Oscillibacter ruminantium (KCTC 15176, NBRC 108824, JCM 18333)

Name: Oscillibacter ruminantium (KCTC 15176, NBRC 108824, JCM 18333)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133851

Type strain

Strain Designation GH1

Culture col. no. KCTC 15176 NBRC 108824 JCM 18333 GH1 DSM 113516

NCBI tax ID(s) 1007096 1263547

Special Collections JCM KCTC Literature strains DSMZ

Links

Oscillibacter ruminantium GH1 is an anaerobe, Gram-negative, motile prokaryote that was isolated from rumen of Korean native cattle.

Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406617

KCTC 15176,NBRC 108824,JCM 18333,DSM 113516

@ref 20215

Last LPSN update 2025-12-16 10:01:54

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Oscillibacter

Species Oscillibacter ruminantium

Full scientific name Oscillibacter ruminantium Lee et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
30675	negative	3.5 µm	0.5 µm	rod-shaped
67771				rod-shaped
67771				curved-shaped
67771	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
68961	PY + X MEDIUM (DSMZ Medium 104b)		Medium recipe at MediaDive	Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 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 Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
30675	positive	growth	30-45
30675	positive	optimum	40	thermophilic
67770	positive	growth	40	thermophilic
67771	positive	growth	37	mesophilic
68961	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30675	positive	optimum	6
30675	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30675	anaerobe
67771	anaerobe
125439	anaerobe	97.5

Spore formation

@ref	Spore formation
30675
67771

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30675	NaCl	positive	growth	0-3.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30675	17234 ChEBI	glucose	+	carbon source
30675	33942 ChEBI	ribose	+	carbon source
30675	18222 ChEBI	xylose	+	carbon source

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	Geographic location	Country	Country ISO 3 Code	Continent
30675	rumen of Korean native cattle
67770	Rumen fluid of Korean native cattle (HanWoo) steer
67771	From rumen fluid of a Korean native cattle(HanWoo) steer		Republic of Korea	KOR	Asia
68961	rumen fluid of a Korean native cattle	Seoul National University, Suwon City	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JF750939 (>99% sequence identity) for Oscillibacter ruminantium subclade from Microbeatlas

Aquatic Samples	2034
Soil Samples	1065
Animal Samples	19734
Plant Samples	346
Total Samples	23179

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
68961	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67771	ASM30726v1 assembly for Oscillibacter ruminantium GH1	scaffold	GCA_000307265	1007096.3	2551306563	1007096	65.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30675	Oscillibacter ruminantium GH1 16S ribosomal RNA gene, partial sequence	JF750939	1409		1007096

GC content

@ref	GC-content (mol%)	Method
30675	54.6
68961	54.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Oscillibacter ruminantium GH1
NCBI: GCA_000307265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.50	no
125439	gram_stain	BacteriaNetⓘ	variable	82.30	no
125439	motility	BacteriaNetⓘ	no	50.60	no
125439	spore_formation	BacteriaNetⓘ	yes	64.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oscillibacter ruminantium GH1
PATRIC: 1007096.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	57.14	no
125438	anaerobic	anaerobicⓘ	yes	84.98	yes
125438	spore-forming	spore-formingⓘ	no	58.89	no
125438	aerobic	aerobicⓘ	no	91.56	no
125438	thermophilic	thermophileⓘ	no	89.44	yes
125438	flagellated	motile2+ⓘ	yes	62.22	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oscillibacter ruminantium sp. nov., isolated from the rumen of Korean native cattle.	Lee GH, Rhee MS, Chang DH, Lee J, Kim S, Yoon MH, Kim BC	Int J Syst Evol Microbiol	10.1099/ijs.0.041749-0	2012

References

#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 )
#27006	IJSEM 1942 2013 ( DOI 10.1099/ijs.0.041749-0 , PubMed 23024142 )
#30675	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27006
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68961	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 113516
#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 )

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Oscillibacter ruminantium (KCTC 15176, NBRC 108824, JCM 18333)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000307265

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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