Strain identifier

BacDive ID: 14125

Type strain: Yes

Species: Sphingobacterium thalpophilum

Strain Designation: K-1173

Strain history: CIP <- 1984, NCTC, Flavobacterium thalpophilum <- California Univ., Los Angeles, USA <- Isolation Hosp., New York, USA

NCBI tax ID(s): 1123265 (strain), 259 (species)

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General

@ref: 4455

BacDive-ID: 14125

DSM-Number: 11723

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

description: Sphingobacterium thalpophilum K-1173 is an obligate aerobe, Gram-negative, rod-shaped bacterium of the family Sphingobacteriaceae.

NCBI tax id

NCBI tax idMatching level
259species
1123265strain

strain history

@refhistory
4455<- IFO <- ATCC (Flavobacterium thalphphilum) <- NCTC
67770IAM 14313 <-- IFO 14963 <-- ATCC 43320 <-- NCTC 11429 <-- Univ. California, LA, USA.
123499CIP <- 1984, NCTC, Flavobacterium thalpophilum <- California Univ., Los Angeles, USA <- Isolation Hosp., New York, USA

doi: 10.13145/bacdive14125.20240916.9.1

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 thalpophilum
  • full scientific name: Sphingobacterium thalpophilum (Holmes et al. 1983) Takeuchi and Yokota 1993

  • synonyms

    • @ref: 20215
    • synonym: Flavobacterium thalpophilum

@ref: 4455

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium thalpophilum

full scientific name: Sphingobacterium thalpophilum (Holmes et al. 1983) Takeuchi and Yokota 1993 emend. Hahnke et al. 2016

strain designation: K-1173

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123499negativerod-shapedno
69480negative97.604

colony morphology

  • @ref: 123499
  • hemolysis ability: 1

pigmentation

  • @ref: 123499
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4455NUTRIENT 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
40269MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123499CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123499CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
4455positivegrowth28
40269positivegrowth30
67770positivegrowth30
123499positivegrowth5-41
123499nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 123499
  • oxygen tolerance: obligate aerobe

spore formation

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

halophily

@refsaltgrowthtested relationconcentration
123499NaClpositivegrowth0-4 %
123499NaClnogrowth6 %
123499NaClnogrowth8 %
123499NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
12349916947citrate-carbon source
1234994853esculin+hydrolysis
123499606565hippurate-hydrolysis
12349917632nitrate-builds gas from
12349917632nitrate+reduction
12349916301nitrite-builds gas from
12349916301nitrite-reduction
12349915792malonate-assimilation
12349917632nitrate-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: 123499
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836935581indoleno
12349935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836935581indole-
12349915688acetoin-
12349917234glucose-

enzymes

@refvalueactivityec
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
123499oxidase+
123499beta-galactosidase+3.2.1.23
123499alcohol dehydrogenase-1.1.1.1
123499gelatinase-
123499catalase+1.11.1.6
123499gamma-glutamyltransferase+2.3.2.2
123499lysine decarboxylase-4.1.1.18
123499ornithine decarboxylase-4.1.1.17
123499phenylalanine ammonia-lyase-4.3.1.24
123499tryptophan deaminase-
123499urease-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+
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
47630-+++-++-+-++++-+++++
123499-+++-++++-++++-+++++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
47630+---++-++++-++------+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
47630---+---+++----+--++----++-----++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123499+++++-+++++++++++++-++++-+-----+--++-+---+------------++---+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
40269New York CityUSAUSANorth America
47630New YorkUSAUSANorth AmericaHuman wound,swab
67770New YorkUSAUSANorth AmericaWound swab
123499New York, New YorkUnited States of AmericaUSANorth AmericaHuman, Wound

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Swab
#Host Body-Site#Other#Wound
#Host#Human

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44552Risk group (German classification)
1234991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobacterium thalpophilum 16S ribosomal RNA gene, partial sequenceM587791478nuccore259
20218Flavobacterium thalpophilum 16S ribosomal RNAD140201264nuccore259
20218Sphingobacterium thalpophilum gene for 16S rRNA, partial sequence, strain: NBRC 14963AB6807251453nuccore259
20218F.thalpophilum (NCTC 11429) gene for 16S rRNAX67851905nuccore259
4455Sphingobacterium thalpophilum partial 16S rRNA, strain DSM 11723TAJ4381771499nuccore259

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium thalpophilum NCTC11429GCA_901482695completencbi259
66792Sphingobacterium thalpophilum DSM 117231123265.3wgspatric1123265
66792Sphingobacterium thalpophilum strain NCTC11429259.5completepatric259
66792Sphingobacterium thalpophilum DSM 117232563366725draftimg1123265
67770Sphingobacterium thalpophilum DSM 11723GCA_000686625scaffoldncbi1123265

GC content

@refGC-contentmethod
445543.6sequence analysis
6777041.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.604no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.467yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.799yes
69480spore-formingspore-formingAbility to form endo- or exosporesno88.312no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.479yes
69480flagellatedmotile2+Ability to perform flagellated movementno87.542no

External links

@ref: 4455

culture collection no.: DSM 11723, ATCC 43320, IFO 14963, NBRC 14963, NCTC 11429, CCUG 22397, JCM 21153, CIP 100935, IAM 14313, NRRL B-14902

straininfo link

  • @ref: 83292
  • straininfo: 7613

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
Phylogeny17267986Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete.Ntougias S, Fasseas C, Zervakis GIInt J Syst Evol Microbiol10.1099/ijs.0.64561-02007Aerobiosis, Amino Acids/metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Greece, Hydrogen-Ion Concentration, *Industrial Waste, Molecular Sequence Data, Movement, Olive Oil, Phylogeny, Pigments, Biological/biosynthesis, *Plant Oils, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Spores, Bacterial, TemperatureMetabolism
Phylogeny17629434Sphingobacterium canadense sp. nov., an isolate from corn roots.Mehnaz S, Weselowski B, Lazarovits GSyst Appl Microbiol10.1016/j.syapm.2007.06.0022007Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingobacterium/chemistry/*classification/genetics/*isolation & purification, Zea mays/*microbiologyGenetics
Phylogeny22307508Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil.Marques AM, Burgos-Diaz C, Aranda FJ, Teruel JA, Manresa A, Ortiz A, Farfan MInt J Syst Evol Microbiol10.1099/ijs.0.036707-02012Azores, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Surface-Active Agents/*metabolismGenetics
Phylogeny24281734Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo.Ahmed I, Ehsan M, Sin Y, Paek J, Khalid N, Hayat R, Chang YHAntonie Van Leeuwenhoek10.1007/s10482-013-0077-02013Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fabaceae/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Growth Regulators/*metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/metabolismGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4455Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11723)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11723
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
40269Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12454
47630Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 22397)https://www.ccug.se/strain?id=22397
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
68374Automatically annotated from API ID32E
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
83292Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7613.1StrainInfo: A central database for resolving microbial strain identifiers
123499Curators of the CIPCollection of Institut Pasteur (CIP 100935)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100935