Strain identifier

BacDive ID: 7847

Type strain: Yes

Species: Actinoplanes abujensis

Strain Designation: A4029

Strain history: <- N Sahin, Ondokuz Mayis Univ., Turkey

NCBI tax ID(s): 882441 (species)

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General

@ref: 17494

BacDive-ID: 7847

DSM-Number: 45518

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

description: Actinoplanes abujensis A4029 is an aerobe, spore-forming, mesophilic bacterium that was isolated from arid soil.

NCBI tax id

  • NCBI tax id: 882441
  • Matching level: species

strain history

@refhistory
17494<- N. Sahin, Ondokuz Mayis University, Turkey; A4029
67770KCTC 19984 <-- N. Sahin A4029.
67771<- N Sahin, Ondokuz Mayis Univ., Turkey

doi: 10.13145/bacdive7847.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinoplanes
  • species: Actinoplanes abujensis
  • full scientific name: Actinoplanes abujensis Sazak et al. 2012

@ref: 17494

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes abujensis

full scientific name: Actinoplanes abujensis Sazak et al. 2012

strain designation: A4029

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
30255positive
67771positive
69480positive100

pigmentation

  • @ref: 30255
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17494TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
17494CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium83.pdf
17494GYM 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

culture temp

@refgrowthtypetemperaturerange
17494positivegrowth28mesophilic
30255positivegrowth20-37
30255positiveoptimum25-30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30255positivegrowth05-09alkaliphile
30255positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30255aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 30255
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3025517057cellobiose+carbon source
3025517234glucose+carbon source
3025517306maltose+carbon source
3025537684mannose+carbon source
302554853esculin+hydrolysis
3025517632nitrate+reduction

enzymes

@refvalueactivityec
30255acid phosphatase+3.1.3.2
30255alkaline phosphatase+3.1.3.1
30255alpha-galactosidase+3.2.1.22
30255catalase+1.11.1.6
30255gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17494arid soilAbujaNigeriaNGAAfrica
67770Arid soilAbujaNigeriaNGAAfrica
67771From arid soilAbujaNigeriaNGAAfrica

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

Safety information

risk assessment

  • @ref: 17494
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17494
  • description: Actinoplanes abujensis strain A4029 16S ribosomal RNA gene, partial sequence
  • accession: HQ157185
  • length: 1490
  • database: ena
  • NCBI tax ID: 882441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes abujensis NBRC 110796GCA_016861995contigncbi882441
66792Actinoplanes abujensis DSM 45518GCA_014204895contigncbi882441
66792Actinoplanes abujensis strain DSM 45518882441.3wgspatric882441
66792Actinoplanes abujensis strain NBRC 110796882441.4wgspatric882441
66792Actinoplanes abujensis DSM 455182870584755draftimg882441

GC content

@refGC-contentmethod
1749470.2fluorimetric
3025570.2
6777070.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes59.766no
flagellatedno91.144no
gram-positiveyes90.518yes
anaerobicno99.194yes
halophileno95.666no
spore-formingyes92.212no
thermophileno99.273yes
glucose-utilyes88.127yes
aerobicyes94.805yes
glucose-fermentno88.905no

External links

@ref: 17494

culture collection no.: DSM 45518, KCTC 19984, NRRL B-24835, JCM 19953, NBRC 110796

straininfo link

  • @ref: 77284
  • straininfo: 400419

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21669926Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil.Sazak A, Sahin N, Camas MInt J Syst Evol Microbiol10.1099/ijs.0.031872-02011Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26243557Actinoplanes bogoriensis sp. nov., a novel actinomycete isolated from leaf litter.Nurkanto A, Lisdiyanti P, Hamada M, Ratnakomala S, Shibata C, Tamura TJ Antibiot (Tokyo)10.1038/ja.2015.812015Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Indonesia, Molecular Sequence Data, Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny29125458Actinoplanes sediminis sp. nov., isolated from marine sediment.Qu Z, Bao XD, Xie QY, Zhao YX, Yan B, Dai HF, Chen HQInt J Syst Evol Microbiol10.1099/ijsem.0.0024512017Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Geologic Sediments, Greece, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17494Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45518)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45518
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
30255Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2659728776041
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
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
77284Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400419.1StrainInfo: A central database for resolving microbial strain identifiers