Strain identifier

BacDive ID: 158180

Type strain: Yes

Species: Siccibacter colletis

Strain Designation: 1383

Strain history: <- CECT <- S.J. Forsythe, Nottingham Trent University, United Kingdom

NCBI tax ID(s): 1505757 (species)

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General

@ref: 64773

BacDive-ID: 158180

DSM-Number: 107916

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Siccibacter colletis 1383 is a mesophilic, Gram-negative bacterium that was isolated from poppy seeds purchased in the UK.

NCBI tax id

  • NCBI tax id: 1505757
  • Matching level: species

strain history

  • @ref: 64773
  • history: <- CECT <- S.J. Forsythe, Nottingham Trent University, United Kingdom

doi: 10.13145/bacdive158180.20250331.9.3

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 colletis
  • full scientific name: Siccibacter colletis Jackson et al. 2015

  • synonyms

    @refsynonym
    20215Siccibacter colletis
    20215Cronobacter colletis

@ref: 64773

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Siccibacter

species: Siccibacter colletis

full scientific name: Siccibacter colletis Jackson et al. 2015

strain designation: 1383

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
125439negative97.6
125438negative100

Culture and growth conditions

culture medium

  • @ref: 64773
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

  • @ref: 64773
  • growth: positive
  • type: growth
  • temperature: 28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: aerobe
  • confidence: 93.9

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 95.9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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
64773+---+------++--+-+++-

Isolation, sampling and environmental information

isolation

  • @ref: 64773
  • sample type: poppy seeds purchased in the UK
  • country: United Kingdom
  • origin.country: GBR
  • continent: Europe

isolation source categories

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

Safety information

risk assessment

  • @ref: 64773
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64773
  • description: Siccibacter colletis partial 16S rRNA gene, type strain 1383T
  • accession: LK054215
  • length: 1451
  • database: nuccore
  • NCBI tax ID: 1505757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Siccibacter colletis 1383GCA_000696575scaffoldncbi1505757
66792Siccibacter colletis 13832579778730draftimg1505757

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.662no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no67.545no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.549no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.5no
125438motile2+flagellatedAbility to perform flagellated movementyes77.463no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno95.9
125439BacteriaNetmotilityAbility to perform movementyes69.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe93.9

External links

@ref: 64773

culture collection no.: DSM 107916, CECT 8567, LMG 28204, NCTC 14934

straininfo link

  • @ref: 111011
  • straininfo: 392516

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics24948763Draft Genome Sequence of "Candidatus Cronobacter colletis" NCTC 14934T, a New Species in the Genus Cronobacter.Masood N, Jackson E, Moore K, Farbos A, Paszkiewicz K, Dickins B, McNally A, Forsythe SGenome Announc10.1128/genomeA.00585-142014
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

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64773Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107916Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107916)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
111011Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID392516.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG