Strain identifier

BacDive ID: 13243

Type strain: Yes

Species: Amycolatopsis rubida

Strain Designation: 13.4

Strain history: CIP <- 2001, JCM <- Z. Liu: strain 13.4

NCBI tax ID(s): 112413 (species)

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

@ref: 11946

BacDive-ID: 13243

DSM-Number: 44637

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

description: Amycolatopsis rubida 13.4 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil of a conifer forest.

NCBI tax id

  • NCBI tax id: 112413
  • Matching level: species

strain history

@refhistory
11946<- T. Kudo, JCM <- Z. Liu; 13.4
67770Z. Liu 13.4.
122282CIP <- 2001, JCM <- Z. Liu: strain 13.4

doi: 10.13145/bacdive13243.20230509.8.1

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 rubida
  • full scientific name: Amycolatopsis rubida Huang et al. 2001

@ref: 11946

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis rubida

full scientific name: Amycolatopsis rubida Huang et al. 2001 emend. Nouioui et al. 2018

strain designation: 13.4

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.476
69480100positive
122282nopositivefilament-shaped

colony morphology

@refcolony colorincubation periodmedium used
20084Beige (1001)10-14 daysISP 2
20084Beige (1001)10-14 daysISP 3
20084Beige (1001)10-14 daysISP 4
20084Beige (1001)10-14 daysISP 5
20084Beige (1001)10-14 daysISP 6
20084Beige (1001)10-14 daysISP 7
122282

multicellular morphology

@refforms multicellular complexmedium name
20084noISP 2
20084noISP 3
20084noISP 4
20084noISP 5
20084noISP 6
20084noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11946GYM 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
20084ISP 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
20084ISP 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:
20084ISP 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
20084ISP 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
20084ISP 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
20084ISP 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
39659MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122282CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11946positivegrowth28mesophilic
20084positiveoptimum28mesophilic
39659positivegrowth30mesophilic
67770positivegrowth28mesophilic
122282positivegrowth25-37mesophilic
122282nogrowth10psychrophilic
122282nogrowth41thermophilic
122282nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122282
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.62

halophily

  • @ref: 122282
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12228216947citrate-carbon source
1222824853esculin-hydrolysis
122282606565hippurate-hydrolysis
12228217632nitrate-reduction
12228216301nitrite-reduction
12228217632nitrate-respiration

antibiotic resistance

  • @ref: 122282
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122282
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12228215688acetoin-
12228217234glucose-

enzymes

@refvalueactivityec
122282oxidase-
122282beta-galactosidase-3.2.1.23
122282alcohol dehydrogenase-1.1.1.1
122282gelatinase+
122282amylase-
122282DNase-
122282caseinase+3.4.21.50
122282catalase+1.11.1.6
122282tween esterase-
122282gamma-glutamyltransferase+2.3.2.2
122282lecithinase-
122282lipase+
122282lysine decarboxylase-4.1.1.18
122282ornithine decarboxylase-4.1.1.17
122282phenylalanine ammonia-lyase-4.3.1.24
122282protease+
122282tryptophan deaminase-
122282urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase+3.2.1.52

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20084+++++++++++-+-+++++
122282-++-+---+++-----+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122282+++++------------+++-+--+-+----+++---+-++-------+++--++-+--++++--+-----+++++---++-----+-+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11946soil of a conifer forestGuangxi ProvinceChinaCHNAsia
67770Soil of a conifer forestGuangxi ProvinceChinaCHNAsia
122282Environment, Soil, conifer forestGuangxiChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_7930.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_606;99_7930&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AF222022
  • Sequence Identity:
  • Total samples: 101
  • soil counts: 59
  • animal counts: 14
  • plant counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119461Risk group (German classification)
200841German classification
1222821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Amycolatopsis rubidus 16S ribosomal RNA gene, partial sequence
  • accession: AF222022
  • length: 1402
  • database: ena
  • NCBI tax ID: 112413

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis rubida strain DSM 44637112413.4wgspatric112413
66792Amycolatopsis rubida DSM 446372675903692draftimg112413
67770Amycolatopsis rubida DSM 44637GCA_900115345contigncbi112413

GC content

@refGC-contentmethod
6777069.8genome sequence analysis
6777067.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.647no
flagellatedno97.598no
gram-positiveyes87.818no
anaerobicno99.099no
aerobicyes92.662no
halophileno89.611no
spore-formingyes93.727no
thermophileno94.922yes
glucose-utilyes89.483no
glucose-fermentno91.966no

External links

@ref: 11946

culture collection no.: DSM 44637, AS 4.1541, CIP 107102, JCM 10871, NRRL B-24150, ATCC BAA 726, CGMCC 4.1541, KCTC 19909, NBRC 100041

straininfo link

  • @ref: 82448
  • straininfo: 100502

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11414266Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil.Huang Y, Qi W, Lu Z, Liu Z, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-51-3-10932001Actinomycetales/*classification/genetics/isolation & purification/ultrastructure, Carbohydrate Metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny34287120Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.Tedsree N, Tanasupawat S, Sritularak B, Kuncharoen N, Likhitwitayawuid KInt J Syst Evol Microbiol10.1099/ijsem.0.0049022021Amycolatopsis/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dendrobium/*microbiology, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hantavirus, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11946Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44637)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44637
20084Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44637.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
39659Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19305
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
82448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100502.1StrainInfo: A central database for resolving microbial strain identifiers
122282Curators of the CIPCollection of Institut Pasteur (CIP 107102)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107102