Name: Oscillibacter valericigenes Sjm 18-20
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17691

Type strain:

Species: Oscillibacter valericigenes

Strain Designation: Sjm 18-20

Culture col. no.: DSM 18026, NBRC 101213

Strain history: <- T. Iino, NBRC; Sjm 18-20 <- T. Iino {2005}

NCBI tax ID(s): 693746 (strain), 351091 (species)

SI-ID 404955

DSM 18026

Section

Oscillibacter valericigenes Sjm 18-20 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from clam, alimentary canal of Corbicula japonica.

Gram-negative
motile
rod-shaped
anaerobe
mesophilic
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 valericigenes**
	Full Scientific Name (LPSN)	Oscillibacter valericigenes Iino et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31960]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31960]	Cell length	2.5-6.0 µm

[Ref.: #31960]	Cell width	0.5 µm

[Ref.: #31960]	Cell shape	rod-shaped

[Ref.: #31960]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7351]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #7351]

Culture medium growth

[Ref.: #7351]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7351]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7351]	growth	30 °C
[Ref.: #31960]	growth	15-35 °C
[Ref.: #31960]	optimum	30 °C

[Ref.: #7351]	Temperature range	mesophilic
[Ref.: #31960]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31960]			optimum	6.25
[Ref.: #31960]			growth	5.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7351]	Oxygen tolerance	anaerobe
[Ref.: #31960]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #31960]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %91
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.092

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31960]		NaCl		growth	0-4	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31960]	arabinose ChEBI	+	carbon source
[Ref.: #31960]	glucose ChEBI	+	carbon source
[Ref.: #31960]	ribose ChEBI	+	carbon source
[Ref.: #31960]	xylose ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7351]	Sample type/isolated from	clam, alimentary canal of Corbicula japonica
[Ref.: #7351]	Host species	Corbicula japonica
[Ref.: #7351]	Geographic location (country and/or sea, region)	sea coast in Shimane
[Ref.: #7351]	Country	Japan
[Ref.: #7351]	Country ISO 3 Code	JPN
[Ref.: #7351]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB238598 (>99% sequence identity) for Oscillibacter valericigenes subclade from Microbeatlas

Aquatic Samples	509
Soil Samples	86
Animal Samples	16381
Plant Samples	80
Total Samples	17056

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

[Ref.: #7351]

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.: #7351]	Oscillibacter valericigenes gene for 16S rRNA, partial sequence	AB238598	1453	ENA	351091 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Oscillibacter valericigenes Sjm18-20	693746.10	plasmid	PATRIC	693746 tax ID	*
[Ref.: #66792]	Oscillibacter valericigenes Sjm18-20	693746.9	complete	PATRIC	693746 tax ID	*

[Ref.: #7351]

GC-content

52.9 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Oscillibacter valericigenes Sjm18-20 PATRIC: 693746.9
[Ref.: #69481]	spore-forming	no	91	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oscillibacter valericigenes Sjm18-20 PATRIC: 693746.9
[Ref.: #69480]	gram-positive	no	64.736	yes
[Ref.: #69480]	anaerobic	yes	98.62	yes
[Ref.: #69480]	halophile	no	74.833	no
[Ref.: #69480]	spore-forming	no	67.653	yes
[Ref.: #69480]	glucose-util	yes	84.637	yes
[Ref.: #69480]	thermophile	no	99.404	no
[Ref.: #69480]	flagellated	no	76.857	no
[Ref.: #69480]	motile	yes	87.711	yes
[Ref.: #69480]	aerobic	no	98.735	no
[Ref.: #69480]	glucose-ferment	yes	61.892	no

Availability in culture collections External links

[Ref.: #7351]

Culture collection no.

DSM 18026, NBRC 101213

[Ref.: #86682]

SI-ID 404955

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam.	Iino T, Mori K, Tanaka K, Suzuki KI, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.64717-0	2007	*
Genetics	Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)).	Katano Y, Fujinami S, Kawakoshi A, Nakazawa H, Oji S, Iino T, Oguchi A, Ankai A, Fukui S, Terui Y, Kamata S, Harada T, Tanikawa S, Suzuki K, Fujita N	Stand Genomic Sci	10.4056/sigs.2826118	2012	*
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

#7351

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18026

#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 )

#31960

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 #28216 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#86682

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-ID404955.1 )

#28216

IJSEM 1840 2007 ( DOI 10.1099/ijs.0.64717-0 , PubMed 17684268 )

* These data were automatically processed and therefore are not curated

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Oscillibacter valericigenes Sjm18-20

Oscillibacter valericigenes Sjm18-20

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