Siccibacter colletis (DSM 107916, CECT 8567, LMG 28204)

Name: Siccibacter colletis (DSM 107916, CECT 8567, LMG 28204)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158180

Type strain

Strain Designation 1383

Culture col. no. DSM 107916 CECT 8567 LMG 28204 NCTC 14934 1383

NCBI tax ID(s) 1505757

Special Collections DSMZ

History <- CECT <- S.J. Forsythe, Nottingham Trent University, United Kingdom

Links

Siccibacter colletis 1383 is a mesophilic prokaryote that was isolated from poppy seeds purchased in the UK.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 392516

LMG 28204,CECT 8567,NCTC 14934,DSM 107916

@ref 20215

Last LPSN update 2025-12-16 10:07:58

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Siccibacter

Species Siccibacter colletis

Full scientific name Siccibacter colletis Jackson et al. 2015

Synonyms (2)

"Candidatus Cronobacter colletis"
"Candidatus Siccibacter colletis"

BacDive ID	Other strains from **Siccibacter colletis** (1)	Type strain
153883	S. colletis CCUG 51494

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.6
125438	negative	100

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64773	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	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	Growth	Type	Temperature (°C)	Range
64773	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	93.9

Spore formation

@ref	Spore formation	Confidence
125439		95.9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
64773	+	-	-	-	+	-	-	-	-	-	-	+	+	-	-	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
64773	poppy seeds purchased in the UK	United Kingdom	GBR	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64773	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	C_colletis_1383 assembly for Siccibacter colletis 1383	scaffold	GCA_000696575	1499086.3	2579778730	1505757	67.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64773	Siccibacter colletis partial 16S rRNA gene, type strain 1383T	LK054215	1451		1505757

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Siccibacter colletis 1383
NCBI: GCA_000696575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	69.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Siccibacter colletis 1383
NCBI: GCA_000696575.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	96.66	no
125438	aerobic	aerobicⓘ	no	67.55	no
125438	spore-forming	spore-formingⓘ	no	88.55	no
125438	thermophilic	thermophileⓘ	no	99.50	no
125438	flagellated	motile2+ⓘ	yes	77.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	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	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

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#64773	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; 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) .
#68368	Automatically annotated from API 20E .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Siccibacter colletis (DSM 107916, CECT 8567, LMG 28204)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000696575

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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