Name: Ligilactobacillus ruminis RFl
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6510

Type strain:

Species: Ligilactobacillus ruminis

Strain Designation: RFl, RF 1

Culture col. no.: DSM 20403, ATCC 27780, CCUG 39465, JCM 1152, LMG 10756, CIP 103153, BCRC 14620, CECT 4061, KCTC 3601, NBRC 102161, NCFB 2029, NCIMB 702029, NRIC 1689, NRRL B-14853, VTT E-97852, NCDO 2029

Strain history: CIP <- 1988, NCFB <- 1973, M.J. Lathan: strain RF 1

NCBI tax ID(s): 1623 (species)

SI-ID 3363

LMG 10756, ATCC 27780, CIP 103153, DSM 20403, JCM 1152, NCFB 2029, CCUG 39465, NCDO 2029, CCRC 14620, NCIMB 702029, CECT 4061, KCTC 3601, NRRL B-14853, BCRC 14620, NBRC 102161, VTT E-97852, CECT 7785

Special Collections

Other strains from Ligilactobacillus ruminis

Section

When using BacDive for research please cite our paper

Ligilactobacillus ruminis RFl is an anaerobe, mesophilic bacterium that was isolated from bovine rumen.

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	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Ligilactobacillus*
	Species	**Ligilactobacillus ruminis**
	Full Scientific Name (LPSN)	Ligilactobacillus ruminis (Sharpe et al. 1973) Zheng et al. 2020

Synonym

Lactobacillus ruminis

Information on morphological and physiological properties Morphology

[Ref.: #54804]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8789]

Culture medium

MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)

[Ref.: #8789]

Culture medium growth

[Ref.: #8789]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8789]

Culture medium composition

expand / minimize

[Ref.: #40544]

Culture medium

MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminis

[Ref.: #40544]

Culture medium growth

[Ref.: #40544]

Culture medium composition

expand / minimize

[Ref.: #122313]

Culture medium

CIP Medium 41

[Ref.: #122313]

Culture medium growth

[Ref.: #122313]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8789]	growth	37 °C
[Ref.: #40544]	growth	37 °C
[Ref.: #54804]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8789]	Oxygen tolerance	anaerobe
[Ref.: #54804]	Oxygen tolerance	anaerobe
[Ref.: #54804]	Oxygen tolerance	microaerophile
[Ref.: #125439]	Oxygen tolerance	microaerophile Confidence in %93.6

[Ref.: #8789]	Murein short key	A31
[Ref.: #8789]	Murein types	A1gamma m-Dpm-direct

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[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-mannitol 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.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[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.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[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.: #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.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[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
	Only first 10 entries are displayed. Click here to see all.

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.: #8789]	15701	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #8789]	15451	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #8789]	Sample type/isolated from	bovine rumen

[Ref.: #54804]	Sample type/isolated from	Bovine rumen

[Ref.: #67770]	Sample type/isolated from	Bovine rumen

[Ref.: #122313]	Sample type/isolated from	Animal, Cattle, 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 LC064897 (>99% sequence identity) for Ligilactobacillus ruminis subclade from Microbeatlas

Aquatic Samples	6299
Soil Samples	2943
Animal Samples	110193
Plant Samples	977
Total Samples	120412

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

[Ref.: #8789]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122313]	Biosafety level	1	Risk group (French classification)

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]	Lactobacillus ruminis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1152	LC064897	1465	GenBank ENA	1623 tax ID
[Ref.: #124043]	Ligilactobacillus ruminis JCM:1152 gene for 16S rRNA, partial sequence.	LC723858	1506	GenBank ENA	1623 tax ID	*
[Ref.: #20218]	Lactobacillus ruminis 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer region, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF080103	533	GenBank ENA	1623 tax ID	*
[Ref.: #20218]	Lactobacillus ruminus 16S ribosomal RNA	M58828	1567	GenBank ENA	1623 tax ID	*
[Ref.: #20218]	Lactobacillus ruminis gene for 16S rRNA, partial sequence, strain: JCM 1152	AB289286	659	GenBank ENA	1623 tax ID	*
[Ref.: #20218]	Lactobacillus ruminis gene for 16S rRNA, partial sequence, strain: NBRC 102161	AB326354	1488	GenBank ENA	1623 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]	Ligilactobacillus ruminis DSM 20403 = NBRC 102161	GCA_001436475	contig	GenBank ENA	1423798 tax ID
[Ref.: #67770]	Ligilactobacillus ruminis DSM 20403 = NBRC 102161	GCA_001591905	contig	GenBank ENA	1423798 tax ID
[Ref.: #67770]	Ligilactobacillus ruminis DSM 20403 = NBRC 102161	GCA_900113455	scaffold	GenBank ENA	1423798 tax ID
[Ref.: #67770]	Ligilactobacillus ruminis ATCC 27780	GCA_001008755	contig	GenBank ENA	1623 tax ID
[Ref.: #66792]	Lactobacillus ruminis DSM 20403 = NBRC 102161	1423798.5	wgs	PATRIC	1423798 tax ID	*
[Ref.: #66792]	Ligilactobacillus ruminis ATCC 27780	2627853909	draft	JGI IMG/M	1623 tax ID	*

[Ref.: #8789]	GC-content	43.8 mol%
[Ref.: #67770]	GC-content	43.4 mol%	genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus ruminis DSM 20403 = NBRC 102161 PATRIC: 1423798.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	85.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	67.484	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	76.928	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	97.053	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.208	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	55.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ligilactobacillus ruminis DSM 20403 = NBRC 102161 NCBI: GCA_900113455
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	69.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	74.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	86.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	microaerophile	93.6

Availability in culture collections External links

[Ref.: #8789]

Culture collection no.

DSM 20403, ATCC 27780, CCUG 39465, JCM 1152, LMG 10756, CIP 103153, BCRC 14620, CECT 4061, KCTC 3601, NBRC 102161, NCFB 2029, NCIMB 702029, NRIC 1689, NRRL B-14853, VTT E-97852, NCDO 2029

[Ref.: #75982]

SI-ID 3363

Literature:

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	A Comparative Characterization of Different Host-sourced Lactobacillus ruminis Strains and Their Adhesive, Inhibitory, and Immunomodulating Functions.	Yu X, Avall-Jaaskelainen S, Koort J, Lindholm A, Rintahaka J, von Ossowski I, Palva A, Hynonen U	Front Microbiol	10.3389/fmicb.2017.00657	2017	*

References

#8789

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20403

#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 )

#40544 ; Curators of the CIP;
#54804 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 39465

#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 .

#75982

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-ID3363.1 )

#122313 Collection of Institut Pasteur ; Curators of the CIP; CIP 103153

#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 .

* These data were automatically processed and therefore are not curated

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Lactobacillus ruminis DSM 20403 = NBRC 102161

Ligilactobacillus ruminis DSM 20403 = NBRC 102161

Change proposal

Change proposal