Strain identifier

BacDive ID: 14038

Type strain: Yes

Species: Sanguibacter keddieii

Strain Designation: ST-74

Strain history: CIP <- 1999, CECT <- J.F. Fernandez-Garayzabal: strain ST-74

NCBI tax ID(s): 446469 (strain), 60920 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3971

BacDive-ID: 14038

DSM-Number: 10542

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, animal pathogen

description: Sanguibacter keddieii ST-74 is an aerobe, mesophilic, Gram-positive animal pathogen that was isolated from bovine blood.

NCBI tax id

NCBI tax idMatching level
60920species
446469strain

strain history

@refhistory
3971<- NCFB <- J.F. Fernández-Garayzábal, ST-74
67770IFO 16158 <-- NCIMB 703025 <-- J. F. Fernández-Garayzábal ST-74.
120395CIP <- 1999, CECT <- J.F. Fernandez-Garayzabal: strain ST-74

doi: 10.13145/bacdive14038.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Jonesiaceae
  • genus: Sanguibacter
  • species: Sanguibacter keddieii
  • full scientific name: Sanguibacter keddieii Fernández-Garayzábal et al. 1995

@ref: 3971

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Jonesiaceae

genus: Sanguibacter

species: Sanguibacter keddieii

full scientific name: Sanguibacter keddieii Fernández-Garayzábal et al. 1995 emend. Pikuta et al. 2017 emend. Nouioui et al. 2018

strain designation: ST-74

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120395positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
18429Ivory (1014)10-14 daysISP 2
18429Zinc yellow (1018)10-14 daysISP 3
18429Zinc yellow (1018)10-14 daysISP 4
18429Ivory (1014)10-14 daysISP 5
18429Zinc yellow (1018)10-14 daysISP 6
18429Ivory (1014)10-14 daysISP 7
120395

multicellular morphology

@refforms multicellular complexmedium name
18429noISP 2
18429noISP 3
18429noISP 4
18429noISP 5
18429noISP 6
18429noISP 7

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_10542_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3971TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18429ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18429ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18429ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18429ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18429ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18429ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
35134MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120395CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338
120395CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120395CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3971positivegrowth30mesophilic
18429positiveoptimum28
35134positivegrowth30
53328positivegrowth30
67770positivegrowth28mesophilic
120395positivegrowth10-30
120395nogrowth37mesophilic
120395nogrowth41thermophilic
120395nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53328aerobe
120395facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
18429NaClpositivemaximum7.5 %
120395NaClpositivegrowth0-6 %
120395NaClnogrowth8 %
120395NaClnogrowth10 %

murein

  • @ref: 3971
  • murein short key: A11.48
  • type: A4alpha L-Lys-L-Ser-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1842962968cellulose+
1842916634raffinose+
1842926546rhamnose+
1842928757fructose+
1842929864mannitol+
1842917268myo-inositol+
1842918222xylose+
1842917992sucrose+
1842922599arabinose+
1842917234glucose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12039516947citrate-carbon source
1203954853esculin+hydrolysis
120395606565hippurate-hydrolysis
12039517632nitrate-reduction
12039516301nitrite-reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

antibiotic resistance

  • @ref: 120395
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12039535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12039515688acetoin-
12039517234glucose+

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
120395oxidase-
120395beta-galactosidase+3.2.1.23
120395alcohol dehydrogenase-1.1.1.1
120395gelatinase+/-
120395amylase+
120395DNase+
120395caseinase+3.4.21.50
120395catalase+1.11.1.6
120395tween esterase-
120395gamma-glutamyltransferase-2.3.2.2
120395lecithinase-
120395lipase-
120395lysine decarboxylase-4.1.1.18
120395ornithine decarboxylase-4.1.1.17
120395phenylalanine ammonia-lyase-4.3.1.24
120395protease-
120395tryptophan deaminase-
120395urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    53328C13:00.313
    53328C14:04.314
    53328C15:05.515
    53328C16:07.716
    53328C17:00.817
    53328C13:0 ANTEISO0.812.701
    53328C14:0 ISO113.618
    53328C15:0 ANTEISO5714.711
    53328C15:0 ISO2.614.621
    53328C15:1 ANTEISO A9.214.526
    53328C16:0 iso3.315.626
    53328C16:1 ω7c0.415.819
    53328C17:0 anteiso3.516.722
    53328C17:1 ISO I/C16:0 DMA1.316.481
    53328C18:2 ω6,9c/C18:0 ANTE1.417.724
    53328Unidentified0.416.107
    53328Unidentified0.617.194
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18429+-+++/-+++++-++++++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18429+++-+---+++++-++++-
120395-++-++--+++++-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18429----+-+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120395+--+++--+++++-+-----++++++++++++--+++-+++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120395+++++-++-+++++-++++++++--------+---+--------------------------------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3971bovine bloodSpainESPEurope
53328Bovine blood
67770Venous blood from healthy cow
120395Animal, Bovine, bloodSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_6615.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3136;97_3840;98_4877;99_6615&stattab=map
  • Last taxonomy: Sanguibacter
  • 16S sequence: X79450
  • Sequence Identity:
  • Total samples: 28524
  • soil counts: 6877
  • aquatic counts: 4433
  • animal counts: 13080
  • plant counts: 4134

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
3971yes, in single cases1Risk group (German classification)
184292German classification
1203951Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3971
  • description: Sanguibacter keddieii ST74 16S rDNA
  • accession: X79450
  • length: 1495
  • database: ena
  • NCBI tax ID: 446469

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sanguibacter keddieii DSM 10542GCA_000024925completencbi446469
66792Sanguibacter keddieii DSM 10542446469.6completepatric446469
66792Sanguibacter keddieii ST-74, DSM 10542646564565completeimg446469

GC content

@refGC-contentmethod
397170.0thermal denaturation, midpoint method (Tm)
6777070thermal denaturation, midpoint method (Tm)
6777071.89genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes78.085no
flagellatedno87.761no
gram-positiveyes90.498no
anaerobicno98.669yes
aerobicyes87.597yes
halophileno88.113no
spore-formingno76.871no
glucose-utilyes88.808yes
thermophileno99.73yes
glucose-fermentno52.681yes

External links

@ref: 3971

culture collection no.: DSM 10542, ATCC 51767, CECT 4540, NCFB 3025, CCUG 36690, JCM 11429, CGMCC 1.3608, CIP 106323, IFO 16158, NBRC 16158, NCIMB 703025

straininfo link

@refstraininfo
8320545316
83206312112

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18319451Sanguibacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Pulla RK, Kim SY, Yi TH, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65399-02008Actinomycetales/classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Genetics21304646Complete genome sequence of Sanguibacter keddieii type strain (ST-74).Ivanova N, Sikorski J, Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Pati A, Mavromatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Goker M, Pukall R, Klenk HP, Kyrpides NCStand Genomic Sci10.4056/sigs.161972009

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3971Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10542)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10542
18429Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10542.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
35134Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18441
53328Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36690)https://www.ccug.se/strain?id=36690
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
83205Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45316.1StrainInfo: A central database for resolving microbial strain identifiers
83206Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312112.1StrainInfo: A central database for resolving microbial strain identifiers
120395Curators of the CIPCollection of Institut Pasteur (CIP 106323)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106323