Name: Oscillibacter ruminantium GH1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133851

Type strain:

Species: Oscillibacter ruminantium

Strain Designation: GH1

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

Strain history: <- KCTC; KCTC 15176 <- B.-C. Kim, KRIBB; GH1

NCBI tax ID(s): 1007096 (strain), 1263547 (species)

SI-ID 406617

DSM 113516

Section

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

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Oscillospiraceae*
	Genus	*Oscillibacter*
	Species	**Oscillibacter ruminantium**
	Full Scientific Name (LPSN)	Oscillibacter ruminantium Lee et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30675]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #30675]	Cell length	3.5 µm

[Ref.: #30675]	Cell width	0.5 µm

[Ref.: #30675]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	curved-shaped

[Ref.: #30675]	Motility	yes
[Ref.: #67771]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #68961]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #68961]

Culture medium growth

[Ref.: #68961]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #30675]	growth	30-45 °C
[Ref.: #30675]	optimum	40 °C
[Ref.: #67770]	growth	40 °C
[Ref.: #67771]	growth	37 °C
[Ref.: #68961]	growth	37 °C

[Ref.: #30675]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #67771]	Temperature range	mesophilic
[Ref.: #68961]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30675]			optimum	6
[Ref.: #30675]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30675]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #30675]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30675]		NaCl		growth	0-3.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30675]	glucose ChEBI	+	carbon source
[Ref.: #30675]	ribose ChEBI	+	carbon source
[Ref.: #30675]	xylose ChEBI	+	carbon source

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

[Ref.: #30675]	Sample type/isolated from	rumen of Korean native cattle

[Ref.: #67770]	Sample type/isolated from	Rumen fluid of Korean native cattle (HanWoo) steer

[Ref.: #67771]	Sample type/isolated from	From rumen fluid of a Korean native cattle(HanWoo) steer
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #68961]	Sample type/isolated from	rumen fluid of a Korean native cattle
[Ref.: #68961]	Geographic location (country and/or sea, region)	Seoul National University, Suwon City
[Ref.: #68961]	Country	Republic of Korea
[Ref.: #68961]	Country ISO 3 Code	KOR
[Ref.: #68961]	Continent	Asia
* 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 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

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

[Ref.: #68961]

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:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #30675]	Oscillibacter ruminantium GH1 16S ribosomal RNA gene, partial sequence	JF750939	1409	GenBank	1007096 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Oscillibacter ruminantium GH1	GCA_000307265	scaffold	GenBank	1007096 tax ID
[Ref.: #66792]	Oscillibacter ruminantium GH1	1007096.3	wgs	PATRIC	1007096 tax ID	*
[Ref.: #66792]	Oscillibacter ruminantium GH1	2551306563	draft	JGI IMG/M	1007096 tax ID	*

[Ref.: #30675]	GC-content	54.6 mol%
[Ref.: #68961]	GC-content	54.6 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oscillibacter ruminantium GH1 PATRIC: 1007096.3
[Ref.: #69480]	motile	yes	80.36	no
[Ref.: #69480]	flagellated	no	77.44	no
[Ref.: #69480]	gram-positive	no	63.218	yes
[Ref.: #69480]	anaerobic	yes	98.768	no
[Ref.: #69480]	aerobic	no	98.067	no
[Ref.: #69480]	halophile	no	85.009	no
[Ref.: #69480]	spore-forming	no	70.298	yes
[Ref.: #69480]	thermophile	no	98.687	no
[Ref.: #69480]	glucose-util	yes	83.828	yes
[Ref.: #69480]	glucose-ferment	yes	56.786	no

Availability in culture collections External links

[Ref.: #30675]

Culture collection no.

KCTC 15176, NBRC 108824, JCM 18333, DSM 113516

[Ref.: #91619]

SI-ID 406617

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 )

#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 (see below)

#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;
#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 .

#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) .

#91619

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-ID406617.1 )

#27006

IJSEM 1942 2013 ( DOI 10.1099/ijs.0.041749-0 , PubMed 23024142 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Oscillibacter ruminantium in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF