Name: Citrobacter werkmanii 876-58
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4342

Type strain:

Species: Citrobacter werkmanii

Strain Designation: 876-58, 83I

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

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

NCBI tax ID(s): 67827 (species)

SI-ID 42810

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

Other strains from Citrobacter werkmanii

C. werkmanii 3323-75, CIP 104928
C. werkmanii 2444-78, 884-6426, CIP 105012, ...
C. werkmanii CIP 111301

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Citrobacter*
	Species	**Citrobacter werkmanii**
	Full Scientific Name (LPSN)	Citrobacter werkmanii Brenner et al. 1993

Information on morphological and physiological properties Morphology

[Ref.: #123945]	Gram stain	negative

[Ref.: #123945]	Cell shape	rod-shaped

[Ref.: #123945]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7066]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #7066]

Culture medium growth

[Ref.: #7066]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7066]

Culture medium composition

expand / minimize

[Ref.: #39042]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #39042]

Culture medium growth

[Ref.: #39042]

Culture medium composition

expand / minimize

[Ref.: #123945]

Culture medium

CIP Medium 3

[Ref.: #123945]

Culture medium growth

[Ref.: #123945]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #123945]

Culture medium

CIP Medium 72

[Ref.: #123945]

Culture medium growth

[Ref.: #123945]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7066]		growth	30 °C
[Ref.: #39042]		growth	30 °C
[Ref.: #50273]		growth	37 °C
[Ref.: #123945]		growth	30 °C
[Ref.: #123945]	no	growth	5 °C
[Ref.: #123945]	no	growth	10 °C

[Ref.: #7066]	Temperature range	mesophilic
[Ref.: #39042]	Temperature range	mesophilic
[Ref.: #50273]	Temperature range	mesophilic
[Ref.: #123945]	Temperature range	mesophilic
[Ref.: #123945]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7066]	Oxygen tolerance	aerobe
[Ref.: #123945]	Oxygen tolerance	facultative anaerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68371]	D-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #123945]	glucose ChEBI	+	fermentation
[Ref.: #123945]	glucose ChEBI	+	degradation
[Ref.: #68371]	glycerol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68371]	L-sorbose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #123945]	lactose ChEBI	-	fermentation
[Ref.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #123945]	mannitol ChEBI	+	fermentation
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #123945]	nitrate ChEBI	+	reduction
[Ref.: #123945]	nitrite ChEBI	+	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #123945]	sodium thiosulfate ChEBI	+	builds gas from
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #123945]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite	Production
[Ref.: #123945]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	yes	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #123945]	acetoin ChEBI	-
[Ref.: #123945]	glucose ChEBI		+
[Ref.: #68368]	acetoin ChEBI	+			* from API 20E
[Ref.: #68368]	indole ChEBI			-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #123945]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123945]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #123945]	gelatinase	-
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #123945]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #123945]	tryptophan deaminase	-
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #123945]	urease	-	3.5.1.5
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #7066]	16756	+	+	-	-	+	+	-	-	-	+	-	+	+	-	+	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #123945]	9653	not determinedn.d.	+	-	+	+	+	+	-	-	-	+	+	+	+	+	+	-	-	+	+	-	-	+	-	+/-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	+	-	+/-	-	-	+	-	-	+	+	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123945]	8036	-	+	+	-	-	+	+	+	+	-	+	+	-	+	-	+	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7066]	Sample type/isolated from	human blood
[Ref.: #7066]	Geographic location (country and/or sea, region)	Ohio
[Ref.: #7066]	Country	USA
[Ref.: #7066]	Country ISO 3 Code	USA
[Ref.: #7066]	Continent	North America

[Ref.: #50273]	Sample type/isolated from	Human blood

[Ref.: #123945]	Sample type/isolated from	Human, Blood
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Fluids	#Blood

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7066]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #123945]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7066]	Citrobacter werkmanii 16S ribosomal RNA gene, partial sequence	AF025373	1521	ENA	67827 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Citrobacter werkmanii strain FDAARGOS_1524	67827.86	complete	PATRIC	67827 tax ID	*
[Ref.: #66792]	Citrobacter werkmanii strain FDAARGOS_1524	67827.74	complete	PATRIC	67827 tax ID	*
[Ref.: #66792]	Citrobacter werkmanii strain FDAARGOS_1524	67827.80	complete	PATRIC	67827 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Citrobacter werkmanii strain FDAARGOS_1524 strain Not applicable PATRIC: 67827.86
[Ref.: #69480]	gram-positive	no	98.37	no
[Ref.: #69480]	anaerobic	no	94.097	yes
[Ref.: #69480]	halophile	no	91.103	no
[Ref.: #69480]	spore-forming	no	93.259	no
[Ref.: #69480]	glucose-util	yes	95.202	no
[Ref.: #69480]	thermophile	no	99.443	no
[Ref.: #69480]	flagellated	yes	51.284	no
[Ref.: #69480]	motile	yes	89.184	no
[Ref.: #69480]	aerobic	yes	79.651	yes
[Ref.: #69480]	glucose-ferment	yes	94.713	yes

Availability in culture collections External links

[Ref.: #7066]

Culture collection no.

DSM 17579, ATCC 51114, CDC 876-58, CIP 104555, CCUG 30793

[Ref.: #73834]

SI-ID 42810

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#73834

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID42810.1 )

#123945 Collection of Institut Pasteur ; Curators of the CIP; CIP 104555
* These data were automatically processed and therefore are not curated

Change proposal

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Search for species Citrobacter werkmanii in external resources:
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Citrobacter werkmanii strain FDAARGOS_1524 strain Not applicable

Change proposal

Change proposal