Strain identifier

BacDive ID: 14294

Type strain: Yes

Species: Sphingosinicella xenopeptidilytica

Strain Designation: 3-2W4

Strain history: CIP <- 2007, CCUG <- 2006, B. Geueke, Swiss Fed. Inst. Aquatic Sci., Dübendorf, Switzerland: strain 3-2W4

NCBI tax ID(s): 364098 (species)

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General

@ref: 6777

BacDive-ID: 14294

DSM-Number: 17130

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

description: Sphingosinicella xenopeptidilytica 3-2W4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from aeration tank of sewage treatment plant.

NCBI tax id

  • NCBI tax id: 364098
  • Matching level: species

strain history

@refhistory
6777<- B. Geueke, EAWAG Dübendorf; 3-2W4
123972CIP <- 2007, CCUG <- 2006, B. Geueke, Swiss Fed. Inst. Aquatic Sci., Dübendorf, Switzerland: strain 3-2W4

doi: 10.13145/bacdive14294.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingosinicellaceae
  • genus: Sphingosinicella
  • species: Sphingosinicella xenopeptidilytica
  • full scientific name: Sphingosinicella xenopeptidilytica Geueke et al. 2007

@ref: 6777

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingosinicellaceae

genus: Sphingosinicella

species: Sphingosinicella xenopeptidilytica

full scientific name: Sphingosinicella xenopeptidilytica Geueke et al. 2007

strain designation: 3-2W4

type strain: yes

Morphology

cell morphology

  • @ref: 123972
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6777LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
6777CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
37315MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
123972CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
6777positivegrowth28mesophilic
37315positivegrowth25mesophilic
59581positivegrowth20-30

culture pH

  • @ref: 59581
  • ability: positive
  • type: growth
  • pH: 7.0-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59581aerobe
123972obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12397217632nitrate+reduction
12397216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12397235581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123972oxidase+
123972catalase+1.11.1.6
123972urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123972-+++-+++++++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6777+-----+-----------+++
6777+-----+-----------+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6777aeration tank of sewage treatment plantSwitzerlandCHEEurope
59581Wastewater treatment plant,aeration tankSwitzerlandCHEEuropeZürich,Leutschenbach
123972Environment, Wastewater treatment plant, aeration tankSwitzerlandCHEEuropeZurich

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#Engineered#Waste#Wastewater
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_29701.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_14601;97_17816;98_22148;99_29701&stattab=map
  • Last taxonomy: Sphingosinicella
  • 16S sequence: AY950663
  • Sequence Identity:
  • Total samples: 17610
  • soil counts: 5974
  • aquatic counts: 7685
  • animal counts: 2606
  • plant counts: 1345

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67771Risk group (German classification)
1239721Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Sphingosinicella xenopeptidilytica strain 3-2W4 16S ribosomal RNA gene, partial sequence
  • accession: AY950663
  • length: 1411
  • database: ena
  • NCBI tax ID: 364098

External links

@ref: 6777

culture collection no.: DSM 17130, CCUG 52537, CIP 109497

straininfo link

  • @ref: 83447
  • straininfo: 297322

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220451Description of Sphingosinicella xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans.Geueke B, Busse HJ, Fleischmann T, Kampfer P, Kohler HEInt J Syst Evol Microbiol10.1099/ijs.0.64509-02007Aminopeptidases/*metabolism, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Microcystins/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Peptides/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonadaceae/chemistry/*classification/genetics/metabolism, Switzerland, Waste Disposal, Fluid/*methods, *Water MicrobiologyMetabolism
Phylogeny17625188Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes.Kim MK, Schubert K, Im WT, Kim KH, Lee ST, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.64579-02007Bacterial Proteins/analysis/*genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Light-Harvesting Protein Complexes/*genetics, Molecular Sequence Data, Photosynthetic Reaction Center Complex Proteins/*genetics, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/*genetics/isolation & purificationGenetics
Enzymology17886858Enzyme-catalyzed formation of beta-peptides: beta-peptidyl aminopeptidases BapA and DmpA acting as beta-peptide-synthesizing enzymes.Heck T, Kohler HP, Limbach M, Flogel O, Seebach D, Geueke BChem Biodivers10.1002/cbdv.2007901682007Amino Acids/chemistry, Aminopeptidases/*chemistry, Bacterial Proteins/*chemistry, Catalysis, Kinetics, *Peptide Biosynthesis, Peptides/*chemistry, Substrate Specificity
Enzymology19449346Kinetic resolution of aliphatic beta-amino acid amides by beta-aminopeptidases.Heck T, Seebach D, Osswald S, Ter Wiel MK, Kohler HP, Geueke BChembiochem10.1002/cbic.2009001842009Alphaproteobacteria/enzymology, Amides/*chemistry, Amino Acids/chemistry/*isolation & purification, Aminopeptidases/*metabolism, Biocatalysis, Kinetics, Ochrobactrum anthropi/enzymology, StereoisomerismPhylogeny
Phylogeny19654337Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella.Yasir M, Aslam Z, Song GC, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.010777-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny26315363Sphingosinicella cucumeris sp. nov., isolated from soil of a cucumber garden.Akter S, Du J, Won K, Yin CS, Kook M, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0572-62015Base Composition, *Cucumis sativus/microbiology, DNA, Bacterial, Fatty Acids/chemistry, Lipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/isolation & purification/physiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6777Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17130)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17130
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
37315Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7247
59581Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52537)https://www.ccug.se/strain?id=52537
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
83447Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297322.1StrainInfo: A central database for resolving microbial strain identifiers
123972Curators of the CIPCollection of Institut Pasteur (CIP 109497)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109497