Citrobacter werkmanii (DSM 17579, ATCC 51114, CDC 876-58)

Name: Citrobacter werkmanii (DSM 17579, ATCC 51114, CDC 876-58)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4342

Type strain

Strain Designation 876-58, 83I

Culture col. no. DSM 17579 ATCC 51114 CDC 876-58 CIP 104555 CCUG 30793 2 more

NCBI tax ID(s) 67827

Special Collections DSMZ CCUG CIP

History DSMZ <- CIP <- P. A. D. Grimont, Institut Pasteur, Paris <- CDC <- Ohio State Health Dept. CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 876-58 <- Ohio State Hlth. Dept.: strain 83I

Links

Citrobacter werkmanii 876-58 is an aerobe, Gram-negative, motile bacterium that was isolated from human blood.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42810

NBRC 105721,ATCC 51114,CCUG 30793,CIP 104555,DSM 17579,CNCTC 5067

@ref 20215

Last LPSN update 2026-05-29 08:25:54

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Citrobacter

Species Citrobacter werkmanii

Full scientific name Citrobacter werkmanii Brenner et al. 1993

BacDive ID	Other strains from **Citrobacter werkmanii** (3)	Type strain
137174	C. werkmanii 3323-75, CIP 104928
137345	C. werkmanii 2444-78, 884-6426, CIP 105012, ATCC 51636
174324	C. werkmanii CIP 111301

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
123945	negative	rod-shaped
125438	negative			99.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7066	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
39042	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
123945	CIP Medium 3	Medium recipe at CIP
123945	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7066	positive	growth	30
39042	positive	growth	30
50273	positive	growth	37
123945	positive	growth	30
123945	negative	growth	5
123945	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7066	aerobe
123945	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.745

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
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
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
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
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
123945	17234 ChEBI	glucose	+	fermentation
123945	17234 ChEBI	glucose	+	degradation
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
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
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
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
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68371	17266 ChEBI	L-sorbose	+	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
123945	17716 ChEBI	lactose	-	fermentation
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
123945	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
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
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
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
123945	17632 ChEBI	nitrate	+	reduction
123945	16301 ChEBI	nitrite	+	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371	0 ChEBI	Potassium 2-ketogluconate	+	builds acid from	from API 50CH acid
68371	0 ChEBI	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
123945	132112 ChEBI	sodium thiosulfate	+	builds gas from
68368	30911 ChEBI	sorbitol	+	fermentation	from API 20E
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
123945	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
123945	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
123945	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	+			from API 20E
123945	17234 ChEBI	glucose		+
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	+	3.2.1.23	from API zym
123945	beta-galactosidase	+	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123945	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
123945	gelatinase	-
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
123945	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
123945	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
123945	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

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
7066	+	+	-	-	+	+	-	-	-	+	-	+	+	-	+	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
123945	-	+	+	-	-	+	+	+	+	-	+	+	-	+	-	+	-	-	-	-

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
123945	not determinedn.d.	+	-	+	+	+	+	-	-	-	+	+	+	+	+	+	-	-	+	+	-	-	+	-	+/-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	+	-	+/-	-	-	+	-	-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
7066	human blood	Homo sapiens	Ohio	USA	USA	North America
50273	Human blood	Homo sapiens
123945	Human, Blood	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AF025373 (>99% sequence identity) for Citrobacter from Microbeatlas

Aquatic Samples	7413
Soil Samples	3252
Animal Samples	52478
Plant Samples	2947
Total Samples	66090

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7066	2	Risk group (German classification) According to TRBA 466
123945	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	Citrobacter werkmanii strain FDAARGOS_1524	complete		67827.86	67827	98.21
66792	Citrobacter werkmanii strain FDAARGOS_1524	complete		67827.80	67827	98.21
124043	ASM2034149v1 assembly for Citrobacter werkmanii FDAARGOS_1524	chromosome	GCA_020341495	67827.74	67827	87.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7066	Citrobacter werkmanii 16S ribosomal RNA gene, partial sequence	AF025373	1521		67827
124043	Citrobacter werkmanii strain CIP 104555 16S ribosomal RNA gene, partial sequence.	KM515974	1386		67827

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Citrobacter werkmanii strain FDAARGOS_1524
BV-BRC: 67827.86

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.51	no
125439	gram_stain	BacteriaNetⓘ	negative	89.41	no
125439	motility	BacteriaNetⓘ	yes	59.43	no
125439	spore_formation	BacteriaNetⓘ	no	95.75	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Citrobacter werkmanii strain FDAARGOS_1524 strain Not applicable
PATRIC: 67827.86

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	97.09	yes
125438	spore-forming	spore-formingⓘ	no	88.13	no
125438	aerobic	aerobicⓘ	no	73.54	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	73.52	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Bacteria from gut microbiota associated with diarrheal infections in children promote virulence of Shiga toxin-producing and enteroaggregative Escherichia coli pathotypes.	Izquierdo M, Lopez J, Gallardo P, Vidal RM, Ossa JC, Farfan MJ.	Front Cell Infect Microbiol	10.3389/fcimb.2022.867205	2022
	Genetically Engineered Strains: Application and Advances for 1,3-Propanediol Production from Glycerol.	Yang M, Yun J, Zhang H, Magocha TA, Zabed H, Xue Y, Fokum E, Sun W, Qi X, Qi X.	Food Technol Biotechnol	10.17113/ftb.56.01.18.5444	2018
	Natural peptides and their synthetic congeners acting against Acinetobacter baumannii through the membrane and cell wall: latest progress.	Kumar G.	RSC Med Chem	10.1039/d4md00745j	2025
	Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants.	Yu B, Roy Choudhury M, Yang X, Benoit SL, Womack E, Van Mouwerik Lyles K, Acharya A, Kumar A, Yang C, Pavlova A, Zhu M, Yuan Z, Gumbart JC, Boykin DW, Maier RJ, Eichenbaum Z, Wang B.	ACS Infect Dis	10.1021/acsinfecdis.2c00121	2022
Enzymology	Molecular method for detection of total coliforms in drinking water samples.	Maheux AF, Boudreau DK, Bisson MA, Dion-Dupont V, Bouchard S, Nkuranga M, Bergeron MG, Rodriguez MJ.	Appl Environ Microbiol	10.1128/aem.00546-14	2014
Enzymology	Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples.	Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG.	Appl Environ Microbiol	10.1128/aem.02337-10	2011
Metabolism	1,3-propanediol production with Citrobacter werkmanii DSM17579: effect of a dhaD knock-out.	Maervoet VE, De Maeseneire SL, Avci FG, Beauprez J, Soetaert WK, De Mey M	Microb Cell Fact	10.1186/1475-2859-13-70	2014
Metabolism	Unraveling the dha cluster in Citrobacter werkmanii: comparative genomic analysis of bacterial 1,3-propanediol biosynthesis clusters.	Maervoet VE, De Maeseneire SL, Soetaert WK, De Mey M	Bioprocess Biosyst Eng	10.1007/s00449-013-1041-0	2013

References

#7066	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17579
#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 )
#39042	; Curators of the CIP;
#50273	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30793
#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 .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#123945	Collection of Institut Pasteur ; Curators of the CIP; CIP 104555
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Citrobacter werkmanii (DSM 17579, ATCC 51114, CDC 876-58)

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 20E

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_020341495

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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