Strain identifier

BacDive ID: 3941

Type strain: Yes

Species: Kineosphaera limosa

Strain Designation: Lpha5, 225

Strain history: S. Hanada 225 (=strain Lpha5).

NCBI tax ID(s): 1184609 (strain), 111564 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
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 8.1 (current version)

General

@ref: 5382

BacDive-ID: 3941

DSM-Number: 14548

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

description: Kineosphaera limosa Lpha5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
1184609strain
111564species

strain history

@refhistory
5382<- S. Hanada; 225
67770S. Hanada 225 (=strain Lpha5).

doi: 10.13145/bacdive3941.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermatophilaceae
  • genus: Kineosphaera
  • species: Kineosphaera limosa
  • full scientific name: Kineosphaera limosa Liu et al. 2002

@ref: 5382

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermatophilaceae

genus: Kineosphaera

species: Kineosphaera limosa

full scientific name: Kineosphaera limosa Liu et al. 2002

strain designation: Lpha5, 225

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 5382
  • name: MICROLUNATUS MEDIUM (DSMZ Medium 776)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/776
  • composition: Name: MICROLUNATUS MEDIUM (DSMZ Medium 776) Composition: KH2PO4 0.5 g/l Na glutamate 0.5 g/l Yeast extract 0.5 g/l Peptone 0.5 g/l Glucose 0.5 g/l (NH4)2SO4 0.1 g/l MgSO4 x 7 H2O 0.1 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18515positiveoptimum28mesophilic
5382positivegrowth28mesophilic
61194positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 61194
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.988

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5382activated sludgeIbaraki Pref.JapanJPNAsia
61194Activated sludgeIbaraki Pref.JapanJPNAsia
67770Activated sludgeIbaraki Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_8188.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2814;97_4639;98_5955;99_8188&stattab=map
  • Last taxonomy: Kineosphaera limosa subclade
  • 16S sequence: AF109792
  • Sequence Identity:
  • Total samples: 152
  • soil counts: 10
  • aquatic counts: 52
  • animal counts: 76
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185151Risk group (German classification)
53821Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5382Uncultured High G+C Gram-positive bacterium lpha5 16S ribosomal RNA gene, partial sequenceAF1097921461ena1184609
67770Kineosphaera limosa gene for 16S rRNA, partial sequence, strain: NBRC 100340AB5508021474ena1184609

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineosphaera limosa NBRC 1003401184609.3wgspatric1184609
66792Kineosphaera limosa strain DSM 14548111564.3wgspatric111564
66792Kineosphaera limosa DSM 145482844806747draftimg111564
66792Kineosphaera limosa NBRC 1003402524023180draftimg1184609
67770Kineosphaera limosa NBRC 100340GCA_000298215contigncbi1184609
67770Kineosphaera limosa DSM 14548GCA_013409325contigncbi111564

GC content

@refGC-contentmethod
538271high performance liquid chromatography (HPLC)
6777071.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno57no
motileno50no
gram-positiveyes80no
anaerobicno97.314no
aerobicyes80.732no
halophileno91.561no
spore-formingno81.382no
flagellatedno91.546no
thermophileno98.464no
glucose-utilyes90.6no
glucose-fermentno82.748no

External links

@ref: 5382

culture collection no.: CCUG 57105, DSM 14548, JCM 11399, NBRC 100340

straininfo link

@refstraininfo
73449100704
73450409553

literature

  • topic: Phylogeny
  • Pubmed-ID: 12361296
  • title: Kineosphaera limosa gen. nov., sp. nov., a novel Gram-positive polyhydroxyalkanoate-accumulating coccus isolated from activated sludge.
  • authors: Liu WT, Hanada S, Marsh TL, Kamagata Y, Nakamura K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-5-1845
  • year: 2002
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Bioreactors, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, Polyesters/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as Topic
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5382Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14548)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14548
18515Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14548.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
61194Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57105)https://www.ccug.se/strain?id=57105
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/
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)
73449Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100704.1StrainInfo: A central database for resolving microbial strain identifiers
73450Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID409553.1StrainInfo: A central database for resolving microbial strain identifiers