Strain identifier

BacDive ID: 14126

Type strain: Yes

Species: Sphingobacterium mizutaii

Strain Designation: Teraoka, K M 1203

Strain history: CIP <- 1984, ATCC <- E. Yabuuchi, Japan: strain K M 1203 <- S. Mizuta, Japan <- N. Satoh: strain Teraoka

NCBI tax ID(s): 1220576 (strain), 1010 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4456

BacDive-ID: 14126

DSM-Number: 11724

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, human pathogen

description: Sphingobacterium mizutaii Teraoka is an obligate aerobe, mesophilic human pathogen that was isolated from ventricular fluid.

NCBI tax id

NCBI tax idMatching level
1010species
1220576strain

strain history

@refhistory
4456<- IFO <- GIFU <- S. Mizuta
67770IAM 14315 <-- IFO 14946 <-- GIFU 1203 <-- S. Mizuta <-- N. Satoh strain Teraoka.
120984CIP <- 1984, ATCC <- E. Yabuuchi, Japan: strain K M 1203 <- S. Mizuta, Japan <- N. Satoh: strain Teraoka

doi: 10.13145/bacdive14126.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium mizutaii
  • full scientific name: Sphingobacterium mizutaii corrig. Yabuuchi et al. 1983

  • synonyms

    @refsynonym
    20215Sphingobacterium mizutae
    20215Flavobacterium mizutaii

@ref: 4456

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium mizutaii

full scientific name: Sphingobacterium mizutaii Yabuuchi et al. 1983 emend. Choi and Lee 2012 emend. Wauters et al. 2012

strain designation: Teraoka, K M 1203

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.396
6948099.988negative
120984norod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4456NUTRIENT 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
39762MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120984CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4456positivegrowth28mesophilic
39762positivegrowth25mesophilic
67770positivegrowth30mesophilic
120984positivegrowth25-30mesophilic
120984nogrowth10psychrophilic
120984nogrowth18psychrophilic
120984nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120984
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

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
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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-ribose-builds acid from16988
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
120984esculin+hydrolysis4853
120984nitrate-reduction17632
120984nitrite+reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12098435581indoleno

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
120984oxidase+
120984beta-galactosidase+3.2.1.23
120984alcohol dehydrogenase-1.1.1.1
120984amylase-
120984catalase+1.11.1.6
120984tween esterase-
120984lysine decarboxylase-4.1.1.18
120984ornithine decarboxylase-4.1.1.17
120984urease-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
46376-+-+-+----+----+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
46376-----+-++-+-++------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120984--+/-+/--+/-----+/-+/-+/---------+/---+--+/-+/-+/-+/-+/----+/-+/--+/-+/-+/---+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120984---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4456ventricular fluid
46376Human ventricular fluid,fetus
67770Ventricular fluid of fetusNagasakiJapanJPNAsia
120984Human, Fetus, ventricular fluid

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Brain
#Host Body Product#Fluids#Cerebrospinal fluid

taxonmaps

  • @ref: 69479
  • File name: preview.99_9651.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_3818;97_4710;98_7131;99_9651&stattab=map
  • Last taxonomy: Sphingobacterium mizutaii subclade
  • 16S sequence: JF708889
  • Sequence Identity:
  • Total samples: 752
  • soil counts: 181
  • aquatic counts: 192
  • animal counts: 333
  • plant counts: 46

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
4456yes, in single cases1Risk group (German classification)
1209841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobacterium mizutaii gene for 16S rRNA, partial sequence, strain: NBRC 14946AB6807161453ena1010
20218Sphingobacterium mizutae 16S ribosomal RNAD140241270ena1010
20218Sphingobacterium mizutaii strain LMG 8340 16S ribosomal RNA gene, partial sequenceJF7088891454ena1010
20218Flavobacterium mizutaii 16S ribosomal RNA gene, partial sequenceM587961478ena1010
20218S.mizutae (ATCC 33299T) gene for 16S rRNAX67853795ena1010
4456Flavobacterium mizutaii partial 16S rRNA, strain DSM 11724TAJ4381751491ena1010

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium mizutaii NCTC12149GCA_900187125completencbi1010
66792Sphingobacterium mizutaii NBRC 14946 = DSM 117241220576.3wgspatric1220576
66792Sphingobacterium mizutaii strain DSM 117241010.7wgspatric1010
66792Sphingobacterium mizutaii strain NCTC121491010.5completepatric1010
66792Sphingobacterium mizutaii NCTC 121492773857900completeimg1010
66792Sphingobacterium mizutaii DSM 117242634166301draftimg1220576
67770Sphingobacterium mizutaii NBRC 14946 = DSM 11724GCA_007990895contigncbi1220576
67770Sphingobacterium mizutaii DSM 11724GCA_900102835scaffoldncbi1010

GC content

  • @ref: 67770
  • GC-content: 40
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.355no
flagellatedno96.929no
gram-positiveno97.925no
anaerobicno98.996no
aerobicyes86.102no
halophileno91.593no
spore-formingno95.905no
thermophileno99.287yes
glucose-utilyes85.704no
glucose-fermentno88.715yes

External links

@ref: 4456

culture collection no.: NCTC 12149, DSM 11724, ATCC 33299, CCUG 15907, GIFU 1203, IFO 14946, LMG 8340, NBRC 14946, JCM 21155, CIP 101122, IAM 14315

straininfo link

  • @ref: 83293
  • straininfo: 2827

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology14729071Structural analysis of sphingophospholipids derived from Sphingobacterium spiritivorum, the type species of genus Sphingobacterium.Naka T, Fujiwara N, Yano I, Maeda S, Doe M, Minamino M, Ikeda N, Kato Y, Watabe K, Kumazawa Y, Tomiyasu I, Kobayashi KBiochim Biophys Acta10.1016/j.bbalip.2003.10.0102003Ceramides/analysis, Chromatography, Thin Layer, Fatty Acids/analysis, Magnetic Resonance Spectroscopy, Molecular Structure, Phospholipids/*chemistry/isolation & purification, Solubility, Spectrometry, Mass, Fast Atom Bombardment, Spectrophotometry, Infrared, Sphingobacterium/*chemistry, Sphingolipids/*chemistry/isolation & purificationPhylogeny
Phylogeny16957095Sphingobacterium daejeonense sp. nov., isolated from a compost sample.Kim KH, Ten LN, Liu QM, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64406-02006Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial/*analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Sphingobacterium/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny17625199Sphingobacterium composti sp. nov., isolated from cotton-waste composts.Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64948-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gossypium/microbiology, Korea, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil, *Soil Microbiology, Sphingobacterium/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny18768611Sphingobacterium anhuiense sp. nov., isolated from forest soil.Wei W, Zhou Y, Wang X, Huang X, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.65864-02008Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/physiology, Temperature, *TreesGenetics
Phylogeny19933581Sphingobacterium shayense sp. nov., isolated from forest soil.He X, Xiao T, Kuang H, Lan X, Tudahong M, Osman G, Fang C, Rahman EInt J Syst Evol Microbiol10.1099/ijs.0.018481-02009Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, Populus/growth & development, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/physiology, Temperature, TreesGenetics
Phylogeny21551333Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge.Zhang J, Zheng JW, Cho BC, Hwang CY, Fang C, He J, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.033118-02011Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Pyrethrins/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sodium Chloride/metabolism, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism, Temperature, Vitamin K 2/analysisMetabolism
Phylogeny22180612Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii.Choi HA, Lee SSInt J Syst Evol Microbiol10.1099/ijs.0.024737-02011Bacterial Typing Techniques, Base Composition, Ceramides/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Sphingobacterium/*classification/genetics/isolation & purification, Tetrachloroethylene, Trichloroethylene, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny22199213Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium.Wauters G, Janssens M, De Baere T, Vaneechoutte M, Deschaght PInt J Syst Evol Microbiol10.1099/ijs.0.037325-02011Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Indoles/*metabolism, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/metabolismMetabolism
Phylogeny22611196Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense.Xiao T, He X, Cheng G, Kuang H, Ma X, Yusup K, Hamdun M, Gulsimay A, Fang C, Rahman EInt J Syst Evol Microbiol10.1099/ijs.0.030155-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Sphingomyelins/analysis, Trees/microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny28699577Sphingobacteriumsoli sp. nov., isolated from soil.Fu YS, Hussain F, Habib N, Khan IU, Chu X, Duan YQ, Zhi XY, Chen X, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0019462017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31967955Sphingobacterium olei sp. nov., isolated from oil-contaminated soil.Liu B, Yang X, Sheng M, Yang Z, Qiu J, Wang C, He JInt J Syst Evol Microbiol10.1099/ijsem.0.0040002020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, *Petroleum Pollution, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4456Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11724)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11724
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
39762Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12663
46376Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15907)https://www.ccug.se/strain?id=15907
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
83293Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2827.1StrainInfo: A central database for resolving microbial strain identifiers
120984Curators of the CIPCollection of Institut Pasteur (CIP 101122)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101122