Name: Bifidobacterium ruminantium Ru687
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1723

Type strain:

Species: Bifidobacterium ruminantium

Strain Designation: Ru687

Culture col. no.: DSM 6489, ATCC 49390, CCUG 34975, JCM 8222, CGMCC 1.2241, KCTC 3425, LMG 12588, LMG 21811

Strain history: B. Biavati Ru687.

NCBI tax ID(s): 1410647 (strain), 78346 (species)

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

Special Collections

Other strains from Bifidobacterium ruminantium

Section

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

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Bifidobacteriales*
	Family	*Bifidobacteriaceae*
	Genus	*Bifidobacterium*
	Species	**Bifidobacterium ruminantium**
	Full Scientific Name (LPSN)	Bifidobacterium ruminantium Biavati and Mattarelli 1991

Information on morphological and physiological properties Morphology

[Ref.: #23364]	Gram stain	positive

[Ref.: #23364]	Cell length	3.0-6.0 µm

[Ref.: #23364]	Cell shape	rod-shaped

[Ref.: #23364]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.5

[Ref.: #23364]	Colony color	cream to white
[Ref.: #23364]	Colony shape	irregular
[Ref.: #23364]	Cultivation medium used	Trypticase-Phytone-yeast extract agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2694]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #2694]

Culture medium growth

[Ref.: #2694]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2694]

Culture medium composition

expand / minimize

[Ref.: #23364]

Culture medium

Trypticase-Phytone-yeast extract agar

[Ref.: #23364]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #2694]		growth	37 °C
[Ref.: #23364]	no	growth	25 °C
[Ref.: #23364]	no	growth	45 °C
[Ref.: #23364]		optimum	38-42 °C
[Ref.: #52427]		growth	37 °C
[Ref.: #67770]		growth	37 °C

	Kind of pH		pH
[Ref.: #23364]		optimum	6.5-6.9
[Ref.: #23364]	no	growth	4.5
[Ref.: #23364]	no	growth	8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2694]	Oxygen tolerance	anaerobe
[Ref.: #23364]	Oxygen tolerance	anaerobe
[Ref.: #52427]	Oxygen tolerance	anaerobe

[Ref.: #23364]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #2694]	Murein short key	A11.21
[Ref.: #2694]	Murein types	A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala₂

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	arabinose ChEBI	-	fermentation
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	cellobiose ChEBI	-	builds acid from
[Ref.: #23364]	cellobiose ChEBI	-	fermentation
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[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.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[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.: #23364]	dextrin ChEBI	+	fermentation
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	fructose ChEBI	+	fermentation
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	galactose ChEBI	+	fermentation
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	gluconate ChEBI	-	builds acid from
[Ref.: #23364]	gluconate ChEBI	-	fermentation
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	glucose ChEBI	+	fermentation
[Ref.: #23364]	glycerol ChEBI	-	fermentation
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	indole ChEBI	-
[Ref.: #23364]	inulin ChEBI	-	builds acid from
[Ref.: #23364]	inulin ChEBI	-	fermentation
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[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.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	lactate ChEBI	-	fermentation
[Ref.: #23364]	lactose ChEBI	+	fermentation
[Ref.: #23364]	maltose ChEBI	+	fermentation
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	mannitol ChEBI	+	builds acid from
[Ref.: #23364]	mannitol ChEBI	+	fermentation
[Ref.: #23364]	mannose ChEBI	-	fermentation
[Ref.: #23364]	melezitose ChEBI	-	builds acid from
[Ref.: #23364]	melezitose ChEBI	-	fermentation
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	melibiose ChEBI	+	fermentation
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[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.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	nitrate ChEBI	-	reduction
[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.: #23364]	propionate ChEBI	-
[Ref.: #23364]	raffinose ChEBI	+	fermentation
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	rhamnose ChEBI	-	fermentation
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	ribose ChEBI	+	builds acid from
[Ref.: #23364]	ribose ChEBI	+	fermentation
[Ref.: #23364]	salicin ChEBI	+/-	builds acid from
[Ref.: #23364]	salicin ChEBI	+/-	fermentation
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	sorbitol ChEBI	-	fermentation
[Ref.: #23364]	starch ChEBI	+	fermentation
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	sucrose ChEBI	+	fermentation
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23364]	trehalose ChEBI	-	fermentation
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23364]	xylose ChEBI	-	builds acid from
[Ref.: #23364]	xylose ChEBI	-	fermentation
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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® 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.: #2694]	15753	-	-	-	-	-	+	-	-	-	-	+	+	+	-	-	-	-	-	+	-	-	+	-	-	+	+	+	-	+	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #2694]	15055	-	-	-	-	-	+	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #2694]	Sample type/isolated from	rumen of cattle

[Ref.: #52427]	Sample type/isolated from	Cattle rumen

[Ref.: #67770]	Sample type/isolated from	Bovine rumen
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #2694]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Bifidobacterium ruminantium gene for 16S ribosomal RNA, partial sequence, strain: JCM 8222	LC071848	1398	GenBank ENA	78346 tax ID
[Ref.: #20218]	Bifidobacterium ruminantium strain DSM 6489 16S ribosomal RNA gene, partial sequence	GQ438820	358	GenBank ENA	78346 tax ID	*
[Ref.: #20218]	Bifidobacterium ruminantium strain DSM 6489 16S ribosomal RNA gene, partial sequence	GQ487644	154	GenBank ENA	78346 tax ID	*
[Ref.: #20218]	Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222	AB116347	477	GenBank ENA	78346 tax ID	*
[Ref.: #20218]	Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222	AB507151	796	GenBank ENA	78346 tax ID	*
[Ref.: #20218]	Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222	D86197	1437	GenBank ENA	78346 tax ID	*
[Ref.: #20218]	Bifidobacterium ruminantium strain JCM 8222 16S ribosomal RNA gene, partial sequence	GQ227715	317	GenBank ENA	78346 tax ID	*
[Ref.: #20218]	Bifidobacterium ruminantium strain KCTC 3425 16S ribosomal RNA gene, partial sequence	GU361831	1480	GenBank ENA	78346 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Bifidobacterium ruminantium LMG 21811	GCA_000741365	contig	GenBank ENA	78346 tax ID
[Ref.: #67770]	Bifidobacterium ruminantium DSM 6489	GCA_000687635	contig	GenBank ENA	1410647 tax ID
[Ref.: #67770]	Bifidobacterium ruminantium DSM 6489	GCA_000770925	contig	GenBank ENA	1410647 tax ID
[Ref.: #66792]	Bifidobacterium ruminantium strain LMG 21811	78346.3	wgs	PATRIC	78346 tax ID	*
[Ref.: #66792]	Bifidobacterium ruminantium DSM 6489	2558860117	draft	JGI IMG/M	1410647 tax ID	*
[Ref.: #66792]	Bifidobacterium ruminantium LMG 21811	2597490258	draft	JGI IMG/M	78346 tax ID	*

[Ref.: #2694]	GC-content	57.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #23364]	GC-content	57.0 mol%	Thermal denaturation, fluorometry
[Ref.: #67770]	GC-content	57 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bifidobacterium ruminantium DSM 6489 PATRIC: 1410647.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bifidobacterium ruminantium DSM 6489 PATRIC: 1410647.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	88.664	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	84.86	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.071	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.571	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	91.618	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	93.5	no

Availability in culture collections External links

[Ref.: #2694]

Culture collection no.

DSM 6489, ATCC 49390, CCUG 34975, JCM 8222, CGMCC 1.2241, KCTC 3425, LMG 12588, LMG 21811

[Ref.: #71370]

SI-ID 7859

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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) .

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71370

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-ID7859.1 )

* These data were automatically processed and therefore are not curated

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Bifidobacterium ruminantium DSM 6489

Bifidobacterium ruminantium DSM 6489

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Change proposal