Strain identifier

BacDive ID: 6280

Type strain: Yes

Species: Ornithinimicrobium pekingense

Strain Designation: LW6

Strain history: S.-J. Liu LW6.

NCBI tax ID(s): 1122622 (strain), 384677 (species)

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General

@ref: 15791

BacDive-ID: 6280

DSM-Number: 21552

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

description: Ornithinimicrobium pekingense LW6 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge, wastewater treatment bioreactor.

NCBI tax id

NCBI tax idMatching level
1122622strain
384677species

strain history

@refhistory
15791<- JCM <- S.-J. Liu; LW6
67770S.-J. Liu LW6.

doi: 10.13145/bacdive6280.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Ornithinimicrobiaceae
  • genus: Ornithinimicrobium
  • species: Ornithinimicrobium pekingense
  • full scientific name: Ornithinimicrobium pekingense Liu et al. 2008

@ref: 15791

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Ornithinimicrobiaceae

genus: Ornithinimicrobium

species: Ornithinimicrobium pekingense

full scientific name: Ornithinimicrobium pekingense Liu et al. 2008 emend. Nouioui et al. 2018

strain designation: LW6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32268positive1.3 µm0.65 µmrod-shapedno
69480positive100

pigmentation

  • @ref: 32268
  • production: yes

multimedia

  • @ref: 15791
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_21552.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15791BHI 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
15791TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
15791TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

@refgrowthtypetemperaturerange
15791positivegrowth28mesophilic
32268positivegrowth26-38mesophilic
32268positiveoptimum35mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32268positivegrowth06-09alkaliphile
32268positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 32268
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.98

halophily

  • @ref: 32268
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 7 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3226830089acetate+carbon source
3226818403L-arabitol+carbon source
3226817057cellobiose+carbon source
3226816947citrate+carbon source
3226828757fructose+carbon source
3226828260galactose+carbon source
3226816634raffinose+carbon source
3226817632nitrate+reduction

enzymes

@refvalueactivityec
32268catalase+1.11.1.6
32268gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15791activated sludge, wastewater treatment bioreactorPekingChinaCHNAsia
67770Activated sludge of a bioreactor treating wastewaterBeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Activated sludge
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_6537.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3098;97_3799;98_4825;99_6537&stattab=map
  • Last taxonomy: Ornithinimicrobium
  • 16S sequence: DQ512860
  • Sequence Identity:
  • Total samples: 1308
  • soil counts: 222
  • aquatic counts: 205
  • animal counts: 798
  • plant counts: 83

Safety information

risk assessment

  • @ref: 15791
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15791
  • description: Ornithinimicrobium pekingense strain LW6 16S ribosomal RNA gene, partial sequence
  • accession: DQ512860
  • length: 1396
  • database: ena
  • NCBI tax ID: 1122622

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinimicrobium pekingense CGMCC 1.5362GCA_014644955scaffoldncbi384677
66792Ornithinimicrobium pekingense DSM 215521122622.9wgspatric1122622
66792Ornithinimicrobium pekingense strain CGMCC 1.5362384677.7wgspatric384677
66792Ornithinimicrobium pekingense DSM 215522524614884draftimg1122622
67770Ornithinimicrobium pekingense DSM 21552GCA_000421185scaffoldncbi1122622

GC content

@refGC-contentmethod
1579169
6777072.9genome sequence analysis
6777069thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
motileno93.552yes
flagellatedno98.755yes
gram-positiveyes88.923no
anaerobicno99.33no
aerobicyes92.361yes
halophileno77.993no
spore-formingno92.344no
glucose-utilyes88.685no
thermophileno96.378yes
glucose-fermentno89.271no

External links

@ref: 15791

culture collection no.: DSM 21552, CGMCC 1.5362, JCM 14001

straininfo link

  • @ref: 75756
  • straininfo: 323988

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175694Ornithinimicrobium pekingense sp. nov., isolated from activated sludge.Liu XY, Wang BJ, Jiang CY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.65229-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, *Bioreactors, China, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species SpecificityGenetics
Phylogeny26395130Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva.Ramaprasad EVV, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijsem.0.0006242015Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ulva/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31935182Ornithinimicrobium cerasi sp. nov., isolated from the fruit of Cerasus pseudocerasus and emended description of the genus Ornithinimicrobium.Fang XM, Du HJ, Bai JL, He WN, Li J, Wang H, Su J, Liu HY, Zhang YQ, Yu LYInt J Syst Evol Microbiol10.1099/ijsem.0.0039572020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fruit/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Prunus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15791Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21552)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21552
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
32268Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2850928776041
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/
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)
75756Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323988.1StrainInfo: A central database for resolving microbial strain identifiers