Strain identifier

BacDive ID: 14264

Type strain: Yes

Species: Sphingomonas rubra

Strain Designation: BH3

Strain history: CIP <- 2012, JCM <- 2009, Y.Y. Huo: strain BH3

NCBI tax ID(s): 634430 (species)

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General

@ref: 18168

BacDive-ID: 14264

DSM-Number: 26135

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

description: Sphingomonas rubra BH3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from bioreactor for wastewater from a leather plant.

NCBI tax id

  • NCBI tax id: 634430
  • Matching level: species

strain history

@refhistory
18168<- JCM <- Y.-Y. Huo, Zhejiang Univ., Hangzhou, China; BH3
67770Y.-Y. Huo BH3.
122288CIP <- 2012, JCM <- 2009, Y.Y. Huo: strain BH3

doi: 10.13145/bacdive14264.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas rubra
  • full scientific name: Sphingomonas rubra Huo et al. 2011

@ref: 18168

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas rubra

full scientific name: Sphingomonas rubra Huo et al. 2011

strain designation: BH3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29787negative2.35 µm0.25 µmrod-shapedyes
69480negative99.814
122288negativerod-shapedyes

pigmentation

  • @ref: 29787
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18168R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
36891MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122288CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18168positivegrowth28mesophilic
29787positivegrowth04-37
29787positiveoptimum28mesophilic
36891positivegrowth25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29787positivegrowth06-09alkaliphile
29787positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29787
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.997

halophily

  • @ref: 29787
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-8 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2978722599arabinose+carbon source
2978728260galactose+carbon source
2978717234glucose+carbon source
2978717306maltose+carbon source
297874853esculin+hydrolysis

enzymes

@refvalueactivityec
29787acid phosphatase+3.1.3.2
29787alkaline phosphatase+3.1.3.1
29787catalase+1.11.1.6
29787cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
18168bioreactor for wastewater from a leather plantChinaCHNAsia
67770Wastewater of a sequential batch reactor treating wastewater from a leather plant
122288Environment, Wastewater of a sequential batch reactor treating wastewater taken from a leather plant

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Wastewater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
181681Risk group (German classification)
1222881Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18168
  • description: Sphingomonas rubra strain BH3 16S ribosomal RNA gene, partial sequence
  • accession: FJ834325
  • length: 1448
  • database: ena
  • NCBI tax ID: 634430

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas rubra strain CGMCC 1.9113634430.3wgspatric634430
66792Sphingomonas rubra CGMCC 1.91132617270762draftimg634430
67770Sphingomonas rubra CGMCC 1.9113GCA_900115745contigncbi634430

GC content

@refGC-contentmethod
1816865.6thermal denaturation, midpoint method (Tm)
2978765.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
gram-positiveno96.937yes
anaerobicno99.351no
halophileno93.441no
spore-formingno96.346no
glucose-utilyes89.644yes
thermophileno96.61yes
flagellatedno90.878no
aerobicyes95.342no
motileyes64.734no
glucose-fermentno90.74no

External links

@ref: 18168

culture collection no.: DSM 26135, CGMCC 1.9113, CIP 110396, JCM 16230

straininfo link

  • @ref: 83422
  • straininfo: 377307

literature

  • topic: Phylogeny
  • Pubmed-ID: 20511462
  • title: Sphingomonas rubra sp. nov., isolated from bioreactor wastewater.
  • authors: Huo YY, Xu XW, Liu SP, Cui HL, Li X, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.020958-0
  • year: 2010
  • mesh: Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Sphingomonas/*classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18168Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26135)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26135
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
29787Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2616728776041
36891Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8251
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/
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
83422Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377307.1StrainInfo: A central database for resolving microbial strain identifiers
122288Curators of the CIPCollection of Institut Pasteur (CIP 110396)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110396