Strain identifier

BacDive ID: 14274

Type strain: Yes

Species: Sphingopyxis macrogoltabida

Strain Designation: 203

Strain history: CIP <- 1994, IFO <- F. Kawai, Kobe Univ. of Commerce, Japan

NCBI tax ID(s): 1219047 (strain), 33050 (species)

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General

@ref: 3417

BacDive-ID: 14274

DSM-Number: 8826

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

description: Sphingopyxis macrogoltabida 203 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1219047strain
33050species

strain history

@refhistory
3417<- IFO <- F. Kawai, Kobe Univ. Commerce <- Kyoto Univ.
67770IFO 15033 <-- F. Kawai 203.
120743CIP <- 1994, IFO <- F. Kawai, Kobe Univ. of Commerce, Japan

doi: 10.13145/bacdive14274.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingopyxis
  • species: Sphingopyxis macrogoltabida
  • full scientific name: Sphingopyxis macrogoltabida (Takeuchi et al. 1993) Takeuchi et al. 2001

  • synonyms

    @refsynonym
    20215Sphingomonas macrogoltabida
    20215Sphingomonas macrogolitabida
    20215Sphingomonas macrogoltabidus

@ref: 3417

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingopyxis

species: Sphingopyxis macrogoltabida

full scientific name: Sphingopyxis macrogoltabida (Takeuchi et al. 1993) Takeuchi et al. 2001

strain designation: 203

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.976
120743negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3417REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39986MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120743CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3417positivegrowth30mesophilic
39986positivegrowth30mesophilic
67770positivegrowth30mesophilic
120743positivegrowth30mesophilic
120743nogrowth5psychrophilic
120743nogrowth41thermophilic
120743nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120743
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.976

compound production

  • @ref: 3417
  • compound: polyethyleneglycol dehydrogenase

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12074316947citrate-carbon source
12074317632nitrate-reduction
12074316301nitrite-reduction

antibiotic resistance

  • @ref: 120743
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120743
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120743oxidase+
120743beta-galactosidase+3.2.1.23
120743alcohol dehydrogenase-1.1.1.1
120743gelatinase-
120743DNase-
120743catalase+1.11.1.6
120743lysine decarboxylase-4.1.1.18
120743ornithine decarboxylase-4.1.1.17
120743phenylalanine ammonia-lyase+4.3.1.24
120743urease-3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120743+--+-----------++++-------------------------------------------+----------+-+------------++++-++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3417soilKyotoJapanJPNAsia
120743Environment, SoilKyotoJapanJPNAsia1974

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2245.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1020;97_1190;98_1749;99_2245&stattab=map
  • Last taxonomy: Sphingopyxis
  • 16S sequence: CP009429
  • Sequence Identity:
  • Total samples: 497
  • soil counts: 91
  • aquatic counts: 121
  • animal counts: 232
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34171Risk group (German classification)
1207431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingopyxis macrogoltabida 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGQ907177546ena33050
20218Sphingopyxis macrogoltabida gene for 16S rRNA, partial sequenceD137231415ena33050
20218Sphingopyxis macrogoltabida gene for 16S ribosomal RNAD845301411ena33050
20218Sphingopyxis macrogoltabida gene for 16S rRNA, partial sequence, strain: NBRC 15033AB6807531414ena33050
3417Sphingopyxis macrogoltabida strain 203, complete genomeCP0094295174928ena33050

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingopyxis macrogoltabida 203GCA_001314325completencbi33050
66792Sphingopyxis macrogoltabida 2032654588046completeimg1219047

GC content

  • @ref: 67770
  • GC-content: 63.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 99
  • training_data: no

External links

@ref: 3417

culture collection no.: DSM 8826, ATCC 51380, IFO 15033, NBRC 15033, JCM 10192, CIP 104196, IAM 14459, KCTC 2813, LMG 17324

straininfo link

  • @ref: 83429
  • straininfo: 9367

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508864Sphingopyxis witflariensis sp. nov., isolated from activated sludge.Kampfer P, Witzenberger R, Denner EB, Busse HJ, Neef AInt J Syst Evol Microbiol10.1099/00207713-52-6-20292002Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiologyGenetics
Phylogeny12710615Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov.Godoy F, Vancanneyt M, Martinez M, Steinbuchel A, Swings J, Rehm BHAInt J Syst Evol Microbiol10.1099/ijs.0.02375-02003Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification/*metabolism, Base Composition, Biodegradation, Environmental, Chlorophenols/*metabolism, Fatty Acids/analysis/*chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Stearic AcidsMetabolism
Phylogeny15880090Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria.Kim MK, Im WT, Ohta H, Lee M, Lee STJ Microbiol21692005Base Composition, Nucleic Acid Hybridization, Phylogeny, Sphingomonadaceae/*classification/enzymology/genetics, beta-Glucosidase/*biosynthesisEnzymology
Metabolism17630126Biosynthesis of poly-beta-hydroxyalkanoate by Brevundimonas vesicularis LMG P-23615 and Sphingopyxis macrogoltabida LMG 17324 using acid-hydrolyzed sawdust as carbon source.Silva JA, Tobella LM, Becerra J, Godoy F, Martinez MAJ Biosci Bioeng10.1263/jbb.103.5422007Acids, Biodegradation, Environmental, Biopolymers/*biosynthesis, Carbon/metabolism, Caulobacteraceae/*metabolism, Hydrolysis, Hydroxy Acids/*metabolism, Polyesters/*metabolism, Sphingomonadaceae/*metabolism, Wood
Phylogeny19933588Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M, Kalaiselvi S, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.019414-02009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/genetics/*isolation & purificationGenetics
Genetics26659674Complete Genome Sequence of Sphingopyxis macrogoltabida Type Strain NBRC 15033, Originally Isolated as a Polyethylene Glycol Degrader.Ohtsubo Y, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai FGenome Announc10.1128/genomeA.01401-152015Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3417Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8826)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8826
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39986Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16077
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)
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
83429Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9367.1StrainInfo: A central database for resolving microbial strain identifiers
120743Curators of the CIPCollection of Institut Pasteur (CIP 104196)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104196