Shigella dysenteriae (CIP 58.1, 588)

Name: Shigella dysenteriae (CIP 58.1, 588)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 135721

Type strain

Strain Designation 588

Culture col. no. CIP 58.1 588

NCBI tax ID(s) 622

Special Collections CIP

History 1958, Huet: strain 588 CIP <- 1958, Huet: strain 588

Links

Shigella dysenteriae 588 is a facultative anaerobe, Gram-negative, rod-shaped bacterium of the family Enterobacteriaceae.

Gram-negative rod-shaped facultative anaerobe Bacteria

Name and taxonomic classification

SI-ID 70121

CIP 58.1

@ref 20215

Last LPSN update 2026-02-09 11:32:29

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Shigella

Species Shigella dysenteriae

Full scientific name Shigella dysenteriae (Shiga 1897) Castellani and Chalmers 1919 (Approved Lists 1980)

Synonyms (1)

"Bacillus dysentericus"

BacDive ID	Other strains from **Shigella dysenteriae** (51)	Type strain
138456	S. dysenteriae CIP 57.28, ATCC 13313, CCUG 9565, NCTC 4837 (type strain)
131935	S. dysenteriae RKI00-04776, DSM 103303
134426	S. dysenteriae M158, 34, CIP 106191
134427	S. dysenteriae Bagdad 7/66, CIP 67.60
134428	S. dysenteriae 252, CIP 59.3
134431	S. dysenteriae Bagdad 5/66, CIP 67.59
134738	S. dysenteriae CIP 58.26, NCTC 9347
134739	S. dysenteriae 418/55, CIP 58.28
135177	S. dysenteriae 599-52, CIP 53.134, NCTC 9345
135203	S. dysenteriae 43, CIP 106200
135301	S. dysenteriae 4219-50, CIP 52.120
135385	S. dysenteriae 54188, CIP 54.57
135580	S. dysenteriae CIP 54.51
135603	S. dysenteriae 589, CIP 57.42
135604	S. dysenteriae 3873-50, CIP 58.16, NCTC 9349
135606	S. dysenteriae 3307-53, 58, CIP 58.25, NCTC 9348
135718	S. dysenteriae 54921, CIP 56.17
135719	S. dysenteriae 54268, CIP 54.77
135722	S. dysenteriae 309, CIP 59.1
135723	S. dysenteriae 41, CIP 59.2
135724	S. dysenteriae 6270, CIP 59.4
136016	S. dysenteriae CIP 52.31
136061	S. dysenteriae 1048-50, CIP 52.122
137043	S. dysenteriae 4325, CIP 54.95
137393	S. dysenteriae Bucarest S, CIP 55.137
137398	S. dysenteriae CIP 82.34, ATCC 11835
138512	S. dysenteriae Bagdad 57/46, CIP 67.58
138544	S. dysenteriae Bucarest R, CIP 55.139
139001	S. dysenteriae Bucarest R, CIP 55.90
139003	S. dysenteriae CIP 53.127
139005	S. dysenteriae Norwich, CIP 52.27
139006	S. dysenteriae 9D, CIP 52.28
139007	S. dysenteriae CIP 52.30
139008	S. dysenteriae CIP 52.32
139009	S. dysenteriae 1012, CIP 54.49
139010	S. dysenteriae CIP 54.50
139012	S. dysenteriae 4388-50, CIP 58.15, NCTC 9350
139013	S. dysenteriae 1046-50, CIP 52.121
139014	S. dysenteriae CIP 52.123, NCTC 9763
139015	S. dysenteriae 1768-53, CIP 53.135
139016	S. dysenteriae 52287, CIP 53.136
139017	S. dysenteriae 120, CIP 56.16
139018	S. dysenteriae CIP 56.33
139150	S. dysenteriae CIP 52.33
139306	S. dysenteriae 41, M183, CIP 106198
143352	S. dysenteriae CCUG 18713
145726	S. dysenteriae CCUG 29414
149515	S. dysenteriae CCUG 37887
149516	S. dysenteriae CCUG 37888
149517	S. dysenteriae CCUG 37889
150348	S. dysenteriae CCUG 39701

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		99.75
125439	negative		94.4
34902	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
34902	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
34902	CIP Medium 72			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
34902	positive	growth	30
34902	positive	growth	30-41
34902	negative	growth	5
34902	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
34902	facultative anaerobe
125439	aerobe	96.2

Spore formation

@ref	Spore formation	Confidence
125439		93.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
34902	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
34902	17234 ChEBI	glucose	+	fermentation
34902	17234 ChEBI	glucose	+	degradation
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
34902	17716 ChEBI	lactose	-	fermentation
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
34902	15792 ChEBI	malonate	-	assimilation
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
34902	29864 ChEBI	mannitol	-	fermentation
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
34902	17632 ChEBI	nitrate	+	reduction
34902	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
34902	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
34902	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
34902	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
34902	15688 ChEBI	acetoin	-
34902	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
34902	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
34902	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
34902	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
34902	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
34902	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
34902	ornithine decarboxylase	-	4.1.1.17
34902	oxidase	-
34902	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
34902	tryptophan deaminase	-
34902	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
34902	-	+	-	-	-	+	-	-	+	-	+	+	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
34902	not determinedn.d.	+/-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
34902	not determinedn.d.	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Geographic location	Country	Country ISO 3 Code	Continent
34902	Tunis	Tunisia	TUN	Africa

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
34902	3	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	BV-BRC accession	NCBI tax ID
66792	Shigella dysenteriae strain CIP58.1	contig	622.146	622

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shigella dysenteriae strain CIP58.1
PATRIC: 622.146

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.50	no
125439	motility	BacteriaNetⓘ	yes	66.00	no
125439	gram_stain	BacteriaNetⓘ	negative	94.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shigella dysenteriae strain CIP58.1
PATRIC: 622.146

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	93.42	yes
125438	spore-forming	spore-formingⓘ	no	89.95	no
125438	aerobic	aerobicⓘ	no	73.86	yes
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	53.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Differential invasiveness & expression of antimicrobial peptides in Shigella serotypes.	Narayan C, Kant V, Mahajan JK, Mohan B, Taneja N.	Indian J Med Res	10.4103/ijmr.ijmr_4864_20	2023
Phylogeny	Selection and validation of a multilocus variable-number tandem-repeat analysis panel for typing Shigella spp.	Gorge O, Lopez S, Hilaire V, Lisanti O, Ramisse V, Vergnaud G.	J Clin Microbiol	10.1128/jcm.02027-07	2008

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 )
#34902	Collection of Institut Pasteur ; Curators of the CIP; CIP 58.1
#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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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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Shigella dysenteriae (CIP 58.1, 588)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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