Strain identifier

BacDive ID: 13255

Type strain: Yes

Species: Amycolatopsis rifamycinica

Strain Designation: Baxter NT 19, NT 19

Strain history: DSM 46095 <-- IMET 7668 <-- M. P. Lechevalier <-- ATCC 27643 <-- E. H. Baxter NT 19 (Nocardia mediterranei).

NCBI tax ID(s): 287986 (species)

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General

@ref: 12434

BacDive-ID: 13255

DSM-Number: 46095

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production

description: Amycolatopsis rifamycinica Baxter NT 19 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 287986
  • Matching level: species

strain history

@refhistory
12434<- IMET <- M.P. Lechevalier <- ATCC <- E.H. Baxter, NT 19 (Nocardia mediterranei)
67770DSM 46095 <-- IMET 7668 <-- M. P. Lechevalier <-- ATCC 27643 <-- E. H. Baxter NT 19 (Nocardia mediterranei).

doi: 10.13145/bacdive13255.20230509.8.1

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 rifamycinica
  • full scientific name: Amycolatopsis rifamycinica Bala et al. 2004

@ref: 12434

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis rifamycinica

full scientific name: Amycolatopsis rifamycinica Bala et al. 2004 emend. Nouioui et al. 2018

strain designation: Baxter NT 19, NT 19

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.785
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
20190Dahlia yellow (1033)10-14 daysISP 2
20190Dahlia yellow (1033)10-14 daysISP 3
20190Dahlia yellow (1033)10-14 daysISP 4
20190Dahlia yellow (1033)10-14 daysISP 5
20190Beige (1001)10-14 daysISP 6
20190Nut brown (8011)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20190noISP 2
20190noISP 3
20190noISP 4
20190noISP 5
20190noISP 6
20190noISP 7

multimedia

  • @ref: 12434
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_46095.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12434GYM 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
20190ISP 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
20190ISP 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:
20190ISP 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
20190ISP 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
20190ISP 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
20190ISP 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
12434positivegrowth28mesophilic
20190positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes97
69480yes100

compound production

  • @ref: 12434
  • compound: rifamycin SV

metabolite production

  • @ref: 67770
  • Chebi-ID: 29673
  • metabolite: rifamycin SV
  • production: yes

enzymes

@refvalueactivityec
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
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
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20190+++++++++++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12434soilNorthern territory, Alice springsAustraliaAUSAustralia and Oceania
67770Soil in an arid region near Alice SpringsNorthern TerritoryAustraliaAUSAustralia and Oceania

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_660.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_532;99_660&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AY083603
  • Sequence Identity:
  • Total samples: 5860
  • soil counts: 4583
  • aquatic counts: 156
  • animal counts: 306
  • plant counts: 815

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
124341Risk group (German classification)
201901German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Amycolatopsis rifamycinica strain DSM 46095 16S ribosomal RNA gene, partial sequenceAY0836031465ena287986
67770Amycolatopsis rifamycinica strain DSM 46095 GyrB (gyrB) gene, partial cdsEU8229101379ena287986

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis rifamycinica strain DSM 46095287986.3wgspatric287986
67770Amycolatopsis rifamycinica DSM 46095GCA_000695625contigncbi287986

GC content

  • @ref: 67770
  • GC-content: 71.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
gram-positiveyes88.133no
anaerobicno99.457no
halophileno90.608no
spore-formingyes91.726no
glucose-utilyes90.831no
motileno91.533no
flagellatedno97.556no
aerobicyes93.158no
thermophileno97.495no
glucose-fermentno92.106no

External links

@ref: 12434

culture collection no.: DSM 46095, ATCC 27643, IMET 7668, JCM 12674, KCTC 9403

straininfo link

  • @ref: 82459
  • straininfo: 125797

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280283Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.Bala S, Khanna R, Dadhwal M, Prabagaran SR, Shivaji S, Cullum J, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.02901-02004Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Electrophoresis, Gel, Pulsed-Field, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis/isolation & purification, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rifamycins/biosynthesis, Sequence Analysis, DNA, Sequence HomologyEnzymology
Genetics24994803Draft Genome Sequence of the Rifamycin Producer Amycolatopsis rifamycinica DSM 46095.Saxena A, Kumari R, Mukherjee U, Singh P, Lal RGenome Announc10.1128/genomeA.00662-142014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12434Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46095)https://www.dsmz.de/collection/catalogue/details/culture/DSM-46095
20190Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM46095.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/
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
82459Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125797.1StrainInfo: A central database for resolving microbial strain identifiers