Strain identifier

BacDive ID: 14226

Type strain: Yes

Species: Sphingomonas trueperi

Strain history: CIP <- 1997, E.B.M. Denner, Univ. Wien, Austria <- H.J. Busse <- G. Auling <- M. Gillis <- 1955, G.R. Anderson

NCBI tax ID(s): 1219059 (strain), 53317 (species)

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General

@ref: 3060

BacDive-ID: 14226

DSM-Number: 7225

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

description: Sphingomonas trueperi DSM 7225 is an obligate aerobe, mesophilic, motile bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1219059strain
53317species

strain history

@refhistory
3060<- LMG <- NCIB <- ATCC (Pseudomonas azotocolligans) <- G. Anderson
67770E. Yabuuchi EY4218 <-- ATCC 12417 <-- G. R. Anderson.
123596CIP <- 1997, E.B.M. Denner, Univ. Wien, Austria <- H.J. Busse <- G. Auling <- M. Gillis <- 1955, G.R. Anderson

doi: 10.13145/bacdive14226.20230509.8.1

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 trueperi
  • full scientific name: Sphingomonas trueperi Kämpfer et al. 1997

@ref: 3060

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas trueperi

full scientific name: Sphingomonas trueperi Kämpfer et al. 1997

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes91.666
6948099.971negative
123596yesnegativerod-shaped

pigmentation

  • @ref: 123596
  • production: yes
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3060NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605)yeshttps://mediadive.dsmz.de/medium/605Name: NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l Distilled water
3060TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
3060NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
41574MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123596CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3060positivegrowth25mesophilic
41574positivegrowth30mesophilic
67770positivegrowth26mesophilic
3060positivegrowth28mesophilic
123596positivegrowth25-37mesophilic
123596nogrowth5psychrophilic
123596nogrowth10psychrophilic
123596nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123596
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.985

compound production

  • @ref: 3060
  • compound: coenzyme Q-10

halophily

@refsaltgrowthtested relationconcentration
123596NaClpositivegrowth0-2 %
123596NaClnogrowth4 %
123596NaClnogrowth6 %
123596NaClnogrowth8 %
123596NaClnogrowth10 %

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-fucose+builds acid from28847
68371D-tagatose-builds acid from16443
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose-builds acid from17992
68371esculin+builds acid from4853
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-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
123596citrate-carbon source16947
123596esculin+hydrolysis4853
123596nitrate-reduction17632
123596nitrite-reduction16301
123596phenol-degradation15882
123596nitrate-respiration17632

antibiotic resistance

  • @ref: 123596
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12359635581indoleno

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
123596oxidase+
123596beta-galactosidase+3.2.1.23
123596alcohol dehydrogenase-1.1.1.1
123596gelatinase+
123596amylase-
123596DNase-
123596caseinase-3.4.21.50
123596catalase+1.11.1.6
123596tween esterase-
123596lecithinase-
123596lipase-
123596lysine decarboxylase-4.1.1.18
123596ornithine decarboxylase-4.1.1.17
123596tryptophan deaminase-
123596urease-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
123596-+++-++---++-++++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3060-----+-++++-++---+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123596---+/--+/-----+/-+/-----------++/-++/-+/-+/-+/-+/--+/-------+/-+/-+/--+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123596+++++-+++++++++++++-+++-++--------++--+--+-------+----++---+--++-----------+---++-----+-+++--+--++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3060soilUSAUSANorth America
67770Soil
123596Environment, SoilUnited States of AmericaUSANorth America1955

isolation source categories

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

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: X97776
  • 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
30601Risk group (German classification)
1235961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218S.trueperi 16S rRNA geneX977761461ena53317
20218Sphingomonas trueperi gene for 16S rRNA, partial sequence, strain: NBRC 100456AB6811731414ena53317

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas trueperi strain DSM 722553317.4wgspatric53317
66792Sphingomonas trueperi DSM 72252829783330draftimg53317
67770Sphingomonas trueperi DSM 7225GCA_011927635scaffoldncbi53317

GC content

  • @ref: 67770
  • GC-content: 65.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.511no
anaerobicno99.007no
halophileno96.497no
spore-formingno93.879no
glucose-utilyes90.176no
thermophileno98.706yes
motileyes70.874no
aerobicyes92.172no
flagellatedno87.547no
glucose-fermentno92.002yes

External links

@ref: 3060

culture collection no.: DSM 7225, ATCC 12417, LMG 2141, LMG 2142, NCIB 9391, JCM 10278, CIP 105252, IAM 15267, IFO 16157, NBRC 100456, NBRC 16157, NCIMB 9391

straininfo link

  • @ref: 83385
  • straininfo: 3937

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9103654Classification of "Pseudomonas azotocolligans" Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov.Kampfer P, Denner EB, Meyer S, Moore ER, Busse HJInt J Syst Bacteriol10.1099/00207713-47-2-5771997Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Bacteria/*classification/genetics/metabolism, Lipids/analysis, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as TopicMetabolism
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
Phylogeny19406815Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.003285-02009Animals, Anomura/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny24425812Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.055269-02013*Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
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/urltitlejournalpubmed
3060Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7225)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7225
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
41574Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17251
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/
68369Automatically annotated from API 20NE
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
83385Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3937.1StrainInfo: A central database for resolving microbial strain identifiers
123596Curators of the CIPCollection of Institut Pasteur (CIP 105252)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105252