Strain identifier
BacDive ID: 158180
Type strain:
Species: Siccibacter colletis
Strain Designation: 1383
Strain history: <- CECT <- S.J. Forsythe, Nottingham Trent University, United Kingdom
NCBI tax ID(s): 1505757 (species)
General
@ref: 64773
BacDive-ID: 158180
DSM-Number: 107916
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Siccibacter colletis 1383 is a mesophilic, motile 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/bacdive158180.20230509.8.1
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 colletis
- full scientific name: Siccibacter colletis Jackson et al. 2015
synonyms
@ref synonym 20215 Siccibacter colletis 20215 Cronobacter 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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.339 | |
69480 | 99.973 | negative |
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
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69480 | no | 99.587 |
69481 | no | 100 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | + | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | + | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | + | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: ena
- NCBI tax ID: 1505757
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Siccibacter colletis 1383 | GCA_000696575 | scaffold | ncbi | 1505757 |
66792 | Siccibacter colletis 1383 | 2579778730 | draft | img | 1505757 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 93.282 | no |
flagellated | no | 64.475 | no |
gram-positive | no | 98.233 | no |
anaerobic | no | 96.763 | no |
halophile | no | 86.799 | no |
spore-forming | no | 93.284 | no |
glucose-util | yes | 94.951 | no |
aerobic | yes | 62.161 | no |
thermophile | no | 98.202 | yes |
glucose-ferment | yes | 93.385 | no |
External links
@ref: 64773
culture collection no.: DSM 107916, CECT 8567, LMG 28204, NCTC 14934
straininfo link
- @ref: 111011
- straininfo: 392516
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 24948763 | Draft 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 S | Genome Announc | 10.1128/genomeA.00585-14 | 2014 | ||
Phylogeny | 25667396 | Description 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 SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.000108 | 2015 | Bacterial 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, DNA | Genetics |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
64773 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-107916 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107916) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68368 | Automatically annotated from API 20E | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
111011 | Reimer, 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 identifiers | 10.60712/SI-ID392516.1 |