Strain identifier

BacDive ID: 4378

Type strain: Yes

Species: Siccibacter turicensis

Strain Designation: 508/05

Strain history: CIP <- 2007, DSMZ <- R. Stephan, Inst. Food Safety Hyg., Zürich, Switzerland: strain 508/05

NCBI tax ID(s): 1388748 (strain), 357233 (species)

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General

@ref: 7525

BacDive-ID: 4378

DSM-Number: 18397

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, coccus-shaped

description: Siccibacter turicensis 508/05 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from fruit powder.

NCBI tax id

NCBI tax idMatching level
357233species
1388748strain

strain history

@refhistory
7525<- R. Stephan, Inst. for Food Safety and Hygiene; 508/05
67770LMG 23730 <-- R. Stephan 508/05.
124039CIP <- 2007, DSMZ <- R. Stephan, Inst. Food Safety Hyg., Zürich, Switzerland: strain 508/05

doi: 10.13145/bacdive4378.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Siccibacter
  • species: Siccibacter turicensis
  • full scientific name: Siccibacter turicensis (Stephan et al. 2007) Stephan et al. 2014

  • synonyms

    @refsynonym
    20215Cronobacter zurichensis
    20215Enterobacter turicensis

@ref: 7525

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Siccibacter

species: Siccibacter turicensis

full scientific name: Siccibacter turicensis (Stephan et al. 2007) Stephan et al. 2014 emend. Jackson et al. 2015

strain designation: 508/05

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31918negative1.5-2.5 µm1 µmcoccus-shapedyes
69480yes95.385
69480negative99.954
124039negativerod-shapedyes

pigmentation

  • @ref: 31918
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7525COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
7525TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
34216MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
124039CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7525positivegrowth37mesophilic
31918positivegrowth10-44
31918positiveoptimum27mesophilic
34216positivegrowth37mesophilic
60405positivegrowth37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31918facultative anaerobe
60405aerobe
124039facultative anaerobe

spore formation

@refspore formationconfidence
31918no
69481no100
69480no99.241

observation

  • @ref: 31918
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31918168082-dehydro-D-gluconate+carbon source
3191816449alanine+carbon source
3191822599arabinose+carbon source
3191835391aspartate+carbon source
3191817057cellobiose+carbon source
3191828757fructose+carbon source
3191828260galactose+carbon source
319185417glucosamine+carbon source
3191817234glucose+carbon source
3191829987glutamate+carbon source
3191817754glycerol+carbon source
3191824996lactate+carbon source
3191817716lactose+carbon source
3191825115malate+carbon source
3191817306maltose+carbon source
3191829864mannitol+carbon source
3191837684mannose+carbon source
3191828053melibiose+carbon source
3191826271proline+carbon source
3191826546rhamnose+carbon source
3191833942ribose+carbon source
3191817822serine+carbon source
3191827082trehalose+carbon source
3191818222xylose+carbon source
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
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
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
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
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12403917632nitrate+reduction
12403916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12403935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
31918catalase+1.11.1.6
31918cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68368cytochrome oxidase-1.9.3.1
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
124039oxidase-
124039catalase+1.11.1.6
124039urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124039-+++-+----++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7525+---+------++--+-+++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
124039+-+++++/---++++-++-+---++/-+++++++-+--+/----+-------+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7525fruit powderSwitzerlandCHEEurope
67770Fruit powder
124039Fruit powderSwitzerlandCHEEuropeZurich

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant
  • Cat3: #Fruit (Seed)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75251Risk group (German classification)
1240392Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7525Enterobacter turicensis strain LMG 23730 16S ribosomal RNA gene, partial sequenceDQ2736811266ena1388748
67770Enterobacter turicensis strain LMG 23730 16S ribosomal RNA gene, partial sequenceHQ9929471494ena1388748

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cronobacter zurichensis LMG 237301388748.3wgspatric1388748
66792Siccibacter turicensis z5081390075.3wgspatric1390075
66792Siccibacter turicensis LMG 237302617271157draftimg1388748
67770Siccibacter turicensis LMG 23730 LMG23730TGCA_000463155scaffoldncbi1388748

GC content

@refGC-contentmethod
752557.8
6777057.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes93.275no
gram-positiveno98.15no
anaerobicno97.311yes
halophileno82.011no
spore-formingno93.074yes
thermophileno98.681yes
glucose-utilyes95.038yes
aerobicyes71.074no
flagellatedno67.226no
glucose-fermentyes92.543no

External links

@ref: 7525

culture collection no.: DSM 18397, CCUG 54945, CIP 109627, LMG 23730, JCM 16472

straininfo link

  • @ref: 73869
  • straininfo: 302751

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392213Enterobacter turicensis sp. nov. and Enterobacter helveticus sp. nov., isolated from fruit powder.Stephan R, Van Trappen S, Cleenwerck I, Vancanneyt M, De Vos P, Lehner AInt J Syst Evol Microbiol10.1099/ijs.0.64650-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Enterobacter/*classification/genetics/isolation & purification, Fruit/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Genetics24072872Draft Genome Sequences of Three Newly Identified Species in the Genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T.Masood N, Moore K, Farbos A, Hariri S, Paszkiewicz K, Dickins B, McNally A, Forsythe SGenome Announc10.1128/genomeA.00783-132013
Phylogeny25028159Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively.Stephan R, Grim CJ, Gopinath GR, Mammel MK, Sathyamoorthy V, Trach LH, Chase HR, Fanning S, Tall BDInt J Syst Evol Microbiol10.1099/ijs.0.059832-02014Bacterial Typing Techniques, Cronobacter/*classification/genetics, DNA, Bacterial/genetics, Enterobacter/*classification/genetics, Enterobacteriaceae/*classification/genetics, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Polymorphism, Single Nucleotide, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25667396Description of Siccibacter colletis sp. nov., a novel species isolated from plant material, and emended description of Siccibacter turicensis.Jackson EE, Masood N, Ibrahim K, Urvoy N, Hariri S, Forsythe SJInt J Syst Evol Microbiol10.1099/ijs.0.0001082015Bacterial Typing Techniques, Camellia sinensis/*microbiology, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Papaver/*microbiology, *Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Seeds/microbiology, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7525Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18397)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18397
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
31918Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2817528776041
34216Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7391
60405Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54945)https://www.ccug.se/strain?id=54945
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/
68368Automatically annotated from API 20E
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
73869Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302751.1StrainInfo: A central database for resolving microbial strain identifiers
124039Curators of the CIPCollection of Institut Pasteur (CIP 109627)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109627