Strain identifier

BacDive ID: 13271

Type strain: Yes

Species: Amycolatopsis xylanica

Strain history: <- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

NCBI tax ID(s): 589385 (species)

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General

@ref: 16154

BacDive-ID: 13271

DSM-Number: 45285

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

description: Amycolatopsis xylanica DSM 45285 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 589385
  • Matching level: species

strain history

@refhistory
16154<- Y.-Q. Zhang, Inst. Med. Biotechnol., Chinese Academy of Med. Sci. and Peking Union Med. College, Beijing; CPCC 202699
67770CCM 7627 <-- Y.-Q. Zhang; Inst. of Med. Biotechnol., China; CPCC 202699.
67771<- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

doi: 10.13145/bacdive13271.20230509.8.1

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 xylanica
  • full scientific name: Amycolatopsis xylanica Chen et al. 2010

@ref: 16154

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis xylanica

full scientific name: Amycolatopsis xylanica Chen et al. 2010 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29606positiveno
67771positive
69480no93.874
69480positive100

pigmentation

  • @ref: 29606
  • production: yes

multimedia

  • @ref: 16154
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45285.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 16154
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
16154positivegrowth28mesophilic
29606positivegrowth10-45
29606positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29606positivegrowth6-9.5alkaliphile
29606positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29606aerobe
67771aerobe

spore formation

@refspore formationconfidence
29606yes
69481yes100
69480yes99.74

halophily

@refsaltgrowthtested relationconcentration
29606NaClpositivegrowth0-7 %
29606NaClpositiveoptimum0-5 %

observation

@refobservation
29606aggregates in chains
67770quinones: MK-9(H4), MK-9(H6), MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2960622599arabinose+carbon source
2960628757fructose+carbon source
2960628260galactose+carbon source
2960617754glycerol+carbon source
2960629864mannitol+carbon source
2960618222xylose+carbon source
296064853esculin+hydrolysis
2960617632nitrate+reduction
6836925115malate+assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29606alkaline phosphatase+3.1.3.1
29606catalase+1.11.1.6
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
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
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
16154-++/---+----------+/-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
16154----+/-+-++++++-+/--+/-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16154soilQinghai ProvinceChinaCHNAsia
67771From soilQinghai ProvinceChinaCHNAsia
67770SoilQinghai ProvinceChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 16154
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16154
  • description: Amycolatopsis xylanica strain CPCC 202699 16S ribosomal RNA gene, partial sequence
  • accession: FJ529702
  • length: 1451
  • database: ena
  • NCBI tax ID: 589385

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis xylanica strain CPCC 202699589385.3wgspatric589385
66792Amycolatopsis xylanica CPCC 2026992675903050draftimg589385
67770Amycolatopsis xylanica CPCC 202699GCA_900107045scaffoldncbi589385

GC content

@refGC-contentmethod
1615465.9thermal denaturation, midpoint method (Tm)
2960665.9
6777068.9genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes86.335yes
anaerobicno99.208yes
halophileno89.507no
spore-formingyes94.072yes
glucose-utilyes89.73no
thermophileno97.688yes
flagellatedno96.383no
aerobicyes94.399yes
motileno91.586no
glucose-fermentno92.663no

External links

@ref: 16154

culture collection no.: DSM 45285, CCM 7627, KCTC 19581, CPCC 202699, JCM 32380

straininfo link

  • @ref: 82475
  • straininfo: 408138

literature

  • topic: Phylogeny
  • Pubmed-ID: 19880636
  • title: Amycolatopsis xylanica sp. nov., isolated from soil.
  • authors: Chen J, Su JJ, Wei YZ, Li QP, Yu LY, Liu HY, Zhang YQ, Zhang YQ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.016865-0
  • year: 2009
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16154Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45285)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45285
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
29606Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2599628776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
82475Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408138.1StrainInfo: A central database for resolving microbial strain identifiers