Shigella boydii (CIP 58.22, NCTC 9362, CCUG 67177)

Name: Shigella boydii (CIP 58.22, NCTC 9362, CCUG 67177)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 135166

Type strain

Strain Designation 2045-54, 425

Culture col. no. CIP 58.22 NCTC 9362 CCUG 67177 CNCTC 6349 2045-54 1 more

NCBI tax ID(s) 621

Special Collections CCUG CIP

History CIP <- 1958, Dysentery Ref. Lab., Oxford, UK: strain 425 <- W.H. Ewing, CDC: strain 2045-54

Links

Shigella boydii 2045-54 is an aerobe, mesophilic prokaryote that was isolated from Human.

aerobe mesophilic genome sequence

Name and taxonomic classification

SI-ID 70094

NCTC 9362,CIP 58.22,CNCTC 6349,CCUG 67177

@ref 20215

Last LPSN update 2026-02-09 11:32:22

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Shigella

Species Shigella boydii

Full scientific name Shigella boydii Ewing 1949 (Approved Lists 1980)

BacDive ID	Other strains from **Shigella boydii** (38)	Type strain
5174	S. boydii P288, DSM 7532, ATCC 8700, CCUG 49022, CIP ... (type strain)
134546	S. boydii 54264, CIP 54.75
134560	S. boydii 75-25-3, CIP 54.108
134619	S. boydii 901, CIP 57.47, NCTC 9356
134723	S. boydii CIP 56.36
134737	S. boydii 4350-54, CIP 58.18, NCTC 9765
134833	S. boydii 258, CIP 73.2
134919	S. boydii 7001, CIP 54.73
135299	S. boydii 541106, CIP 56.18
135607	S. boydii 2770/51, CIP 58.17, ATCC 12035, NCTC 9766
135608	S. boydii 703, CIP 58.19, ATCC 12034, NCTC 9365
135653	S. boydii 140/56, 5518/56, CIP 67.11
135895	S. boydii D 27, CIP 53.42
135972	S. boydii Nil-2-c, CIP 52.50, NCTC 9329
135996	S. boydii H 21582, CIP 51.6
136410	S. boydii A12, CIP 53.44, NCTC 6721
136484	S. boydii 54125, CIP 54.76
137104	S. boydii 55, CIP 56.35
137108	S. boydii CIP 58.20, NCTC 10024, DRL 120/55
137109	S. boydii 425, CIP 58.21, ATCC 12032, NCTC 9361
137192	S. boydii type, CIP 52.48
137768	S. boydii 426/FA, CIP 52.52, NCTC 9331
137769	S. boydii 6917, CIP 52.54, NCTC 9333
138575	S. boydii 1296/7, CIP 51.4, NCTC 9355
138576	S. boydii Congo, CIP 51.3
138591	S. boydii PSH-125, CIP 52.51, NCTC 9330
138593	S. boydii M 279, CIP 52.53, NCTC 9332
138842	S. boydii 592, CIP 58.4
138844	S. boydii 123, CIP 58.23, ATCC 12033, NCTC 9772
138845	S. boydii 1693, CIP 58.24
141992	S. boydii CCUG 9564, NCTC 9357
143796	S. boydii CCUG 21249
143801	S. boydii CCUG 21261
149519	S. boydii CCUG 37891
149520	S. boydii CCUG 37892
149521	S. boydii CCUG 37893
151867	S. boydii CCUG 45096
171284	S. boydii CIP 111949

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.944

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
34131	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
34131	CIP Medium 3			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
34131	positive	growth	30	mesophilic
63393	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

63393

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.442

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68374	29016 ChEBI	arginine	-	hydrolysis	from API ID32E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68374	17057 ChEBI	cellobiose	-	builds acid from	from API ID32E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68374	18333 ChEBI	D-arabitol	-	builds acid from	from API ID32E
68374	18024 ChEBI	D-galacturonic acid	+	builds acid from	from API ID32E
68374	17634 ChEBI	D-glucose	-	builds acid from	from API ID32E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68374	16899 ChEBI	D-mannitol	+	builds acid from	from API ID32E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68374	30849 ChEBI	L-arabinose	-	builds acid from	from API ID32E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68374	18403 ChEBI	L-arabitol	-	builds acid from	from API ID32E
68374	62345 ChEBI	L-rhamnose	-	builds acid from	from API ID32E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68374	25094 ChEBI	lysine	-	degradation	from API ID32E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68374	15792 ChEBI	malonate	-	assimilation	from API ID32E
68374	17306 ChEBI	maltose	-	builds acid from	from API ID32E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68374	17268 ChEBI	myo-inositol	-	builds acid from	from API ID32E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68374	18257 ChEBI	ornithine	+	degradation	from API ID32E
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68374	18394 ChEBI	palatinose	-	builds acid from	from API ID32E
68374		Potassium 5-ketogluconate	-	builds acid from	from API ID32E
68374	15963 ChEBI	ribitol	-	builds acid from	from API ID32E
68374	30911 ChEBI	sorbitol	-	builds acid from	from API ID32E
68368	30911 ChEBI	sorbitol	+	fermentation	from API 20E
68374	17992 ChEBI	sucrose	-	builds acid from	from API ID32E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68374	27082 ChEBI	trehalose	+	builds acid from	from API ID32E
68374	27897 ChEBI	tryptophan	+	energy source	from API ID32E
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68374	16199 ChEBI	urea	-	hydrolysis	from API ID32E
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
68374	35581 ChEBI	indole	from API ID32E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68374	35581 ChEBI	indole		+	from API ID32E
68368	35581 ChEBI	indole		+	from API 20E

Enzymes

@ref	Value	Activity	Ec
68374	alpha-galactosidase	-	3.2.1.22	from API ID32E
68374	alpha-glucosidase	-	3.2.1.20	from API ID32E
68374	alpha-maltosidase	-		from API ID32E
68374	arginine dihydrolase	-	3.5.3.6	from API ID32E
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68374	beta-galactosidase	+	3.2.1.23	from API ID32E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68374	beta-glucosidase	-	3.2.1.21	from API ID32E
68374	beta-glucuronidase	-	3.2.1.31	from API ID32E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68374	L-aspartate arylamidase	-	3.4.11.21	from API ID32E
68374	lipase	-		from API ID32E
68374	lysine decarboxylase	-	4.1.1.18	from API ID32E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68374	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API ID32E
68374	ornithine decarboxylase	+	4.1.1.17	from API ID32E
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68374	urease	-	3.5.1.5	from API ID32E
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
63393	+	-	-	+	-	-	-	-	+	+	-	+	+	-	+	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API ID32E

@ref	ODC	ADH (Arg)	LDC (Lys)	URE	LARL	GAT	5KG	LipaseLIP	Phenol red (Acidification)RP	beta GLU	MAN	MAL	ADO	PLE	beta GUR	MNT	IND	N-Acetyl-beta-Glucosaminidasebeta NAG	beta GAL	GLU	SAC	LARA	DARL	alpha GLU	alpha GAL	TRE	RHA	INO	CEL	SOR	alpha-MaltosidasealphaMAL	L-aspartic acid arylamidaseAspA
63393	+	-	-	-	-	+	-	-	+	-	+	-	-	-	-	-	+	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent
63393	Human	1955	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
34131	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM386409v1 assembly for Escherichia albertii NCTC 9362	complete	GCA_003864095	208962.89	8058404159	208962	98.09

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Escherichia albertii NCTC 9362
NCBI: GCA_003864095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	75.80	no
125439	motility	BacteriaNetⓘ	yes	68.10	no
125439	gram_stain	BacteriaNetⓘ	negative	76.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Escherichia albertii NCTC 9362
NCBI: GCA_003864095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.94	no
125438	anaerobic	anaerobicⓘ	no	97.37	no
125438	aerobic	aerobicⓘ	no	65.45	yes
125438	spore-forming	spore-formingⓘ	no	91.44	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	53.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Genetics	Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California.	Carter MQ, Quinones B, He X, Pham A, Carychao D, Cooley MB, Lo CC, Chain PSG, Lindsey RL, Bono JL.	Microorganisms	10.3390/microorganisms11112803	2023
	PacBio Genome Sequences of Eight Escherichia albertii Strains Isolated from Humans in the United States.	Lindsey RL, Rowe LA, Batra D, Smith P, Strockbine NA.	Microbiol Resour Announc	10.1128/mra.01663-18	2019

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 )
#34131	Collection of Institut Pasteur ; Curators of the CIP; CIP 58.22
#63393	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 67177
#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 .
#68374	Automatically annotated from API ID32E .
#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 boydii (CIP 58.22, NCTC 9362, CCUG 67177)

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

API ID32E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003864095

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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