Strain identifier

BacDive ID: 11161

Type strain: Yes

Species: Actinopolymorpha cephalotaxi

Strain Designation: 06-2230, I06-2230

Strain history: <- YQ Zhang, Inst. Med. Biotechnol, China

NCBI tax ID(s): 504797 (species)

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General

@ref: 12356

BacDive-ID: 11161

DSM-Number: 45117

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

description: Actinopolymorpha cephalotaxi 06-2230 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil from the rhizosphere of Cephalotaxus fortunei.

NCBI tax id

  • NCBI tax id: 504797
  • Matching level: species

strain history

@refhistory
12356<- Y.-Q. Zhang, Chinese Acad. Med. Sciences & Peking Union Medical College; 06-2230 <- L.-J. Yuan et al.
67770CCM 7466 <-- Y.-Q. Zhang 106-2230.
67771<- YQ Zhang, Inst. Med. Biotechnol, China

doi: 10.13145/bacdive11161.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Actinopolymorphaceae
  • genus: Actinopolymorpha
  • species: Actinopolymorpha cephalotaxi
  • full scientific name: Actinopolymorpha cephalotaxi Yuan et al. 2010

@ref: 12356

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinopolymorphaceae

genus: Actinopolymorpha

species: Actinopolymorpha cephalotaxi

full scientific name: Actinopolymorpha cephalotaxi Yuan et al. 2010

strain designation: 06-2230, I06-2230

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
29341positive
67771positive
125439positive98.4

pigmentation

  • @ref: 29341
  • production: yes

multimedia

  • @ref: 12356
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45117.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12356GYM 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
12356TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
12356BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
12356positivegrowth28
19917positiveoptimum28
29341positivegrowth20-28
67770positivegrowth28
67771positivegrowth28

culture pH

  • @ref: 29341
  • ability: positive
  • type: growth
  • pH: 06-08

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29341aerobe
67771aerobe
125439obligate aerobe98.9

halophily

  • @ref: 29341
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2934122599arabinose+carbon source
2934128757fructose+carbon source
2934128260galactose+carbon source
293415417glucosamine+carbon source
2934117234glucose+carbon source
2934129864mannitol+carbon source
2934117268myo-inositol+carbon source
2934116634raffinose+carbon source
2934126546rhamnose+carbon source
2934130911sorbitol+carbon source
2934117992sucrose+carbon source
2934118222xylose+carbon source
2934117632nitrate+reduction

enzymes

@refvalueactivityec
29341acid phosphatase+3.1.3.2
29341alkaline phosphatase+3.1.3.1
29341alpha-galactosidase+3.2.1.22
29341gelatinase+
29341urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382alpha-chymotrypsin-3.4.21.1

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19917----------+---+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12356forest soil from the rhizosphere of Cephalotaxus fortuneiCephalotaxus fortuneiYunnan ProvinceChinaCHNAsia
67770Rhizosphere soil of the plant Cephalotaxus fortunei from Yunnan ProvinceCephalotaxus fortuneiChinaCHNAsia
67771From forest soilYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_85990.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_779;96_20597;97_25630;98_59531;99_85990&stattab=map
  • Last taxonomy: Actinopolymorpha
  • 16S sequence: EU438909
  • Sequence Identity:
  • Total samples: 633
  • soil counts: 505
  • aquatic counts: 38
  • animal counts: 37
  • plant counts: 53

Safety information

risk assessment

  • @ref: 12356
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12356
  • description: Actinopolymorpha cephalotaxi strain I06-2230 16S ribosomal RNA gene, partial sequence
  • accession: EU438909
  • length: 1441
  • database: nuccore
  • NCBI tax ID: 504797

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinopolymorpha cephalotaxi strain CPCC 202808504797.4wgspatric504797
66792Actinopolymorpha cephalotaxi strain DSM 45117504797.5wgspatric504797
66792Actinopolymorpha cephalotaxi DSM 451172827628540draftimg504797
66792Actinopolymorpha cephalotaxi CPCC 2028082675903058draftimg504797
67770Actinopolymorpha cephalotaxi CPCC 202808GCA_900113145scaffoldncbi504797
67770Actinopolymorpha cephalotaxi DSM 45117GCA_013408535contigncbi504797

GC content

@refGC-contentmethod
1235669.3thermal denaturation, midpoint method (Tm)
2934169.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.586yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no88.902no
125438spore-formingspore-formingAbility to form endo- or exosporesyes73.08no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.388yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.422no
125438motile2+flagellatedAbility to perform flagellated movementno89.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes59.8
125439BacteriaNetmotilityAbility to perform movementno79.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.9

External links

@ref: 12356

culture collection no.: DSM 45117, CCM 7466, KCTC 19293, JCM 17964, CPCC 202808

straininfo link

  • @ref: 80410
  • straininfo: 403972

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648316Actinopolymorpha cephalotaxi sp. nov., a novel actinomycete isolated from rhizosphere soil of the plant Cephalotaxus fortunei.Yuan LJ, Zhang YQ, Yu LY, Sun CH, Wei YZ, Liu HY, Li WJ, Zhang YQInt J Syst Evol Microbiol10.1099/ijs.0.011197-02009Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Base Composition, Cephalotaxus/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny21148677Actinopolymorpha pittospori sp. nov., an endophyte isolated from surface-sterilized leaves of an apricot tree (Pittosporum phylliraeoides).Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.029579-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Australia, Base Composition, DNA, Bacterial/genetics, Endophytes/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Leaves/*microbiology, Prunus/*microbiology, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12356Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45117)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45117
19917Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45117.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
29341Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2575328776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
80410Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403972.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1