Bifidobacterium ruminantium (DSM 6489, ATCC 49390, CCUG 34975)

Name: Bifidobacterium ruminantium (DSM 6489, ATCC 49390, CCUG 34975)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1723

Type strain

Strain Designation Ru687

Culture col. no. DSM 6489 ATCC 49390 CCUG 34975 Ru687 JCM 8222 4 more

NCBI tax ID(s) 1410647 78346

Special Collections DSMZ CCUG JCM KCTC Literature strains

History DSMZ <- B. Biavati, Ru687 JCM <-- B. Biavati Ru687.

Links

Bifidobacterium ruminantium Ru687 is an anaerobe, Gram-positive, rod-shaped bacterium that forms irregular colonies and was isolated from rumen of cattle.

Gram-positive rod-shaped colony-forming anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 7859

LMG 12588,ATCC 49390,CCUG 34975,DSM 6489,JCM 8222,KCTC 3425,AS 1.2241,LMG 21811,CGMCC 1.2241,VTT E-052848

@ref 20215

Last LPSN update 2026-05-29 08:25:19

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium ruminantium

Full scientific name Bifidobacterium ruminantium Biavati and Mattarelli 1991

BacDive ID	Other strains from **Bifidobacterium ruminantium** (5)	Type strain
1724	B. ruminantium Ru679, DSM 6490
1725	B. ruminantium Ru666, DSM 6491
164728	B. ruminantium JCM 34114
165773	B. ruminantium JCM 8221, LMG 18895
165802	B. ruminantium JCM 8509, LMG 18896

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Motility	Confidence
23364	positive	3.0-6.0 µm	rod-shaped
125438					93.5

Colony morphology

@ref	Colony color	Colony shape	Medium used
23364	cream to white	irregular	Trypticase-Phytone-yeast extract agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2694	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)		Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water
23364	Trypticase-Phytone-yeast extract agar

Culture temp

@ref	Growth	Type	Temperature (°C)
2694	positive	growth	37
23364	negative	growth	25
23364	negative	growth	45
23364	positive	optimum	38-42
52427	positive	growth	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
23364	positive	optimum	6.5-6.9
23364		growth	4.5
23364		growth	8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2694	anaerobe
23364	anaerobe
52427	anaerobe
125439	facultative anaerobe	91.897

Spore formation

@ref	Spore formation	Confidence
23364
125439		97.872

Murein

@ref	Murein short key	Type
2694	A11.21	A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala₂

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
23364	22599 ChEBI	arabinose	-	fermentation
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
23364	17057 ChEBI	cellobiose	-	builds acid from
23364	17057 ChEBI	cellobiose	-	fermentation
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
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
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
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
23364	23652 ChEBI	dextrin	+	fermentation
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
23364	28757 ChEBI	fructose	+	fermentation
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
23364	28260 ChEBI	galactose	+	fermentation
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
23364	24265 ChEBI	gluconate	-	builds acid from
23364	24265 ChEBI	gluconate	-	fermentation
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
23364	17234 ChEBI	glucose	+	fermentation
23364	17754 ChEBI	glycerol	-	fermentation
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
23364	35581 ChEBI	indole	-
23364	15443 ChEBI	inulin	-	builds acid from
23364	15443 ChEBI	inulin	-	fermentation
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
23364	30849 ChEBI	L-arabinose	-	builds acid from
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
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
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
23364	24996 ChEBI	lactate	-	fermentation
23364	17716 ChEBI	lactose	+	fermentation
23364	17306 ChEBI	maltose	+	fermentation
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
23364	29864 ChEBI	mannitol	+	builds acid from
23364	29864 ChEBI	mannitol	+	fermentation
23364	37684 ChEBI	mannose	-	fermentation
23364	6731 ChEBI	melezitose	-	builds acid from
23364	6731 ChEBI	melezitose	-	fermentation
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
23364	28053 ChEBI	melibiose	+	fermentation
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
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
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
23364	17632 ChEBI	nitrate	-	reduction
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
23364	17272 ChEBI	propionate	-
23364	16634 ChEBI	raffinose	+	fermentation
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
23364	26546 ChEBI	rhamnose	-	fermentation
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
23364	33942 ChEBI	ribose	+	builds acid from
23364	33942 ChEBI	ribose	+	fermentation
23364	17814 ChEBI	salicin	+/-	builds acid from
23364	17814 ChEBI	salicin	+/-	fermentation
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
23364	30911 ChEBI	sorbitol	-	fermentation
23364	28017 ChEBI	starch	+	fermentation
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
23364	17992 ChEBI	sucrose	+	fermentation
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
23364	27082 ChEBI	trehalose	-	fermentation
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
23364	18222 ChEBI	xylose	-	builds acid from
23364	18222 ChEBI	xylose	-	fermentation

Fatty acid profile

Metadata FA analysis

@ref

52427

Fatty acid	Percentage	ECL
C16:0	25.1	16
C17:0 2OH	24.8	18.249
C18:1 ω9c	19.7	17.769
C14:0	6.5	14
C18:0	4.5	18
C18:2 ω6,9c/C18:0 ANTE	4.4	17.724
C17:1 ω9c	3.9	16.773
C12:0	2.7	12
C13:0 3OH/C15:1 i I/H	2.2	14.469
C17:0 iso 3OH	1.8	18.161
C16:1 ω9c	1.7	15.774
C17:1 ISO I/C16:0 DMA	0.8	16.481
C16:1 ω7c	0.8	15.819
C10:0	0.7	10
Unidentified	0.4	12.472

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
2694	-	-	-	-	-	+	-	-	-	-	+	+	+	-	-	-	-	-	+	-	-	+	-	-	+	+	+	-	+	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-
2694	-	-	-	-	-	+	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen

Isolation

@ref	Sample type
2694	rumen of cattle
52427	Cattle rumen
67770	Bovine rumen

Taxonmaps

69479

Global distribution of 16S sequence LC071848 (>99% sequence identity) for Bifidobacterium ruminantium from Microbeatlas

Aquatic Samples	1061
Soil Samples	311
Animal Samples	57912
Plant Samples	140
Total Samples	59424

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2694	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
67770	Bifrum assembly for Bifidobacterium ruminantium LMG 21811	contig	GCA_000741365	78346.3	2597490258	78346	74.87
67770	ASM68763v1 assembly for Bifidobacterium ruminantium DSM 6489	contig	GCA_000687635	1410647.3	2558860117	1410647	71.01
67770	DSM-6489 assembly for Bifidobacterium ruminantium DSM 6489	contig	GCA_000770925	1410647.4	2657244954	1410647	66.41

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bifidobacterium ruminantium strain DSM 6489 16S ribosomal RNA gene, partial sequence	GQ438820	358	78346
20218	Bifidobacterium ruminantium strain DSM 6489 16S ribosomal RNA gene, partial sequence	GQ487644	154	78346
20218	Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222	AB116347	477	78346
20218	Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222	AB507151	796	78346
20218	Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222	D86197	1437	78346
20218	Bifidobacterium ruminantium strain JCM 8222 16S ribosomal RNA gene, partial sequence	GQ227715	317	78346
20218	Bifidobacterium ruminantium strain KCTC 3425 16S ribosomal RNA gene, partial sequence	GU361831	1480	78346
67770	Bifidobacterium ruminantium gene for 16S ribosomal RNA, partial sequence, strain: JCM 8222	LC071848	1398	78346

GC content

@ref	GC-content (mol%)	Method
2694	57.0	thermal denaturation, midpoint method (Tm)
23364	57.0	Thermal denaturation, fluorometry
67770	57	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifrum assembly for Bifidobacterium ruminantium LMG 21811
BV-BRC: 78346.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.90	no
125439	gram_stain	BacteriaNetⓘ	variable	50.66	no
125439	motility	BacteriaNetⓘ	no	79.13	no
125439	spore_formation	BacteriaNetⓘ	no	97.87	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium ruminantium DSM 6489
PATRIC: 1410647.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.66	yes
125438	anaerobic	anaerobicⓘ	yes	84.86	yes
125438	spore-forming	spore-formingⓘ	no	89.07	yes
125438	thermophilic	thermophileⓘ	no	94.57	yes
125438	aerobic	aerobicⓘ	no	91.62	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains.	Kurata T, Saha CK, Buttress JA, Mets T, Brodiazhenko T, Turnbull KJ, Awoyomi OF, Oliveira SRA, Jimmy S, Ernits K, Delannoy M, Persson K, Tenson T, Strahl H, Hauryliuk V, Atkinson GC.	Proc Natl Acad Sci U S A	10.1073/pnas.2102212119	2022
Phylogeny	Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment.	Baffoni L, Stenico V, Strahsburger E, Gaggia F, Di Gioia D, Modesto M, Mattarelli P, Biavati B.	BMC Microbiol	10.1186/1471-2180-13-149	2013
Metabolism	Diversity, ecology and intestinal function of bifidobacteria.	Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M.	Microb Cell Fact	10.1186/1475-2859-13-s1-s4	2014
Genetics	Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle.	Hernandez-Sanabria E, Goonewardene LA, Wang Z, Durunna ON, Moore SS, Guan LL.	Appl Environ Microbiol	10.1128/aem.05114-11	2012
Metabolism	Influence of sire breed on the interplay among rumen microbial populations inhabiting the rumen liquid of the progeny in beef cattle.	Hernandez-Sanabria E, Goonewardene LA, Wang Z, Zhou M, Moore SS, Guan LL.	PLoS One	10.1371/journal.pone.0058461	2013
Phylogeny	Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits.	Hernandez-Sanabria E, Guan LL, Goonewardene LA, Li M, Mujibi DF, Stothard P, Moore SS, Leon-Quintero MC.	Appl Environ Microbiol	10.1128/aem.01052-10	2010
Phylogeny	Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.	Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C, Viappiani A, Mancabelli L, Mangifesta M, Taminiau B, Delcenserie V, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02004-14	2014
Phylogeny	Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.	Brandt K, Barrangou R.	Front Microbiol	10.3389/fmicb.2016.00657	2016
Phylogeny	Bifidobacterium faecale sp. nov., isolated from human faeces.	Choi JH, Lee KM, Lee MK, Cha CJ, Kim GB	Int J Syst Evol Microbiol	10.1099/ijs.0.063479-0	2014
Phylogeny	Bifidobacterium stercoris sp. nov., isolated from human faeces.	Kim MS, Roh SW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.019943-0	2010
Phylogeny	Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle.	Biavati B, Mattarelli P	Int J Syst Bacteriol	10.1099/00207713-41-1-163	1991

References

#2694	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6489
#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 )
#23364	B. BIAVATI, P. MATTARELLI: Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the Rumens of Cattle. IJSEM 41: 163 - 168 1991 ( DOI 10.1099/00207713-41-1-163 , PubMed 1995032 )
#52427	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 34975
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#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 )

Rate our new design

Content

About us

Bifidobacterium ruminantium (DSM 6489, ATCC 49390, CCUG 34975)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Metabolite utilization

Fatty acid profile

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000741365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media