Strain identifier

BacDive ID: 14219

Type strain: Yes

Species: Sphingomonas adhaesiva

Strain Designation: Op-55

Strain history: CIP <- 2000, CCM <- GIFU <- R. Mamiya: strain Op-55, Pseudomonas paucimobilis

NCBI tax ID(s): 1219038 (strain), 28212 (species)

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General

@ref: 3141

BacDive-ID: 14219

DSM-Number: 7418

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

description: Sphingomonas adhaesiva Op-55 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from "Sterile" water.

NCBI tax id

NCBI tax idMatching level
1219038strain
28212species

strain history

@refhistory
3141<- JCM <- GIFU <- R. Mamiya; Op-55 (Pseudomonas paucimobilis)
67770GIFU 11458 <-- R. Mamiya Op-55.
116041CIP <- 2000, CCM <- GIFU <- R. Mamiya: strain Op-55, Pseudomonas paucimobilis

doi: 10.13145/bacdive14219.20230509.8.1

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 adhaesiva
  • full scientific name: Sphingomonas adhaesiva Yabuuchi et al. 1990

@ref: 3141

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas adhaesiva

full scientific name: Sphingomonas adhaesiva Yabuuchi et al. 1990 emend. Feng et al. 2018

strain designation: Op-55

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.978
116041negativerod-shapedyes

pigmentation

  • @ref: 116041
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3141TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
3141REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
33001MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116041CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116041CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
3141positivegrowth28mesophilic
33001positivegrowth30mesophilic
67770positivegrowth30mesophilic
116041positivegrowth25-30mesophilic
116041nogrowth5psychrophilic
116041nogrowth10psychrophilic
116041nogrowth37mesophilic
116041nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116041
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.996

halophily

@refsaltgrowthtested relationconcentration
116041NaClpositivegrowth0-2 %
116041NaClnogrowth4 %
116041NaClnogrowth6 %
116041NaClnogrowth8 %
116041NaClnogrowth10 %

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
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
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-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
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
116041esculin+hydrolysis4853
116041nitrate-reduction17632
116041nitrite-reduction16301
116041nitrate-respiration17632

antibiotic resistance

  • @ref: 116041
  • 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
11604135581indoleno

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
116041oxidase+
116041beta-galactosidase-3.2.1.23
116041alcohol dehydrogenase-1.1.1.1
116041gelatinase+/-
116041amylase+
116041DNase+
116041caseinase+3.4.21.50
116041catalase+1.11.1.6
116041tween esterase+
116041lecithinase-
116041lipase-
116041lysine decarboxylase-4.1.1.18
116041ornithine decarboxylase-4.1.1.17
116041protease-
116041tryptophan deaminase-
116041urease-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
116041-+++-++-++++---+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3141-----+-++-+-++---+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116041----------+/-+/-+/------------+/-----+/-+/-+/------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116041++-++-++-++----+--+------------+-----------------+----+----+-------------------++--------+++-+-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3141"Sterile" waterJapanJPNAsia
67770Sterile water used before surgery
116041JapanJPNAsia

isolation source categories

Cat1Cat2
#Engineered#Laboratory
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_7051.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_761;97_887;98_5182;99_7051&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: LC504024
  • Sequence Identity:
  • Total samples: 341
  • soil counts: 19
  • aquatic counts: 67
  • animal counts: 216
  • plant counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31411Risk group (German classification)
1160411Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas adhaesiva gene for 16S rRNA, partial sequenceD161461445ena28212
20218Sphingomonas adhaesiva 16S ribosomal RNA, partial sequenceD38430156ena28212
20218Sphingomonas adhaesiva gene for 16S rRNAD845271381ena28212
20218Sphingomonas adhaesiva gene for 16S rRNA, partial sequenceD137221415ena28212
20218Sphingomonas adhaesiva partial 16S rRNA geneX727201460ena28212
20218Sphingomonas adhaesiva gene for 16S rRNA, partial sequence, strain: NBRC 15099AB6807661412ena28212
67770Sphingomonas adhaesiva JCM 7370 gene for 16S ribosomal RNA, partial sequenceLC5040241409ena28212

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas adhaesiva NBRC 150991219038.3wgspatric1219038
66792Sphingomonas adhaesiva strain DSM 741828212.3wgspatric28212
66792Sphingomonas adhaesiva NBRC 150992731957690draftimg1219038
67770Sphingomonas adhaesiva NBRC 15099GCA_001592345contigncbi1219038
67770Sphingomonas adhaesiva DSM 7418GCA_002374855contigncbi28212

GC content

  • @ref: 3141
  • GC-content: 67.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileyes63.492no
gram-positiveno95.984no
anaerobicno99.019no
aerobicyes91.554no
halophileno93.13no
spore-formingno93.445no
thermophileno96.432yes
glucose-utilyes87.628yes
flagellatedno91.932no
glucose-fermentno89.947yes

External links

@ref: 3141

culture collection no.: DSM 7418, ATCC 51229, GIFU 11458, IAM 14270, JCM 7370, CCM 4598, CCUG 27290, CCUG 27819, CIP 106725, IFO 15099, LMG 10922, NBRC 15099, PCM 2581

straininfo link

  • @ref: 83378
  • straininfo: 4982

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2111872Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas.Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto HMicrobiol Immunol10.1111/j.1348-0421.1990.tb00996.x1990Base Composition, Base Sequence, Cluster Analysis, DNA, Bacterial/isolation & purification, Fatty Acids/analysis, Flavobacterium/*classification/genetics/growth & development, Glycosphingolipids/*analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Phenotype, Pseudomonas/*classification/genetics/growth & development, Pseudomonas aeruginosa/classification/genetics/growth & development, RNA, Ribosomal/*analysis, RNA, Ribosomal, 16S/*analysis/isolation & purificationEnzymology
Phylogeny12710615Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov.Godoy F, Vancanneyt M, Martinez M, Steinbuchel A, Swings J, Rehm BHAInt J Syst Evol Microbiol10.1099/ijs.0.02375-02003Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification/*metabolism, Base Composition, Biodegradation, Environmental, Chlorophenols/*metabolism, Fatty Acids/analysis/*chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Stearic AcidsMetabolism
Phylogeny15545449Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina.Rivas R, Abril A, Trujillo ME, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.63102-02004Acacia/*microbiology, Aerobiosis, Argentina, Bacterial Typing Techniques, Base Composition, Catalase/analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Esculin/metabolism, Fatty Acids/analysis/isolation & purification, Gelatin/metabolism, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phenazines, Phospholipids/analysis/isolation & purification, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sphingomonas/*classification/cytology/*isolation & purification/physiology, Urea/metabolism, beta-Galactosidase/analysisEnzymology
Phylogeny16280497Sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate.Zhang YQ, Chen YG, Li WJ, Tian XP, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63697-02005Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Bacterial/chemistry/isolation & purification, Fatty Acids/chemistry/*metabolism, Genes, rRNA, Gentian Violet, Hydrogen-Ion Concentration, Molecular Sequence Data, Phenazines, RNA, Ribosomal, 16S/analysis/genetics, Sphingomonas/classification/cytology/*isolation & purification/physiologyCultivation
Phylogeny31140971Sphingomonas aracearum sp. nov., isolated from rhizospheric soil of Araceae plants.Wang Z, Zeng Q, Fang Z, Zhu D, Xu D, Wang G, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0034772019Araceae/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny32924914Sphingomonas corticis sp. nov., and Sphingobacterium corticibacterium sp. nov., from bark canker.Li Y, Wang S, Chang JP, Bian DR, Guo LM, Yang XQInt J Syst Evol Microbiol10.1099/ijsem.0.0044512020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, Plant Diseases/*microbiology, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/isolation & purification, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3141Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7418)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7418
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
33001Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18887
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
83378Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4982.1StrainInfo: A central database for resolving microbial strain identifiers
116041Curators of the CIPCollection of Institut Pasteur (CIP 106725)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106725