Strain identifier

BacDive ID: 14118

Type strain: Yes

Species: Sphingobacterium spiritivorum

Strain Designation: E7288, 29-83

Strain history: CIP <- 1983, C. Richard, Inst. Pasteur, Paris, France: strain 29-83 <- GIFU <- NCTC <- CDC: strain E7288 <- Kansas Dept. Hlth., USA <- Univ. Kansas Med. Center, USA, Flavobacterium spiritivorum

NCBI tax ID(s): 525373 (strain), 258 (species)

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General

@ref: 4454

BacDive-ID: 14118

DSM-Number: 11722

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

description: Sphingobacterium spiritivorum E7288 is an aerobe, mesophilic bacterium that was isolated from intrauterine specimen.

NCBI tax id

NCBI tax idMatching level
525373strain
258species

strain history

@refhistory
4454<- JCM <- IFO <- GIFU <- CDC
67770NCTC 11386 <-- CDC E7288 <-- Kansas Dept. Health Environ., USA <-- Univ. Kansas Med. Center, USA.
123265CIP <- 1983, C. Richard, Inst. Pasteur, Paris, France: strain 29-83 <- GIFU <- NCTC <- CDC: strain E7288 <- Kansas Dept. Hlth., USA <- Univ. Kansas Med. Center, USA, Flavobacterium spiritivorum

doi: 10.13145/bacdive14118.20230509.8.1

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 spiritivorum
  • full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983

  • synonyms

    @refsynonym
    20215Flavobacterium spiritivorum
    20215Flavobacterium yabuuchiae

@ref: 4454

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium spiritivorum

full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 emend. Lai et al. 2016

strain designation: E7288, 29-83

type strain: yes

Morphology

cell morphology

@refmotilitygram stainconfidencecell shape
25081no
69480negative99.975
123265nonegativerod-shaped

colony morphology

  • @ref: 123265

pigmentation

  • @ref: 123265
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4454NUTRIENT 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
42121MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123265CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123265CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4454positivegrowth28mesophilic
25081positivegrowth15-30
42121positivegrowth30mesophilic
45917positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
123265positivegrowth5-37
123265nogrowth41thermophilic
123265nogrowth45thermophilic

culture pH

  • @ref: 25081
  • ability: positive
  • type: growth
  • pH: 6.0-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45917aerobe
123265obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
25081NaClpositivegrowth0-3.5 %
123265NaClpositivegrowth0-4 %
123265NaClnogrowth6 %
123265NaClnogrowth8 %
123265NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25081167632-oxobutanoate-respiration
25081286442-oxopentanoate-respiration
25081182404-hydroxy-L-proline-respiration
2508130089acetate-respiration
2508117128adipate-assimilation
2508122599arabinose-assimilation
2508116947citrate-assimilation
2508127689decanoate-assimilation
2508117234glucose-fermentation
2508128087glycogen-respiration
2508117196L-asparagine-respiration
2508129991L-aspartate-respiration
2508115729L-ornithine-respiration
2508117203L-proline-respiration
2508117115L-serine-respiration
250816359lactulose-respiration
2508129864mannitol-assimilation
2508175146monomethyl succinate-respiration
2508173784glycyl-l-glutamate-respiration
2508117632nitrate-reduction
2508118401phenylacetate-assimilation
2508132032potassium gluconate-assimilation
2508117272propionate-respiration
2508126986threonine-respiration
2508127897tryptophan-energy source
2508132528turanose-respiration
25081645522-hydroxybutyrate+respiration
2508140585alpha-cyclodextrin+respiration
2508117925alpha-D-glucose+respiration
2508117057cellobiose+respiration
2508116947citrate+respiration
2508118333D-arabitol+respiration
2508115824D-fructose+respiration
2508112936D-galactose+respiration
2508118024D-galacturonic acid+respiration
250818391D-gluconate+respiration
2508117784D-glucosaminic acid+respiration
2508114314D-glucose 6-phosphate+respiration
2508116899D-mannitol+respiration
2508116024D-mannose+respiration
2508127605D-psicose+respiration
2508117924D-sorbitol+respiration
2508123652dextrin+respiration
2508128066gentiobiose+respiration
2508117234glucose+assimilation
2508129042glucose 1-phosphate+respiration
2508132323glucuronamide+respiration
2508117754glycerol+respiration
2508114336glycerol 1-phosphate+respiration
2508173804glycyl L-aspartic acid+respiration
2508130849L-arabinose+respiration
2508118287L-fucose+respiration
2508129985L-glutamate+respiration
2508124996lactate+respiration
2508117716lactose+respiration
2508117306maltose+assimilation
2508117306maltose+respiration
2508137684mannose+assimilation
2508128053melibiose+respiration
25081320055methyl beta-D-glucopyranoside+respiration
2508128037N-acetylgalactosamine+respiration
25081506227N-acetylglucosamine+assimilation
25081506227N-acetylglucosamine+respiration
2508116634raffinose+respiration
2508117992sucrose+respiration
2508127082trehalose+respiration
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
12326516947citrate-carbon source
1232654853esculin+hydrolysis
123265606565hippurate-hydrolysis
12326517632nitrate-builds gas from
12326517632nitrate-reduction
12326516301nitrite-builds gas from
12326516301nitrite-reduction
12326515792malonate-assimilation
12326517632nitrate-respiration
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol-builds acid from
6837417306maltose-builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose-builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose-builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose-builds acid from
6837462345L-rhamnose-builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol-builds acid from

antibiotic resistance

  • @ref: 123265
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
2508135581indoleno
6837435581indoleno
6836935581indoleno
12326535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testindole testvoges-proskauer-test
2508117234glucose-
2508135581indole-
6837435581indole-
6836935581indole-
12326515688acetoin-
12326517234glucose-

enzymes

@refvalueactivityec
25081alpha-fucosidase+3.2.1.51
25081alpha-galactosidase+3.2.1.22
25081alpha-glucosidase+3.2.1.20
25081alpha-mannosidase-3.2.1.24
25081beta-galactosidase+3.2.1.23
25081beta-glucosidase+3.2.1.21
25081chymotrypsin+3.4.4.5
25081trypsin+3.4.21.4
25081urease+3.5.1.5
25081acid phosphatase+3.1.3.2
25081alkaline phosphatase+3.1.3.1
25081arginine dihydrolase-3.5.3.6
25081beta-glucuronidase-3.2.1.31
25081catalase+1.11.1.6
25081cystine arylamidase+3.4.11.3
25081cytochrome oxidase+1.9.3.1
25081esterase-
25081esterase (C 4)+
25081esterase lipase (C 8)+
25081gelatinase-
25081leucine arylamidase+3.4.11.1
25081N-acetyl-beta-glucosaminidase+3.2.1.52
25081naphthol-AS-BI-phosphohydrolase+
25081tryptophan deaminase-4.1.99.1
25081valine arylamidase+
68374L-aspartate arylamidase+3.4.11.21
68374alpha-maltosidase+
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase+3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase+3.2.1.52
68374beta-glucuronidase+3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase+
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123265oxidase+
123265beta-galactosidase-3.2.1.23
123265alcohol dehydrogenase-1.1.1.1
123265gelatinase-
123265amylase-
123265DNase+
123265caseinase-3.4.21.50
123265catalase+1.11.1.6
123265tween esterase+
123265gamma-glutamyltransferase+2.3.2.2
123265lecithinase-
123265lipase-
123265lysine decarboxylase-4.1.1.18
123265ornithine decarboxylase-4.1.1.17
123265phenylalanine ammonia-lyase-4.3.1.24
123265protease-
123265tryptophan deaminase-
123265urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    45917C14:02.214
    45917C16:06.116
    45917C15:0 ISO2814.621
    45917C15:0 ISO 3OH2.216.135
    45917C16:0 3OH5.217.52
    45917C16:1 ω5c1.315.908
    45917C16:1 ω7c23.715.819
    45917C16:1 ω7c/C15:0 ISO 2OH1815.85
    45917C17:0 iso 3OH10.718.161
    45917C17:1 ISO I/C16:0 DMA1.216.481
    45917C17:1 ω9c ISO1.516.416
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
45917-+-+-++---+++--+-+-+
123265-+++-++-+-++++-+++-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
45917-----+-++-+-++------+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
45917-------+++----+--++----++-----++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123265+--++-++-++++++++++--+++-++----+--++-----+------------++---+------------------+-------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4454intrauterine specimen
45917Intra uterineKansasUSAUSANorth America
67770Intrauterine specimensKSUSAUSANorth America
123265Human, Intra uterine specimenKansasUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Specimen
#Host Body-Site#Urogenital tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_3331.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_1738;97_2079;98_2555;99_3331&stattab=map
  • Last taxonomy: Sphingobacterium spiritivorum subclade
  • 16S sequence: EF090267
  • Sequence Identity:
  • Total samples: 7762
  • soil counts: 926
  • aquatic counts: 1560
  • animal counts: 4723
  • plant counts: 553

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44542Risk group (German classification)
1232651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobacterium spiritivorum 16S ribosomal RNA gene, partial sequenceM587781473ena258
20218Sphingobacterium spiritivorum 16S ribosomal RNAD140261285ena258
20218Sphingobacterium spiritivorum gene for 16S rRNA, partial sequence, strain: NBRC 14948AB6807181448ena258
4454Sphingobacterium spiritivorum strain NCTC 11386 16S ribosomal RNA gene, partial sequenceEF0902671445ena258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium spiritivorum ATCC 33861525373.3wgspatric525373
66792Sphingobacterium spiritivorum strain FDAARGOS_1144258.11completepatric258
66792Sphingobacterium spiritivorum strain NCTC11386258.5wgspatric258
66792Sphingobacterium spiritivorum NCTC 113862849498117draftimg258
66792Sphingobacterium spiritivorum ATCC 338612562617179draftimg525373
67770Sphingobacterium spiritivorum NCTC11386GCA_900457435contigncbi258
66792Sphingobacterium spiritivorum ATCC 33861GCA_000143765scaffoldncbi525373

GC content

@refGC-contentmethod
445440.0
6777041thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.181yes
gram-positiveno97.815no
anaerobicno99.24yes
aerobicyes85.632yes
halophileno95.291no
spore-formingno94.95no
glucose-utilyes91.885yes
flagellatedno96.441yes
thermophileno99.076yes
glucose-fermentno89.315no

External links

@ref: 4454

culture collection no.: DSM 11722, ATCC 33861, CDC E7288, GIFU 3101, JCM 1277, NCTC 11386, CCUG 13224, CCM 4603, CIP 100542, IAM 14210, IFO 14948, JCM 6897, LMG 8347, NBRC 14948, NRRL B-23392

straininfo link

  • @ref: 83285
  • straininfo: 4981

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity12904547Bacterial ceramides and sphingophospholipids induce apoptosis of human leukaemic cells.Minamino M, Sakaguchi I, Naka T, Ikeda N, Kato Y, Tomiyasu I, Yano I, Kobayashi KMicrobiology (Reading)10.1099/mic.0.25922-02003Apoptosis/*drug effects, Caspase 3, Caspases/metabolism, Ceramides/chemistry/*pharmacology, Enzyme Activation/drug effects, Gram-Negative Bacteria/*chemistry, HL-60 Cells, Humans, Jurkat Cells, Molecular Structure, Second Messenger Systems, Sphingolipids/chemistry/*pharmacology, U937 Cells, fas Receptor/metabolismMetabolism
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
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4454Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11722)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11722
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
25081W. A. H. Lai, A.,Liu, Y. C.,Hsu, Y. H.,Lin, S. Y.,Young, C. C.10.1099/ijsem.0.001517Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium thermophilum Yabe et al. 2013IJSEM 66: 5336-5344 201627666956
42121Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12018
45917Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 13224)https://www.ccug.se/strain?id=13224
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
68374Automatically annotated from API ID32E
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
83285Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4981.1StrainInfo: A central database for resolving microbial strain identifiers
123265Curators of the CIPCollection of Institut Pasteur (CIP 100542)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100542