Citrobacter youngae (CCUG 30791, DSM 17578, ATCC 29935)

Name: Citrobacter youngae (CCUG 30791, DSM 17578, ATCC 29935)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4341

Type strain

Strain Designation 460-61

Culture col. no. CCUG 30791 DSM 17578 ATCC 29935 CDC 460-61 CECT 5335 2 more

NCBI tax ID(s) 133448

Special Collections DSMZ CCUG CIP

Links

Citrobacter youngae 460-61 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from meat scraps.

Gram-negative motile rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 1753

LMG 3252,NCTC 13709,ATCC 29935,CCUG 30791,CIP 105016,CECT 5335,DSM 17578,CNCTC 5038

@ref 20215

Last LPSN update 2025-12-16 09:47:47

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Citrobacter

Species Citrobacter youngae

Full scientific name Citrobacter youngae Brenner et al. 1993

BacDive ID	Other strains from **Citrobacter youngae** (12)	Type strain
134636	C. youngae CIP 55.6
134638	C. youngae 5131/51, CIP 55.8
134640	C. youngae CIP 55.11
134644	C. youngae Mich 7, CIP 55.10
136124	C. youngae CIP 55.16
136128	C. youngae 3038, CIP 55.18
136360	C. youngae 3062-62, CIP 104931
136364	C. youngae 5118-60, CIP 104959
136630	C. youngae Mich I, CIP 55.3
136634	C. youngae Md 1, CIP 55.7
136643	C. youngae Na 4, CIP 55.12
136655	C. youngae CIP 55.17

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
124017	negative	rod-shaped
125438	negative		100
125439	negative		97.3

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7065	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
36441	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
124017	CIP Medium 3	Medium recipe at CIP
124017	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7065	positive	growth	30	mesophilic
36441	positive	growth	30	mesophilic
50271	positive	growth	37	mesophilic
124017	positive	growth	5-41

Physiology and metabolism

Oxygen tolerance

124017

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
124017	16947 ChEBI	citrate	+	carbon source
124017	17234 ChEBI	glucose	+	degradation
124017	17716 ChEBI	lactose	-	fermentation
124017	15792 ChEBI	malonate	-	assimilation
124017	29864 ChEBI	mannitol	+	fermentation
124017	17632 ChEBI	nitrate	+	reduction
124017	16301 ChEBI	nitrite	+	reduction
124017	132112 ChEBI	sodium thiosulfate	+	builds gas from

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
124017	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
124017	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
124017	15688 ChEBI	acetoin	-
124017	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
124017	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
124017	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
124017	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
124017	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
124017	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
124017	ornithine decarboxylase	-	4.1.1.17
124017	oxidase	-
124017	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
124017	tryptophan deaminase	-
124017	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
124017	-	+	+	+	-	+	+	-	+	-	+	+	-	+	-	+	+	-	-	-

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
124017	not determinedn.d.	+	+	+	+	+	+	-	-	-	+	+	-	-	+	-	-	+	+	-	+	+	+	-	+	+	-	-	-	-	+	-	+	-	+	-	-	+	-	-	+	-	-	-	+	+	-	-	+	+	+	+	-	-	+	+	+	+	+	-	+	+	-	-	-	-	-	-	-	+	+	-	-	-	+	-	+	-	-	-	+	+	-	+	+	-	-	+	-	+	+	+	+	+	+	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Meat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7065	meat scraps	South Carolina	USA	USA	North America
50271	Meat scraps	South Carolina	USA	USA	North America
124017	Food, Meat scraps	South Carolina	United States of America	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7065	2	Risk group (German classification) According to TRBA 466
124017	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM381811v1 assembly for Citrobacter youngae CCUG 30791	contig	GCA_003818115	133448.7	2903312461	133448	67.72

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Citrobacter freundii 16S ribosomal RNA	M59291	1490	546
7065	Citrobacter youngae partial 16S rRNA gene, strain CECT 5335	AJ564736	948	133448
124043	Citrobacter youngae strain CIP 105016 16S ribosomal RNA gene, partial sequence.	KM515975	1368	133448

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Citrobacter youngae CCUG 30791
NCBI: GCA_003818115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	yes	76.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Citrobacter youngae strain CCUG 30791
PATRIC: 133448.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	94.30	yes
125438	spore-forming	spore-formingⓘ	no	87.65	no
125438	aerobic	aerobicⓘ	no	76.78	yes
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	79.66	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification and Genome Analysis of an Arsenic-Metabolizing Strain of Citrobacter youngae IITK SM2 in Middle Indo-Gangetic Plain Groundwater.	Verma A, Murugan PA, Chinnasamy HV, Singh A, Matheshwaran S.	Biomed Res Int	10.1155/2022/6384742	2022
Phylogeny	MALDI-TOF MS Is an Effective Technique To Classify Specific Microbiota.	Chen L, Gao W, Tan X, Han Y, Jiao F, Feng B, Xie J, Li B, Zhao H, Tu H, Yu S, Wang L.	Microbiol Spectr	10.1128/spectrum.00307-23	2023
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
Phylogeny	Biochemical identification of citrobacteria in the clinical laboratory.	Janda JM, Abbott SL, Cheung WK, Hanson DF.	J Clin Microbiol	10.1128/jcm.32.8.1850-1854.1994	1994
Pathogenicity	A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks.	Molina F, Simancas A, Ramirez M, Tabla R, Roa I, Rebollo JE.	Front Microbiol	10.3389/fmicb.2021.564532	2021
Phylogeny	Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.	Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C, Brisse S	Int J Syst Evol Microbiol	10.1099/ijs.0.000122	2015

References

#7065	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17578
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#36441	; Curators of the CIP;
#50271	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30791
#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) .
#68382	Automatically annotated from API zym .
#124017	Collection of Institut Pasteur ; Curators of the CIP; CIP 105016
#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 youngae (CCUG 30791, DSM 17578, ATCC 29935)

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 biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003818115

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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