Strain identifier

BacDive ID: 14242

Type strain: Yes

Species: Sphingomonas panni

Strain Designation: C52

Strain history: CIP <- 2006, DSMZ

NCBI tax ID(s): 237612 (species)

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General

@ref: 6103

BacDive-ID: 14242

DSM-Number: 15761

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

description: Sphingomonas panni C52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sponge, examination room.

NCBI tax id

  • NCBI tax id: 237612
  • Matching level: species

strain history

@refhistory
6103<- H.-J. Busse; C52
374592006, DSMZ
121531CIP <- 2006, DSMZ

doi: 10.13145/bacdive14242.20230509.8.1

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 panni
  • full scientific name: Sphingomonas panni Busse et al. 2005

@ref: 6103

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas panni

full scientific name: Sphingomonas panni Busse et al. 2005

strain designation: C52

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31599negative1.6 µm0.6 µmrod-shapedno
121531negativerod-shapedyes

colony morphology

  • @ref: 121531

pigmentation

  • @ref: 31599
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6103R2A 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
6103YEAST-PEPTONE-SUCCINATE MEDIUM (DSMZ Medium 988)yeshttps://mediadive.dsmz.de/medium/988Name: YEAST-PEPTONE-SUCCINATE MEDIUM (DSMZ Medium 988; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 3.0 g/l Yeast extract 3.0 g/l Distilled water
37459MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121531CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6103positivegrowth28mesophilic
31599positivegrowth15-37
31599positiveoptimum26mesophilic
37459positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31599aerobe
121531obligate aerobe

spore formation

  • @ref: 31599
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31599NaClpositivegrowth<1 %
31599NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3159916947citrate+carbon source
3159917306maltose+carbon source
3159937684mannose+carbon source
3159915361pyruvate+carbon source
3159927082trehalose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
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
12153117632nitrate-reduction
12153116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12153135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31599catalase+1.11.1.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121531oxidase-
121531alcohol dehydrogenase-1.1.1.1
121531catalase+1.11.1.6
121531lysine decarboxylase-4.1.1.18
121531ornithine decarboxylase-4.1.1.17
121531urease-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
121531-++++++++-++++-++++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6103-----+-++++-++---++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121531------------------------+-----------------+/-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6103sponge, examination roomVienna, Veterinary UniversityAustriaAUTEurope
121531Wipe in the Medical Clinic for small animalsViennaAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Indoor
#Engineered#Industrial#Engineered product

taxonmaps

  • @ref: 69479
  • File name: preview.99_1423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_957;98_1126;99_1423&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AJ575818
  • Sequence Identity:
  • Total samples: 894
  • soil counts: 63
  • aquatic counts: 171
  • animal counts: 508
  • plant counts: 152

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61031Risk group (German classification)
1215311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6103
  • description: Sphingomonas panni 16S rRNA gene, strain C52
  • accession: AJ575818
  • length: 1408
  • database: ena
  • NCBI tax ID: 237612

Genome sequences

  • @ref: 66792
  • description: Sphingomonas panni DSM 15761
  • accession: GCA_022664435
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 237612

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno86.574yes
gram-positiveno97.183yes
anaerobicno99.04no
aerobicyes94.176yes
halophileno93.642yes
spore-formingno94.297no
motileyes66.867yes
glucose-fermentno90.645yes
thermophileno98.935yes
glucose-utilyes90.869yes

External links

@ref: 6103

culture collection no.: DSM 15761, CIP 109155, LMG 21979

straininfo link

  • @ref: 83401
  • straininfo: 100212

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280528Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov.Busse HJ, Hauser E, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.63872-02005DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/metabolismGenetics
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6103Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15761)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15761
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
31599Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2788728776041
37459Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6865
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)
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
83401Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100212.1StrainInfo: A central database for resolving microbial strain identifiers
121531Curators of the CIPCollection of Institut Pasteur (CIP 109155)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109155