Strain identifier

BacDive ID: 14124

Type strain: Yes

Species: Sphingobacterium faecium

Strain Designation: KS 0470

Strain history: CIP <- 1994, IFO <- J. Sugiyama, IAM Univ., Tokyo, Japan <- H. Oyaizu, IAM, Japan

NCBI tax ID(s): 1220575 (strain), 34087 (species)

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General

@ref: 4443

BacDive-ID: 14124

DSM-Number: 11690

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

description: Sphingobacterium faecium KS 0470 is an obligate aerobe, Gram-negative bacterium that was isolated from feces of Bos sprunigenius taurus.

NCBI tax id

NCBI tax idMatching level
34087species
1220575strain

strain history

@refhistory
4443<- IFO <- IAM; KS 0470 (Sphingobacterium sp.)
67770IAM 15376 <-- NBRC 15299 <-- IFO 15299 <-- IAM, KS 0470.
119269CIP <- 1994, IFO <- J. Sugiyama, IAM Univ., Tokyo, Japan <- H. Oyaizu, IAM, Japan

doi: 10.13145/bacdive14124.20240916.9.1

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 faecium
  • full scientific name: Sphingobacterium faecium Takeuchi and Yokota 1993

@ref: 4443

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium faecium

full scientific name: Sphingobacterium faecium Takeuchi and Yokota 1993

strain designation: KS 0470

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119269negativerod-shapedno
69480negative98.104

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4443NUTRIENT 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
40327MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119269CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
4443positivegrowth28
40327positivegrowth30
67770positivegrowth30
119269positivegrowth5-30
119269nogrowth37
119269nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 119269
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

observation

  • @ref: 67770
  • observation: quinones: MK-7

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
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371esculin+builds acid from4853
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
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119269citrate-carbon source16947
119269esculin+hydrolysis4853
119269nitrate-reduction17632
119269nitrite-reduction16301
119269sodium thiosulfate-builds gas from132112
119269nitrate-respiration17632

antibiotic resistance

  • @ref: 119269
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119269
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119269oxidase+
119269beta-galactosidase+3.2.1.23
119269alcohol dehydrogenase-1.1.1.1
119269gelatinase-
119269DNase+
119269catalase+1.11.1.6
119269gamma-glutamyltransferase+2.3.2.2
119269lysine decarboxylase-4.1.1.18
119269ornithine decarboxylase-4.1.1.17
119269phenylalanine ammonia-lyase+4.3.1.24
119269tryptophan deaminase-
119269urease+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
119269-+++-++---+++--++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119269---+/------+/-+/-+/-+/-------+/-+/-+/-+/-+/-++/-+/-+/-+/-+/-+/-+/-+/-+/-+/----+/-+/----+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119269+++++-+++++++++++++-+--++---------++-----+------------++---+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
4443feces of Bos sprunigenius taurusBos sprunigenius taurus
67770Feces of Bos sprunigenius taurusBos sprunigenius taurusJapanJPNAsia
119269Sprunigenius taurus, fecesJapanJPNAsiaTokyo1977

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44431Risk group (German classification)
1192691Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobacterium faecium gene for 16S rRNA, partial sequence, strain: NBRC 15299AB6808291455nuccore34087
4443Sphingobacterium faecium partial 16S rRNA, strain DSM 11690TAJ4381761494nuccore34087

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium faecium NBRC 152991220575.3wgspatric1220575
66792Sphingobacterium faecium strain DSM 1169034087.3wgspatric34087
66792Sphingobacterium faecium DSM 116902734482254draftimg34087
67770Sphingobacterium faecium NBRC 15299GCA_007990875contigncbi1220575
67770Sphingobacterium faecium DSM 11690GCA_003054045scaffoldncbi34087

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.104no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.249yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.294no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.153yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.875yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.25no

External links

@ref: 4443

culture collection no.: DSM 11690, CIP 104193, IFO 15299, NBRC 15299, JCM 21820, IAM 15376, LMG 14022, NCIMB 13408

straininfo link

  • @ref: 83291
  • straininfo: 10255

literature

  • topic: Enzymology
  • Pubmed-ID: 14729071
  • title: Structural analysis of sphingophospholipids derived from Sphingobacterium spiritivorum, the type species of genus Sphingobacterium.
  • authors: Naka T, Fujiwara N, Yano I, Maeda S, Doe M, Minamino M, Ikeda N, Kato Y, Watabe K, Kumazawa Y, Tomiyasu I, Kobayashi K
  • journal: Biochim Biophys Acta
  • DOI: 10.1016/j.bbalip.2003.10.010
  • year: 2003
  • mesh: Ceramides/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 & purification
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4443Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11690)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11690
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
40327Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16074
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
83291Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10255.1StrainInfo: A central database for resolving microbial strain identifiers
119269Curators of the CIPCollection of Institut Pasteur (CIP 104193)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104193