Strain identifier

BacDive ID: 12673

Type strain: Yes

Species: Propioniciclava tarda

Strain history: A. Ueki WR061.

NCBI tax ID(s): 433330 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 16149

BacDive-ID: 12673

DSM-Number: 22130

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Propioniciclava tarda DSM 22130 is an anaerobe, mesophilic bacterium that was isolated from rice-straw residue in a methanogenic reactor of cattle waste.

NCBI tax id

  • NCBI tax id: 433330
  • Matching level: species

strain history

@refhistory
16149<- A. Ueki, Yamagata Univ., Tsuruoka, Japan; WR061 <- A. Ueki et al.
67770A. Ueki WR061.

doi: 10.13145/bacdive12673.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Propioniciclava
  • species: Propioniciclava tarda
  • full scientific name: Propioniciclava tarda Sugawara et al. 2011

@ref: 16149

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Propioniciclava

species: Propioniciclava tarda

full scientific name: Propioniciclava tarda Sugawara et al. 2011

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 99.6

Culture and growth conditions

culture medium

  • @ref: 16149
  • name: PY4S (DSMZ Medium 1308)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1308
  • composition: Name: PY4S (DSMZ Medium 1308) Composition: Trypticase peptone 10.0 g/l Yeast extract 5.0 g/l NaCl 0.9 g/l (NH4)2SO4 0.9 g/l L-Cysteine HCl x H2O 0.5 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l Glucose 0.25 g/l Starch 0.25 g/l Maltose 0.25 g/l Cellobiose 0.25 g/l Na2CO3 0.2 g/l CaCl2 x 2 H2O 0.09 g/l MgSO4 x 7 H2O 0.09 g/l Sodium resazurin 0.001 g/l Vitamin B12 1e-05 g/l Distilled water

culture temp

@refgrowthtypetemperature
16149positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16149anaerobe
125439obligate aerobe99.3

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838016024D-mannose-fermentation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380alanine arylamidase+3.4.11.2
68380L-arginine arylamidase+
68380alpha-fucosidase-3.2.1.51
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16149--++-++----------+++/-+/-+/---++/-+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16149rice-straw residue in a methanogenic reactor of cattle wasteHokkaidoJapanJPNAsia
67770Rice-straw residue in a methanogenic reactor treating waste from cattle farms

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste
#Host#Mammals#Bovinae (Cow, Cattle)
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_134815.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_282;96_24993;97_67281;98_89976;99_134815&stattab=map
  • Last taxonomy: Propioniciclava tarda subclade
  • 16S sequence: AB298731
  • Sequence Identity:
  • Total samples: 2521
  • soil counts: 105
  • aquatic counts: 2132
  • animal counts: 226
  • plant counts: 58

Safety information

risk assessment

  • @ref: 16149
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16149
  • description: Propioniciclava tarda gene for 16S rRNA, partial sequence, strain: WR061
  • accession: AB298731
  • length: 1453
  • database: nuccore
  • NCBI tax ID: 433330

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propioniciclava tarda DSM 22130GCA_900182665contigncbi433330
66792Propioniciclava tarda strain DSM 22130433330.3wgspatric433330
66792Propioniciclava tarda strain DSM 22130433330.4wgspatric433330
66792Propioniciclava tarda DSM 221302724679781draftimg433330
67770Propioniciclava tarda DSM 22130GCA_004324765contigncbi433330

GC content

  • @ref: 16149
  • GC-content: 69.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.825no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no74.076no
125438spore-formingspore-formingAbility to form endo- or exosporesno74.224no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes50.192yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.129yes
125438motile2+flagellatedAbility to perform flagellated movementno89.975no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno60.4
125439BacteriaNetmotilityAbility to perform movementno81.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.3

External links

@ref: 16149

culture collection no.: DSM 22130, JCM 15804, WR 061, KCTC 15186

straininfo link

  • @ref: 81884
  • straininfo: 403856

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20971831Propioniciclava tarda gen. nov., sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.Sugawara Y, Ueki A, Abe K, Kaku N, Watanabe K, Ueki KInt J Syst Evol Microbiol10.1099/ijs.0.027482-02010Aerobiosis, Anaerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Carbohydrate Metabolism, Catalase/metabolism, Cattle, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, *Industrial Waste, Japan, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Phylogeny, Propionibacteriaceae/*classification/genetics/*isolation & purification/physiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Vitamin B 12/metabolismMetabolism
Phylogeny28901898Propioniciclava sinopodophylli sp. nov., isolated from leaves of Sinopodophyllum hexandrum (Royle) Ying.Zhang L, Li Q, Chen C, Li X, Li M, Hu J, Shen XInt J Syst Evol Microbiol10.1099/ijsem.0.0022652017Bacterial Typing Techniques, Base Composition, Berberidaceae/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16149Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22130)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22130
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
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/
68380Automatically annotated from API rID32A
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
81884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403856.1StrainInfo: 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