Strain identifier

BacDive ID: 14229

Type strain: Yes

Species: Sphingomonas pituitosa

Strain Designation: EDIV

Strain history: CIP <- 1999, E.B.M. Denner, Vienna Biocenter, Vienna, Austria: strain EDIV

NCBI tax ID(s): 1219051 (strain), 99597 (species)

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General

@ref: 4905

BacDive-ID: 14229

DSM-Number: 13101

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Sphingomonas pituitosa EDIV is an obligate aerobe, mesophilic, motile bacterium that was isolated from water .

NCBI tax id

NCBI tax idMatching level
99597species
1219051strain

strain history

@refhistory
4905<- E. B. M. Denner; EDIV
372851999, E.B.M. Denner, Inst. Mikrob. Gen., Vienna, Austria: strain EDIV
67770IAM 15276 <-- CIP 106154 <-- E. B. M. Denner strain EDIV.
121851CIP <- 1999, E.B.M. Denner, Vienna Biocenter, Vienna, Austria: strain EDIV

doi: 10.13145/bacdive14229.20230509.8.1

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 pituitosa
  • full scientific name: Sphingomonas pituitosa Denner et al. 2001

@ref: 4905

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas pituitosa

full scientific name: Sphingomonas pituitosa Denner et al. 2001

strain designation: EDIV

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.414
6948099.97negative
121851negativerod-shaped

pigmentation

  • @ref: 121851
  • production: no
  • name: Pyocyanin

multimedia

  • @ref: 4905
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_13101.jpg
  • caption: cells
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4905NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37285MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121851CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4905positivegrowth30mesophilic
37285positivegrowth30mesophilic
67770positivegrowth30mesophilic
121851positivegrowth10-37
121851nogrowth5psychrophilic
121851nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121851
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.974

halophily

@refsaltgrowthtested relationconcentration
121851NaClpositivegrowth0-2 %
121851NaClnogrowth4 %
121851NaClnogrowth6 %
121851NaClnogrowth8 %
121851NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121851citrate-carbon source16947
121851esculin+hydrolysis4853
121851nitrate-reduction17632
121851nitrite-reduction16301
121851nitrate-respiration17632

antibiotic resistance

  • @ref: 121851
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121851
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121851oxidase-
121851beta-galactosidase+3.2.1.23
121851alcohol dehydrogenase-1.1.1.1
121851gelatinase-
121851amylase-
121851DNase-
121851caseinase-3.4.21.50
121851catalase+1.11.1.6
121851tween esterase+
121851lecithinase-
121851lipase-
121851lysine decarboxylase-4.1.1.18
121851ornithine decarboxylase-4.1.1.17
121851protease-
121851tryptophan deaminase-
121851urease-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
121851-+-+-++-+-++-++++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121851---+-+---++++-+-------++++++++++/--+/-++--++/---+/-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121851+++++-+++++++--++++-+++++----------+-------------+----+----+--+++----------+---++-----+-+-+--+---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4905water (eutrophic artifical spring)ViennaAustriaAUTEurope
67770Water of eutrophic fountainViennaAustriaAUTEurope
121851Environment, Water, eutrophic fountainViennaAustriaAUTEurope1988

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_2321.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_515;98_592;99_2321&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AJ243751
  • Sequence Identity:
  • Total samples: 108
  • soil counts: 18
  • aquatic counts: 50
  • animal counts: 14
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49051Risk group (German classification)
1218511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4905
  • description: Sphingomonas pituitosa partial 16S rRNA gene, strain EDIV
  • accession: AJ243751
  • length: 1446
  • database: ena
  • NCBI tax ID: 99597

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas pituitosa NBRC 1024911219051.3wgspatric1219051
66792Sphingomonas pituitosa NBRC 1024912731957700draftimg1219051
67770Sphingomonas pituitosa NBRC 102491GCA_001598435contigncbi1219051

GC content

@refGC-contentmethod
490564.5
6777064.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes66.536no
gram-positiveno97.388no
anaerobicno99.065no
aerobicyes94.36no
halophileno96.197no
spore-formingno93.967no
thermophileno98.087yes
glucose-utilyes92.549no
flagellatedno91.884no
glucose-fermentno90.935no

External links

@ref: 4905

culture collection no.: DSM 13101, CIP 106154, JCM 21727, IAM 15276, NBRC 102491

straininfo link

  • @ref: 83388
  • straininfo: 100960

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11411704Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan.Denner EB, Paukner S, Kampfer P, Moore ER, Abraham WR, Busse HJ, Wanner G, Lubitz WInt J Syst Evol Microbiol10.1099/00207713-51-3-8272001Base Composition, Cell Wall/ultrastructure, Chemotaxis, Coenzymes, DNA, Ribosomal/genetics, Fatty Acids/analysis, Glucose/analysis, Molecular Sequence Data, Myristic Acids/analysis, Nucleic Acid Hybridization, *Phylogeny, Polysaccharides, Bacterial/*biosynthesis/chemistry, RNA, Ribosomal, 16S/genetics, Rhamnose/analysis, Sphingomonas/*classification/genetics/*physiology, Ubiquinone/analogs & derivatives/analysis, ViscosityGenetics
Phylogeny17267979Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.64441-02007Aerobiosis, Animals, *Antibiosis, Arcidae/*microbiology, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Glycosphingolipids/analysis/chemistry, Gram-Positive Bacteria/drug effects, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/*classification/cytology/*isolation & purification/physiologyGenetics
Metabolism18286278Structural characterization of the exopolysaccharide PS-EDIV from Sphingomonas pituitosa strain DSM 13101.Schultheis E, Dreger MA, Nimtz M, Wray V, Hempel DC, Nortemann BAppl Microbiol Biotechnol10.1007/s00253-008-1383-82008Chromatography, Gel, Magnetic Resonance Spectroscopy, Methylation, Polysaccharides, Bacterial/*chemistry/metabolism, Sphingomonas/*chemistry/growth & development/metabolism, Tandem Mass SpectrometryProteome
Phylogeny19329595Sphingomonas sanxanigenens sp. nov., isolated from soil.Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RLInt J Syst Evol Microbiol10.1099/ijs.0.000257-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny24523446Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov.Feng GD, Yang SZ, Wang YH, Zhang XX, Zhao GZ, Deng MR, Zhu HHInt J Syst Evol Microbiol10.1099/ijs.0.056853-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Mining, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny30808585Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis.Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar NSyst Appl Microbiol10.1016/j.syapm.2019.02.0032019DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Genome, Bacterial/*genetics, Lipids/analysis, Nucleic Acid Hybridization, Oryza/*microbiology/physiology, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salt Tolerance, Sequence Analysis, DNA, Soil Microbiology, Sphingomonas/chemistry/*classification/*geneticsGenetics

Reference

@idauthorscataloguedoi/urltitle
4905Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13101)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13101
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
37285Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18253
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
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
83388Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100960.1StrainInfo: A central database for resolving microbial strain identifiers
121851Curators of the CIPCollection of Institut Pasteur (CIP 106154)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106154