Strain identifier

BacDive ID: 6329

Type strain: Yes

Species: Quadrisphaera granulorum

Strain Designation: AG-019

Strain history: DSM 44889 <-- A. M. Maszenan AG-019.

NCBI tax ID(s): 317664 (species)

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General

@ref: 12174

BacDive-ID: 6329

DSM-Number: 44889

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

description: Quadrisphaera granulorum AG-019 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from aerobic granule sludge biomass.

NCBI tax id

  • NCBI tax id: 317664
  • Matching level: species

strain history

@refhistory
12174<- A. M. Maszenan; AG-019
67770DSM 44889 <-- A. M. Maszenan AG-019.

doi: 10.13145/bacdive6329.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kineosporiales
  • family: Kineosporiaceae
  • genus: Quadrisphaera
  • species: Quadrisphaera granulorum
  • full scientific name: Quadrisphaera granulorum Maszenan et al. 2005

@ref: 12174

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Quadrisphaera

species: Quadrisphaera granulorum

full scientific name: Quadrisphaera granulorum Maszenan et al. 2005 emend. Nouioui et al. 2018

strain designation: AG-019

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31447positive2.1 µm2.1 µmcoccus-shapedno
69480positive100

pigmentation

  • @ref: 31447
  • production: no

multimedia

@refmultimedia contentintellectual property rightscaption
12174https://www.dsmz.de/microorganisms/photos/DSM_44889-1.jpg© Leibniz-Institut DSMZ
12174https://www.dsmz.de/microorganisms/photos/DSM_44889.jpg© Leibniz-Institut DSMZMedium 621 37°C

Culture and growth conditions

culture medium

  • @ref: 12174
  • name: PYGV AGAR (DSMZ Medium 621)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/621
  • composition: Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water

culture temp

@refgrowthtypetemperaturerange
12174positivegrowth37mesophilic
31447positivegrowth15-40
31447positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31447positivegrowth05-09alkaliphile
31447positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31447
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31447no
69481no97
69480no99.712

observation

@refobservation
31447aggregates in clumps
67770quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3144716000ethanolamine+carbon source
3144715963ribitol+carbon source
3144722599arabinose+carbon source
3144718403L-arabitol+carbon source
3144717057cellobiose+carbon source
3144723652dextrin+carbon source
3144732323glucuronamide+carbon source
3144717754glycerol+carbon source
3144729864mannitol+carbon source
3144728053melibiose+carbon source
3144737657methyl D-glucoside+carbon source
3144751850methyl pyruvate+carbon source
3144715361pyruvate+carbon source
3144730031succinate+carbon source
3144753423tween 40+carbon source
3144753426tween 80+carbon source
3144718222xylose+carbon source

enzymes

  • @ref: 31447
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12174aerobic granule sludge biomassSingaporeSGPAsia
67770Aerobic granules from a laboratory-scale sequencing batch reactor

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_135434.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_6677;97_40456;98_89775;99_135434&stattab=map
  • Last taxonomy: Quadrisphaera granulorum subclade
  • 16S sequence: AY831385
  • Sequence Identity:
  • Total samples: 1281
  • soil counts: 290
  • aquatic counts: 111
  • animal counts: 800
  • plant counts: 80

Safety information

risk assessment

  • @ref: 12174
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12174
  • description: Quadrisphaera granulorum strain AG019 16S ribosomal RNA gene, partial sequence
  • accession: AY831385
  • length: 1483
  • database: ena
  • NCBI tax ID: 317664

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Quadrisphaera granulorum strain DSM 44889317664.3wgspatric317664
66792Quadrisphaera granulorum DSM 448892724679791draftimg317664
67770Quadrisphaera granulorum DSM 44889GCA_003149145contigncbi317664
67770Quadrisphaera granulorum DSM 44889GCA_900218025contigncbi317664

GC content

@refGC-contentmethod
1217474.8
3144775
6777072.6genome sequence analysis
6777075high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveyes91.236yes
anaerobicno98.773no
halophileno91.945no
spore-formingno81.989yes
glucose-utilyes88.227no
motileyes69.042no
flagellatedno91.999yes
aerobicyes87.21yes
thermophileno98.899no
glucose-fermentno84.516no

External links

@ref: 12174

culture collection no.: DSM 44889, ATCC BAA 1104, CIP 108941, JCM 16010, NBRC 106147

straininfo link

  • @ref: 75803
  • straininfo: 215516

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166665Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules.Maszenan AM, Tay JH, Schumann P, Jiang HL, Tay STInt J Syst Evol Microbiol10.1099/ijs.0.63583-02005Actinomycetales/chemistry/*classification/genetics/isolation & purification, Aerobiosis, *Bacterial Adhesion, Bacterial Typing Techniques, Bioreactors, Cells, Immobilized, DNA, Bacterial/analysis, Gram-Positive Cocci/classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, Polyphosphates/*metabolism, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny35925796Quadrisphaera setariae sp. nov., polyphosphate-accumulating bacterium occurring as tetrad or aggregate cocci and isolated from Setaria viridis.Kim I, Chhetri G, Kim J, So Y, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0054652022*Actinomycetales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, Phospholipids/chemistry, Phylogeny, Polyphosphates, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Setaria Plant/microbiology, Vitamin K 2/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12174Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44889)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44889
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
31447Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2775028776041
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)
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
75803Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215516.1StrainInfo: A central database for resolving microbial strain identifiers