-14 daysISP 6
20092Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20092yesAerial MyceliumPure white (9010)ISP 2
20092yesAerial MyceliumPure white (9001)ISP 3
20092yesAerial MyceliumPure white (9001)ISP 4
20092yesAerial MyceliumISP 5
20092noISP 6
20092yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11968GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
20092ISP 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
20092ISP 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:
20092ISP 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
20092ISP 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
20092ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20092ISP 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
37544MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
116647CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11968positivegrowth28mesophilic
20092positiveoptimum28mesophilic
37544positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116647
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-8(H2), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2009217234glucose+
2009222599arabinose+
2009217992sucrose+
2009218222xylose-
2009217268myo-inositol+
2009229864mannitol+
2009228757fructose+
2009226546rhamnose-
2009216634raffinose+
2009262968cellulose+
11664717632nitrate-reduction
11664716301nitrite-reduction

metabolite production

  • @ref: 116647
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116647oxidase-
116647catalase+1.11.1.6
116647urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20092+++++++++++++-+++++
116647+++-+++++++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11968composite soilAustraliaAUSAustralia and Oceania
67770Arid Australian soil
116647Environment, Soil, compositeAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4767.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_532;99_4767&stattab=map
  • Last taxonomy: Amycolatopsis australiensis
  • 16S sequence: AY129753
  • Sequence Identity:
  • Total samples: 146
  • soil counts: 99
  • aquatic counts: 6
  • animal counts: 12
  • plant counts: 29

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119681Risk group (German classification)
1166471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11968
  • description: Amycolatopsis australiensis strain GY048 16S ribosomal RNA gene, partial sequence
  • accession: AY129753
  • length: 1461
  • database: ena
  • NCBI tax ID: 546364

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis australiensis strain DSM 44671546364.3wgspatric546364
66792Amycolatopsis australiensis DSM 446712642422517draftimg546364
67770Amycolatopsis australiensis DSM 44671GCA_900119165contigncbi546364

GC content

  • @ref: 67770
  • GC-content: 71.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes86.804no
anaerobicno99.322no
halophileno88.114no
spore-formingyes89.951no
glucose-utilyes91.262no
thermophileno98.021yes
aerobicyes91.768no
motileno93.19no
flagellatedno97.738no
glucose-fermentno90.789no

External links

@ref: 11968

culture collection no.: DSM 44671, CIP 109398, NBRC 106146, NCIMB 14142, JCM 15587

straininfo link

  • @ref: 82452
  • straininfo: 297126

literature

  • topic: Phylogeny
  • Pubmed-ID: 17012550
  • title: Amycolatopsis australiensis sp. nov., an actinomycete isolated from arid soils.
  • authors: Tan GYA, Robinson S, Lacey E, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64260-0
  • year: 2006
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Australia, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Desert Climate, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
11968Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44671)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44671
20092Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44671.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
37544Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7135
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/
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
82452Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297126.1StrainInfo: A central database for resolving microbial strain identifiers
116647Curators of the CIPCollection of Institut Pasteur (CIP 109398)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109398