Strain identifier

BacDive ID: 11158

Type strain: Yes

Species: Actinopolymorpha singaporensis

Strain Designation: IM 7744

Strain history: CIP <- 2002, Y. Wang, Singapore: strain IM 7744

NCBI tax ID(s): 117157 (species)

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

@ref: 16040

BacDive-ID: 11158

DSM-Number: 22024

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

description: Actinopolymorpha singaporensis IM 7744 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil sample collected from the surface to about 10 cm deep in the primary rainforest.

NCBI tax id

  • NCBI tax id: 117157
  • Matching level: species

strain history

@refhistory
16040<- JCM/RIKEN <- Y. Wang, Microbial Collection and Screening Lab., Inst. of Molecular and Cell Biology, Singapore; IM 7744
331132002, Y. Wang, Singapore: strain IM 7744
67770Y. Wang IM7744.
67771<- JCM
122631CIP <- 2002, Y. Wang, Singapore: strain IM 7744

doi: 10.13145/bacdive11158.20230509.8.1

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 singaporensis
  • full scientific name: Actinopolymorpha singaporensis Wang et al. 2001

@ref: 16040

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinopolymorphaceae

genus: Actinopolymorpha

species: Actinopolymorpha singaporensis

full scientific name: Actinopolymorpha singaporensis Wang et al. 2001 emend. Nouioui et al. 2018

strain designation: IM 7744

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771positive
69480no90.866
69480positive100
122631positivenorod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16040GYM 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
33113MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
16040R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
122631CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
16040positivegrowth28mesophilic
33113positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth42thermophilic
122631positivegrowth22-37
122631nogrowth5psychrophilic
122631nogrowth15psychrophilic
122631nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
122631obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122631NaClpositivegrowth0-4 %
122631NaClnogrowth6 %
122631NaClnogrowth8 %
122631NaClnogrowth10 %

observation

@refobservation
67770quinones: MK-9(H6), MK-9(H4)
67771quinones: MK-9(H(6))

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371D-fucose+builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122631citrate-carbon source16947
122631esculin+hydrolysis4853
122631nitrate-reduction17632
122631nitrite-reduction16301
122631glucose-degradation17234
122631nitrate-respiration17632

antibiotic resistance

  • @ref: 122631
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122631
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12263115688acetoin-
12263117234glucose-

enzymes

@refvalueactivityec
122631oxidase-
122631alcohol dehydrogenase-1.1.1.1
122631gelatinase+
122631amylase-
122631DNase-
122631caseinase+3.4.21.50
122631catalase+1.11.1.6
122631tween esterase-
122631gamma-glutamyltransferase+2.3.2.2
122631lecithinase-
122631lipase-
122631lysine decarboxylase-4.1.1.18
122631ornithine decarboxylase-4.1.1.17
122631phenylalanine ammonia-lyase-4.3.1.24
122631protease-
122631tryptophan deaminase-
122631urease-3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122631-+++-+--++++-+-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122631------------------------+-----+-----------++/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122631+++++-++++++---++-+-+-++-++-+-----+++----------------------+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16040soil sample collected from the surface to about 10 cm deep in the primary rainforestBukit Timah nature reserveSingaporeSGPAsia
67770Soil, the primary rainforest of the Bukit Timah Nature ReserveSingaporeSGPAsia
67771From soilSingaporeSGPAsia
122631Environment, Soil sampleSingaporeSGPAsia1998

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Climate#Hot#Tropical

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: AF237815
  • Sequence Identity:
  • Total samples: 633
  • soil counts: 505
  • aquatic counts: 38
  • animal counts: 37
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
160401Risk group (German classification)
1226311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16040
  • description: Actinosingapura polymorpha 16S ribosomal RNA gene, partial sequence
  • accession: AF237815
  • length: 1442
  • database: ena
  • NCBI tax ID: 117157

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinopolymorpha singaporensis DSM 22024GCA_900104745chromosomencbi117157
66792Actinopolymorpha singaporensis strain DSM 22024117157.3completepatric117157
66792Actinopolymorpha singaporensis DSM 220242636416006draftimg117157

GC content

@refGC-contentmethod
1604069.5high performance liquid chromatography (HPLC)
6777070.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes68no
motileno90.437no
gram-positiveyes87.488no
anaerobicno98.671yes
aerobicyes91.007yes
halophileno88.269no
spore-formingno56.625no
flagellatedno98.785no
thermophileno92.312no
glucose-utilyes86.54no
glucose-fermentno91.04no

External links

@ref: 16040

culture collection no.: DSM 22024, CIP 107343, JCM 10761, KCTC 19907, NBRC 100040, NRRL B-24113, NCIMB 14324

straininfo link

  • @ref: 80407
  • straininfo: 100477

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842872Actinopolymorpha rutila sp. nov., isolated from a forest soil.Wang YX, Zhang YQ, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.65629-02008Cell Wall/chemistry, China, DNA, Bacterial/genetics, Genes, Bacterial, Genes, rRNA, Genotype, Lipids/chemistry, Molecular Sequence Data, Phenotype, Phylogeny, Propionibacteriaceae/chemistry/*classification/*genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/microbiology, Vitamin K 2/chemistryGenetics
Phylogeny19605725Actinopolymorpha alba sp. nov., isolated from a rhizosphere soil.Cao YR, Jiang Y, Wu JY, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.010280-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Maytenus/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny20889769Flindersiella endophytica gen. nov., sp. nov., an endophytic actinobacterium isolated from the root of Grey Box, an endemic eucalyptus tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.026757-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Eucalyptus/*microbiology, Glucose/analysis, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhamnose/analysis, Ribose/analysis, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16040Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22024)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22024
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
33113Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4768
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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)
80407Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100477.1StrainInfo: A central database for resolving microbial strain identifiers
122631Curators of the CIPCollection of Institut Pasteur (CIP 107343)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107343