Enterocloster citroniae (DSM 19261, CCUG 52203, RMA 16102)

Name: Enterocloster citroniae (DSM 19261, CCUG 52203, RMA 16102)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2843

Type strain

Culture col. no. DSM 19261 CCUG 52203 RMA 16102 ATCC BAA-1317

NCBI tax ID(s) 358743

Special Collections DSMZ CCUG

History <- CCUG <- D. M. Citron; RMA 16102

Links

Enterocloster citroniae DSM 19261 is an anaerobe, mesophilic prokaryote that was isolated from human.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 303344

ATCC BAA-1317,DSM 19261,CCUG 52203

@ref 20215

Last LPSN update 2025-12-16 09:47:24

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Enterocloster

Species Enterocloster citroniae

Full scientific name Enterocloster citroniae (Warren et al. 2007) Haas and Blanchard 2020

Synonyms (1)

Clostridium citroniae

BacDive ID	Other strains from **Enterocloster citroniae** (2)	Type strain
2684	E. citroniae FS41, DSM 6877
159538	E. citroniae H2_21, DSM 108162

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7910	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7910	positive	growth	37	mesophilic
59463	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7910	anaerobe
59463	anaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68367	17057 ChEBI	cellobiose	+	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	+	builds acid from	from API 20A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	+	builds acid from	from API 20A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	+	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	+	builds acid from	from API 20A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68367	catalase	+	1.11.1.6	from API 20A
68367	gelatinase	-		from API 20A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
7910	-	-	+	+	+	+	+	+	+	+	-	-	-	+	+	+	+	+	+	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
7910	human	California	USA	USA	North America	36.7783	-119.418 36.7783/-119.418
59463	Human peritoneal fluid

Taxonmaps

69479

Global distribution of 16S sequence DQ279737 (>99% sequence identity) for Enterocloster citroniae subclade from Microbeatlas

Aquatic Samples	226
Soil Samples	37
Animal Samples	25228
Plant Samples	46
Total Samples	25537

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7910	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
124043	ASM4054545v1 assembly for Enterocloster citroniae DSM 19261	contig	GCA_040545455	2928404274	358743	62.34

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Clostridium citroniae strain DSM 19261 16S ribosomal RNA gene, partial sequence	HM245936	839		358743
7910	Clostridium citroniae strain RMA 16102 16S ribosomal RNA gene, partial sequence	DQ279737	1420		358743

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.	Ai X, Huang C, Liu Q, Duan R, Ma X, Li L, Shu Z, Miao Y, Shen H, Lv Y, Jiang Z, Luo H, Long Z.	Front Microbiol	10.3389/fmicb.2025.1629811	2025
	Human Herpesvirus-6B Infection and Alterations of Gut Microbiome in Patients with Fibromyalgia: A Pilot Study.	Ievina L, Fomins N, Gudra D, Kenina V, Vilmane A, Gravelsina S, Rasa-Dzelzkaleja S, Murovska M, Fridmanis D, Nora-Krukle Z.	Biomolecules	10.3390/biom14101291	2024
Metabolism	NMR Spectroscopic Identification of Urolithin G, a Novel Trihydroxy Urolithin Produced by Human Intestinal Enterocloster Species.	Beltran D, Frutos-Lison MD, Garcia-Villalba R, Yuste JE, Garcia V, Espin JC, Selma MV, Tomas-Barberan FA.	J Agric Food Chem	10.1021/acs.jafc.3c01675	2023
Phylogeny	Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa.	Haas KN, Blanchard JL.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003698	2020
Pathogenicity	Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut.	Levy S, Jiang AK, Grant MR, Arp G, Minabou Ndjite G, Jiang X, Hall B.	Nat Commun	10.1038/s41467-025-56332-9	2025
Metabolism	Gut Bacteria Involved in Ellagic Acid Metabolism To Yield Human Urolithin Metabotypes Revealed.	Iglesias-Aguirre CE, Garcia-Villalba R, Beltran D, Frutos-Lison MD, Espin JC, Tomas-Barberan FA, Selma MV.	J Agric Food Chem	10.1021/acs.jafc.2c08889	2023
	Clinical evidence of the link between gut microbiome and myalgic encephalomyelitis/chronic fatigue syndrome: a retrospective review.	Wang JH, Choi Y, Lee JS, Hwang SJ, Gu J, Son CG.	Eur J Med Res	10.1186/s40001-024-01747-1	2024
	Increased fecal ethanol and enriched ethanol-producing gut bacteria Limosilactobacillus fermentum, Enterocloster bolteae, Mediterraneibacter gnavus and Streptococcus mutans in nonalcoholic steatohepatitis.	Mbaye B, Magdy Wasfy R, Borentain P, Tidjani Alou M, Mottola G, Bossi V, Caputo A, Gerolami R, Million M.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1279354	2023
Metabolism	Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.	Krasenbrink J, Hanson BT, Weiss AS, Borusak S, Tanabe TS, Lang M, Aichinger G, Hausmann B, Berry D, Richter A, Marko D, Mussmann M, Schleheck D, Stecher B, Loy A.	Microbiome	10.1186/s40168-025-02175-x	2025
Pathogenicity	Gut microbiota composition is altered in postural orthostatic tachycardia syndrome and post-acute COVID-19 syndrome.	Hamrefors V, Kahn F, Holmqvist M, Carlson K, Varjus R, Gudjonsson A, Fedorowski A, Ohlsson B.	Sci Rep	10.1038/s41598-024-53784-9	2024
	Baseline gut microbiota and metabolome predict durable immunogenicity to SARS-CoV-2 vaccines.	Peng Y, Zhang L, Mok CKP, Ching JYL, Zhao S, Wong MKL, Zhu J, Chen C, Wang S, Yan S, Qin B, Liu Y, Zhang X, Cheung CP, Cheong PK, Ip KL, Fung ACH, Wong KKY, Hui DSC, Chan FKL, Ng SC, Tun HM.	Signal Transduct Target Ther	10.1038/s41392-023-01629-8	2023
Metabolism	Bioactive small molecules produced by the human gut microbiome modulate Vibrio cholerae sessile and planktonic lifestyles.	Pauer H, Teixeira FL, Robinson AV, Parente TE, De Melo MAF, Lobo LA, Domingues RMCP, Allen-Vercoe E, Ferreira RBR, Antunes LCM.	Gut Microbes	10.1080/19490976.2021.1918993	2021
Pathogenicity	Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo.	Burckhardt JC, Chong DHY, Pett N, Tropini C.	Microbiome	10.1186/s40168-023-01496-z	2023
	An online atlas of human plasma metabolite signatures of gut microbiome composition.	Dekkers KF, Sayols-Baixeras S, Baldanzi G, Nowak C, Hammar U, Nguyen D, Varotsis G, Brunkwall L, Nielsen N, Eklund AC, Bak Holm J, Nielsen HB, Ottosson F, Lin YT, Ahmad S, Lind L, Sundstrom J, Engstrom G, Smith JG, Arnlov J, Orho-Melander M, Fall T.	Nat Commun	10.1038/s41467-022-33050-0	2022
Phylogeny	Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. isolated from human clinical infections.	Warren YA, Tyrrell KL, Citron DM, Goldstein EJ	J Clin Microbiol	10.1128/JCM.00116-06	2006

References

#7910	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19261
#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 )
#59463	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52203
#68367	Automatically annotated from API 20A .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Enterocloster citroniae (DSM 19261, CCUG 52203, RMA 16102)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_040545455

16S sequences

Genome-based predictions

Literature

Literature

References

BacDive

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