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Strain identifier

BacDive ID: 4378

Type strain: Yes

Species: Siccibacter turicensis

Strain Designation: 508/05

Strain history: LMG 23730 <-- R. Stephan 508/05.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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
1388748strain
357233species

strain history

doi: 10.13145/bacdive4378.20221219.7.1

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
69480yes71.754
69480negative98.954

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)

culture temp

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31918facultative anaerobe
60405aerobe

spore formation

@refspore formationconfidence
31918no
69480no95.078

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 96.947

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
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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
31918catalase+1.11.1.6
31918cytochrome oxidase+1.9.3.1
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

API 20E

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

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7525fruit powderSwitzerlandCHEEurope
67770Fruit powder

isolation source categories

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

Safety information

risk assessment

  • @ref: 7525
  • biosafety level: 1
  • biosafety level comment: Risk group (German 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 LMG 23730GCA_000463155scaffoldncbi1388748
66792Citrobacter freundii RHB36-C06GCA_013815045completepatric546

GC content

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

External links

@ref: 7525

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

straininfo link

@refpassport
20218http://www.straininfo.net/strains/701720
20218http://www.straininfo.net/strains/840452
20218http://www.straininfo.net/strains/701721

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/urltitlejournalpubmedID_cross_reference
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
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
2817510.1099/ijs.0.64650-017392213
31918Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128175
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
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)