Salmonella enterica subsp. enterica (DSM 107308, strain 641)

Name: Salmonella enterica subsp. enterica (DSM 107308, strain 641)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 157865

Type strain

Strain Designation strain 641

Culture col. no. DSM 107308 strain 641

NCBI tax ID(s) 59201

Special Collections DSMZ

History <- N. Chanishvili, The Eliava Institute of Bacteriophage, MIcrobiology & Virology; strain 641 <- unknown

Links

Salmonella enterica subsp. enterica strain 641 is a bacterium that was isolated from sepsis; male patient with diarrhea.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 405032

DSM 107308

@ref 20215

Last LPSN update 2026-02-09 11:38:10

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Salmonella

Species Salmonella enterica subsp. enterica

Full scientific name Salmonella enterica subsp. enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987

Synonyms (1)

Salmonella choleraesuis subsp. choleraesuis

BacDive ID	Other strains from **Salmonella enterica subsp. enterica** (54)	Type strain
5117	S. enterica subsp. enterica LT2, DSM 17058, ATCC 43971, CIP 60.62, NCIMB ... (type strain)
5103	S. enterica subsp. enterica LT2 hisG46, DSM 554
5104	S. enterica subsp. enterica K 103, DSM 4224, CIP 80.39, NCTC 6017, WDCM ...
5105	S. enterica subsp. enterica DSM 4883, ATCC 9184
5106	S. enterica subsp. enterica F98, DSM 26529, CECT 4156, CIP 110278, NCTC ...
5107	S. enterica subsp. enterica Mutton, DSM 5569, ATCC 13311, CCM 7933, NCTC ...
5108	S. enterica subsp. enterica Hochberg 2460, DSM 9145, ATCC 7378
5109	S. enterica subsp. enterica pSK1002, TA 1535/pSK 1002, DSM 9274
5110	S. enterica subsp. enterica 16, DSM 9379, ATCC 8326
5111	S. enterica subsp. enterica 775/W, Col Sal 385/57, 493, W 775, 775W, ...
5113	S. enterica subsp. enterica Zoosaloral H, DSM 11320
5114	S. enterica subsp. enterica DSM 13674, RKI 00-07121
5115	S. enterica subsp. enterica DSM 14221, RKI 01-02637
5116	S. enterica subsp. enterica 1348, DSM 14846, ATCC 13312, CIP 55.133, ...
5118	S. enterica subsp. enterica K-1891, DSM 17420, ATCC 13076, DSM 9898, ...
5120	S. enterica subsp. enterica DSM 19587, ATCC 14028, CDC 6516-60, CIP 104115, ...
5121	S. enterica subsp. enterica SL1344, DSM 24522
5122	S. enterica subsp. enterica Menendez 245, DSM 26655, ATCC 49214, CECT ...
23943	S. enterica subsp. enterica 110 (K 108), CNCT SK 108, GISK 100331, 110, ...
23944	S. enterica subsp. enterica Vi4, DSM 50912, ICPB 3247
23945	S. enterica subsp. enterica GISK 100354, StBL 4519, DSM 27686, CECT 4154, ...
131928	S. enterica subsp. enterica S15, DSM 101475
131929	S. enterica subsp. enterica S23, DSM 101476
131930	S. enterica subsp. enterica DSM 102345, NCCP 12232
131931	S. enterica subsp. enterica DSM 102851, NCCP 12241
131932	S. enterica subsp. enterica DSM 102864, NCCP 12231
157848	S. enterica subsp. enterica strain 6, DSM 107291
157849	S. enterica subsp. enterica strain 45, DSM 107292
157850	S. enterica subsp. enterica strain 104, DSM 107293
157851	S. enterica subsp. enterica strain 117, DSM 107294
157852	S. enterica subsp. enterica strain 191, DSM 107295
157853	S. enterica subsp. enterica strain 232, DSM 107296
157854	S. enterica subsp. enterica strain 240, DSM 107297
157855	S. enterica subsp. enterica strain 241, DSM 107298
157856	S. enterica subsp. enterica strain 256, DSM 107299
157857	S. enterica subsp. enterica strain 261, DSM 107300
157858	S. enterica subsp. enterica strain 310, DSM 107301
157859	S. enterica subsp. enterica strain 311, DSM 107302
157860	S. enterica subsp. enterica strain 375, DSM 107303
157861	S. enterica subsp. enterica strain 386, DSM 107304
157862	S. enterica subsp. enterica strain 399, DSM 107305
157863	S. enterica subsp. enterica strain 407, DSM 107306
157864	S. enterica subsp. enterica strain 422, DSM 107307
157866	S. enterica subsp. enterica strain 765, DSM 107309
157867	S. enterica subsp. enterica strain 1150, DSM 107310
157868	S. enterica subsp. enterica strain 164, DSM 107311
157869	S. enterica subsp. enterica strain 259, DSM 107312
164871	S. enterica subsp. enterica JCM 3919
165439	S. enterica subsp. enterica JCM 6977, IFO 14193, NBRC 14193
165440	S. enterica subsp. enterica JCM 6978, IFO 14194, NBRC 14194
165441	S. enterica subsp. enterica JCM 6979, IFO 14209, NBRC 14209
165442	S. enterica subsp. enterica JCM 6980, IFO 14210, NBRC 14210
165443	S. enterica subsp. enterica JCM 6981, IFO 14211, NBRC 14211
165444	S. enterica subsp. enterica JCM 6982, IFO 14212, NBRC 14212

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64438	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
64438	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
64438	positive	growth	37

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		91.8

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
64438	-	+	+	+	+	+	-	-	-	+	-	+	+	+	+	+	-	+	-	+	-	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	#Microbial	#Bacteria
#Host Body Product	#Fluids	#Blood
#Infection	#Patient	-
#Host	#Human	#Male

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64438	sepsis; male patient with diarrhea	Tbilisi	Georgia	GEO	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64438	2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1486160v1 assembly for Salmonella enterica subsp. enterica serovar Typhimurium 641	contig	GCA_014861605	90371.4769	90371	66.78

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Salmonella enterica subsp. enterica serovar Typhimurium strain 641
PATRIC: 90371.4769

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.80	no
125439	motility	BacteriaNetⓘ	yes	67.30	no
125439	gram_stain	BacteriaNetⓘ	negative	88.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	86.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Salmonella enterica subsp. enterica serovar Typhimurium strain 641
PATRIC: 90371.4769

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	95.01	no
125438	aerobic	aerobicⓘ	no	72.91	no
125438	spore-forming	spore-formingⓘ	no	89.53	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	75.89	no

Literature

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 )
#64438	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107308
#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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