Strain identifier

BacDive ID: 14243

Type strain: Yes

Species: Sphingomonas abaci

Strain Designation: C42

Strain history: CIP <- 2006, DSMZ

NCBI tax ID(s): 237611 (species)

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General

@ref: 6129

BacDive-ID: 14243

DSM-Number: 15867

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

description: Sphingomonas abaci C42 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from examination table.

NCBI tax id

  • NCBI tax id: 237611
  • Matching level: species

strain history

@refhistory
6129<- H.-J. Busse; C42
397712006, DSMZ
115971CIP <- 2006, DSMZ

doi: 10.13145/bacdive14243.20230509.8.1

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

@ref: 6129

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas abaci

full scientific name: Sphingomonas abaci Busse et al. 2005

strain designation: C42

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31599negative2.25 µm0.45 µmrod-shapedno
69480negative99.854
115971negativerod-shapedno

colony morphology

  • @ref: 115971

pigmentation

  • @ref: 31599
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6129NUTRIENT 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
6129R2A 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
6129YEAST-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
39771MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
115971CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6129positivegrowth28mesophilic
31599positivegrowth15-28
31599positiveoptimum21.5psychrophilic
39771positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31599aerobe
115971obligate aerobe

spore formation

@refspore formationconfidence
31599no
69481no94
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
31599NaClpositivegrowth<1 %
31599NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3159924265gluconate+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
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11597117632nitrate-reduction
11597116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11597135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31599catalase+1.11.1.6
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
115971oxidase+
115971alcohol dehydrogenase-1.1.1.1
115971catalase+1.11.1.6
115971lysine decarboxylase-4.1.1.18
115971ornithine decarboxylase-4.1.1.17
115971urease-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
115971-+++++++--++++-+++-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6129-----+-++++--++--++--
6129-----++++++-+++--++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
115971------------------------+-----------------+/-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6129examination tableVienna, Veterinary UniversityAustriaAUTEurope
115971Treatment table in the Medical Clinic for small AnimalsViennaAustriaAUTEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Engineered product

taxonmaps

  • @ref: 69479
  • File name: preview.99_70482.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_8913;97_38091;98_49448;99_70482&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AJ575817
  • Sequence Identity:
  • Total samples: 1088
  • soil counts: 67
  • aquatic counts: 42
  • animal counts: 571
  • plant counts: 408

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61291Risk group (German classification)
1159711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6129
  • description: Sphingomonas abaci 16S rRNA gene, strain C42
  • accession: AJ575817
  • length: 1407
  • database: ena
  • NCBI tax ID: 237611

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas abaci DSM 15867GCA_014199625scaffoldncbi237611
66792Sphingomonas abaci strain DSM 15867237611.3wgspatric237611
66792Sphingomonas abaci DSM 158672828624843draftimg237611

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
flagellatedno90.494yes
gram-positiveno96.858yes
anaerobicno98.926yes
aerobicyes90.874no
halophileno92.572no
spore-formingno94.673no
glucose-utilyes88.19yes
thermophileno99.14yes
glucose-fermentno90.583no
motileyes64.639yes

External links

@ref: 6129

culture collection no.: DSM 15867, CIP 109154, LMG 21978

straininfo link

  • @ref: 83402
  • straininfo: 126365

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
Phylogeny26908362Sphingomonas metalli sp. nov., isolated from an abandoned lead-zinc mine.Feng GD, Yang SZ, Xiong X, Li HP, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0009892016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lead, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistry, ZincTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6129Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15867)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15867
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
39771Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6864
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
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
83402Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID126365.1StrainInfo: A central database for resolving microbial strain identifiers
115971Curators of the CIPCollection of Institut Pasteur (CIP 109154)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109154