Eubacterium ramulus (DSM 15684, ATCC 29099, DSM 3995)

Name: Eubacterium ramulus (DSM 15684, ATCC 29099, DSM 3995)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5439

Type strain

Culture col. no. DSM 15684 ATCC 29099 DSM 3995 KCTC 5972 VPI C6-27

NCBI tax ID(s) 1256908 39490

Special Collections DSMZ KCTC

History <- ATCC <- L. V. Holdeman

Links

Eubacterium ramulus DSM 15684 is an anaerobe bacterium that was isolated from human feces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 39352

ATCC 29099,DSM 3995,DSM 15684,VTT E-052782

@ref 20215

Last LPSN update 2026-02-09 11:18:58

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Eubacteriaceae

Genus Eubacterium

Species Eubacterium ramulus

Full scientific name Eubacterium ramulus Moore et al. 1976 (Approved Lists 1980)

BacDive ID	Other strains from **Eubacterium ramulus** (2)	Type strain
5440	E. ramulus WK1, DSM 16296
164024	E. ramulus JCM 31335

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6044	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
6044	SCHAEDLER BROTH (ROTH; 5772) (DSMZ Medium 1669)	Medium recipe at MediaDive	Name: SCHAEDLER BROTH (Roth; 5772) (DSMZ Medium 1669) Composition: Glucose 5.83 g/l Casein peptone 5.66 g/l Yeast extract 5.0 g/l Peptone mixture 5.0 g/l Tris 3.0 g/l NaCl 1.66 g/l Soy peptone 1.0 g/l K2HPO4 0.83 g/l L-Cysteine HCl x H2O 0.4 g/l Hemin 0.01 g/l Resazurin 0.001 g/l Distilled water
6044	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)
6044	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6044	anaerobe
125438	anaerobe	90.328
125439	anaerobe	98.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6044	human feces	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6044	1	Risk group (German 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	ASM46934v1 assembly for Eubacterium ramulus ATCC 29099	scaffold	GCA_000469345	1256908.6	2597490300	1256908	32.3
66792	Eubacterium ramulus ATCC 29099	contig		1256908.3		1256908	31.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Eubacterium ramulus ATCC 29099 16S ribosomal RNA gene, partial sequence	L34623	1474		1256908

GC content

6044

GC-content (mol%)39

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Eubacterium ramulus ATCC 29099
NCBI: GCA_000469345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.30	no
125439	gram_stain	BacteriaNetⓘ	variable	83.30	no
125439	motility	BacteriaNetⓘ	yes	80.90	no
125439	spore_formation	BacteriaNetⓘ	yes	74.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium ramulus ATCC 29099 ATCC 29099
NCBI: GCA_000469345.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	73.51	no
125438	anaerobic	anaerobicⓘ	yes	90.33	yes
125438	aerobic	aerobicⓘ	no	94.23	yes
125438	spore-forming	spore-formingⓘ	no	59.19	no
125438	thermophilic	thermophileⓘ	no	91.60	yes
125438	flagellated	motile2+ⓘ	no	80.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond.	Lordan C, Roche AK, Delsing D, Nauta A, Groeneveld A, MacSharry J, Cotter PD, van Sinderen D.	Microbiol Mol Biol Rev	10.1128/mmbr.00094-23	2024
Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
Metabolism	Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways.	Pichler MJ, Yamada C, Shuoker B, Alvarez-Silva C, Gotoh A, Leth ML, Schoof E, Katoh T, Sakanaka M, Katayama T, Jin C, Karlsson NG, Arumugam M, Fushinobu S, Abou Hachem M.	Nat Commun	10.1038/s41467-020-17075-x	2020
Enzymology	Identification of gut bacteria reductases that biotransform steroid hormones.	Arp G, Jiang AK, Dufault-Thompson K, Levy S, Zhong A, Wassan JT, Grant MR, Li Y, Hall B, Jiang X.	Nat Commun	10.1038/s41467-025-61425-6	2025
	Affinity- and activity-based probes synthesized from structurally diverse hops-derived xanthohumol flavonoids reveal highly varied protein profiling in Escherichia coli.	Webber LC, Anderson LN, Paraiso IL, Metz TO, Bradley R, Stevens JF, Wright AT.	RSC Adv	10.1039/d3ra05296f	2023
	Role of Novel Glucagon-like Peptide-1 Receptor Analogue Polyethylene Glycol Loxenatide in Type 2 Diabetes: A Systematic Review and Meta-analysis.	Dutta D, Chatterjee S, Datta PK, Mohindra R, Sharma M.	Indian J Endocrinol Metab	10.4103/ijem.ijem_162_23	2023
	Bacteroides thetaiotaomicron Starch Utilization Promotes Quercetin Degradation and Butyrate Production by Eubacterium ramulus.	Rodriguez-Castano GP, Dorris MR, Liu X, Bolling BW, Acosta-Gonzalez A, Rey FE.	Front Microbiol	10.3389/fmicb.2019.01145	2019
Metabolism	Chalcone Isomerase from Eubacterium ramulus Catalyzes the Ring Contraction of Flavanonols.	Braune A, Engst W, Elsinghorst PW, Furtmann N, Bajorath J, Gutschow M, Blaut M.	J Bacteriol	10.1128/jb.00490-16	2016
Genetics	O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases.	Labourel A, Parrou JL, Deraison C, Mercier-Bonin M, Lajus S, Potocki-Veronese G.	Essays Biochem	10.1042/ebc20220153	2023
Pathogenicity	Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.	Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L.	PLoS One	10.1371/journal.pone.0009836	2010
Phylogeny	Dominant gut Prevotella copri in gastrectomised non-obese diabetic Goto-Kakizaki rats improves glucose homeostasis through enhanced FXR signalling.	Pean N, Le Lay A, Brial F, Wasserscheid J, Rouch C, Vincent M, Myridakis A, Hedjazi L, Dumas ME, Grundberg E, Lathrop M, Magnan C, Dewar K, Gauguier D.	Diabetologia	10.1007/s00125-020-05122-7	2020
Metabolism	Quantification of the flavonoid-degrading bacterium Eubacterium ramulus in human fecal samples with a species-specific oligonucleotide hybridization probe.	Simmering R, Kleessen B, Blaut M.	Appl Environ Microbiol	10.1128/aem.65.8.3705-3709.1999	1999
	Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism.	Jernberg C, Sullivan A, Edlund C, Jansson JK.	Appl Environ Microbiol	10.1128/aem.71.1.501-506.2005	2005
Phylogeny	Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.	Schwiertz A, Le Blay G, Blaut M.	Appl Environ Microbiol	10.1128/aem.66.1.375-382.2000	2000
Phylogeny	Characterization of an O-desmethylangolensin-producing bacterium isolated from human feces.	Yokoyama S, Niwa T, Osawa T, Suzuki T	Arch Microbiol	10.1007/s00203-009-0524-5	2009
	Polyethylene Glycol Loxenatide Injection (GLP-1) Protects Vascular Endothelial Cell Function in Middle-Aged and Elderly Patients With Type 2 Diabetes by Regulating Gut Microbiota.	Chen F, He L, Li J, Yang S, Zhang B, Zhu D, Wu Z, Zhang S, Hou D, Ouyang C, Yi J, Xiao C, Hou K	Front Mol Biosci	10.3389/fmolb.2022.879294	2022

References

#6044	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15684
#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 )
#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) .
#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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Eubacterium ramulus (DSM 15684, ATCC 29099, DSM 3995)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000469345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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