Strain identifier

BacDive ID: 13230

Type strain: Yes

Species: Amycolatopsis alba

Strain history: IFO 15602 <-- F. P. Mertz A83850.

NCBI tax ID(s): 1125972 (strain), 76020 (species)

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General

@ref: 11634

BacDive-ID: 13230

DSM-Number: 44262

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

description: Amycolatopsis alba DSM 44262 is a mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
76020species
1125972strain

strain history

@refhistory
11634<- IFO <- F. P. Mertz, Eli Lilly & Co., A 83850 <- R. C. Yao
67770IFO 15602 <-- F. P. Mertz A83850.

doi: 10.13145/bacdive13230.20230509.8.1

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 alba
  • full scientific name: Amycolatopsis alba Mertz and Yao 1993

@ref: 11634

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis alba

full scientific name: Amycolatopsis alba Mertz and Yao 1993 emend. Nouioui et al. 2018

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
20035Colorless10-14 daysISP 2
20035Colorless10-14 daysISP 3
20035Colorless10-14 daysISP 4
20035Colorless10-14 daysISP 5
20035Colorless10-14 daysISP 6
20035Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20035yesAerial MyceliumWhiteISP 2
20035noISP 3
20035yesAerial MyceliumWhiteISP 4
20035yesAerial MyceliumWhiteISP 5
20035noISP 6
20035yesAerial MyceliumWhiteISP 7

multimedia

  • @ref: 11634
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44262.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11634N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
11634GYM 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
20035ISP 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
20035ISP 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:
20035ISP 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
20035ISP 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
20035ISP 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
20035ISP 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

culture temp

@refgrowthtypetemperaturerange
11634positivegrowth28mesophilic
20035positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 20035
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2003517234glucose+
2003522599arabinose-
2003517992sucrose-
2003518222xylose-
2003517268myo-inositol-
2003529864mannitol+
2003528757fructose+
2003526546rhamnose-
2003516634raffinose+
2003562968cellulose-
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368beta-galactosidase+3.2.1.23
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase+3.2.1.52
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
20035+++-+++++++-+-++++-
11634+-+-++/-+/--+/-++/------+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARANO2N2
20035+++++-+---+
11634+--------++-----------

Isolation, sampling and environmental information

isolation

@refsample type
11634soil
67770Soil

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: AF051340
  • Sequence Identity:
  • Total samples: 106
  • soil counts: 92
  • aquatic counts: 3
  • animal counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116341Risk group (German classification)
200351German classification

Sequence information

16S sequences

  • @ref: 20218
  • description: Amycolatopsis alba 16S ribosomal RNA gene, partial sequence
  • accession: AF051340
  • length: 1477
  • database: ena
  • NCBI tax ID: 1125972

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis alba DSM 442621125972.3wgspatric1125972
66792Amycolatopsis alba DSM 442621125972.8wgspatric1125972
66792Amycolatopsis alba DSM 442622854996976draftimg1125972
66792Amycolatopsis alba DSM 442622516143008draftimg1125972
67770Amycolatopsis alba DSM 44262GCA_000384215scaffoldncbi1125972
67770Amycolatopsis alba DSM 44262GCA_002234385contigncbi1125972

GC content

  • @ref: 67770
  • GC-content: 68.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.355no
flagellatedno96.977no
gram-positiveyes86.481no
anaerobicno99.495no
aerobicyes94.303no
halophileno90.675no
spore-formingyes93.405no
thermophileno98.271yes
glucose-utilyes89.84yes
glucose-fermentno94.583yes

External links

@ref: 11634

culture collection no.: DSM 44262, ATCC 51368, IFO 15602, NBRC 15602, NRRL 18532, JCM 10030, IMSNU 22095, KCTC 9611

straininfo link

  • @ref: 82435
  • straininfo: 46905

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8240953Amycolatopsis alba sp. nov., isolated from soil.Mertz FP, Yao RCInt J Syst Bacteriol10.1099/00207713-43-4-7151993Actinobacteria/*classification/*isolation & purification/metabolism/ultrastructure, Anti-Bacterial Agents/biosynthesis, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, Fatty Acids/analysis, Microbial Sensitivity Tests, *Soil Microbiology, Vancomycin/analogs & derivatives, Vitamin K/analysisEnzymology
Phylogeny17184341PCR screening reveals unexpected antibiotic biosynthetic potential in Amycolatopsis sp. strain UM16.Wood SA, Kirby BM, Goodwin CM, Le Roes M, Meyers PRJ Appl Microbiol10.1111/j.1365-2672.2006.03043.x2007Actinobacteria/classification/genetics/*metabolism, Anti-Bacterial Agents/*biosynthesis, Bacterial Proteins/genetics, Base Sequence, Genes, Bacterial/genetics, Glycopeptides/genetics, Hydro-Lyases/genetics, Molecular Sequence Data, Mycobacterium tuberculosis/growth & development, Phylogeny, Polyketide Synthases/genetics, Polymerase Chain Reaction/*methods, Receptors, Steroid/genetics, Ristocetin/biosynthesisGenetics
Phylogeny20495035Amycolatopsis thailandensis sp. nov., a poly(L-lactic acid)-degrading actinomycete, isolated from soil.Chomchoei A, Pathom-Aree W, Yokota A, Kanongnuch C, Lumyong SInt J Syst Evol Microbiol10.1099/ijs.0.023564-02010Actinomycetales/*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, ThailandMetabolism
Pathogenicity28276761Abscisic acid-type sesquiterpenes and ansamycins from Amycolatopsis alba DSM 44262.Li XM, Li XM, Lu CHJ Asian Nat Prod Res10.1080/10286020.2017.12859092017Abscisic Acid/chemistry/*isolation & purification/pharmacology, Actinomycetales/*chemistry, Bacillus subtilis/drug effects, Candida albicans/drug effects, Fatty Acids, Monounsaturated, Lactams, Macrocyclic/chemistry/*isolation & purification/pharmacology, Microbial Sensitivity Tests, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Pseudomonas aeruginosa/drug effects, Sesquiterpenes/chemistry/*isolation & purification/pharmacology, Staphylococcus aureus/drug effects, StereoisomerismEnzymology
Pathogenicity31299158Identification of the Bacterial Maytansinoid Gene Cluster asc Provides Insights into the Post-PKS Modifications of Ansacarbamitocin Biosynthesis.Li X, Wu X, Shen YOrg Lett10.1021/acs.orglett.9b018912019Actinomycetales/*genetics, Cell Line, Tumor, Genes, Bacterial/*genetics, HCT116 Cells, HeLa Cells, Humans, Methyltransferases/*genetics, Multigene Family/*genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11634Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44262)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44262
20035Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44262.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
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
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/
68368Automatically annotated from API 20E
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
82435Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46905.1StrainInfo: A central database for resolving microbial strain identifiers