Name: Caldicoprobacter oshimai JW/HY-331
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17803

Type strain:

Species: Caldicoprobacter oshimai

Strain Designation: JW/HY-331

Culture col. no.: DSM 21659, ATCC BAA-1711

Strain history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/HY-331 <- H. Yokoyama

NCBI tax ID(s): 1304880 (strain), 551788 (species)

SI-ID 400242

DSM 21659

Section

Caldicoprobacter oshimai JW/HY-331 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sheep feces.

Gram-positive
rod-shaped
spore-forming
anaerobe
thermophilic
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	*Caldicoprobacteraceae*
	Genus	*Caldicoprobacter*
	Species	**Caldicoprobacter oshimai**
	Full Scientific Name (LPSN)	Caldicoprobacter oshimai Yokoyama et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29349]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.72

[Ref.: #29349]	Cell length	9 µm

[Ref.: #29349]	Cell width	0.45 µm

[Ref.: #29349]	Cell shape	rod-shaped

[Ref.: #29349]	Motility	no

Multimedia content

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Caption:

electron microscopic image

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Intellectual property rights:

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electron microscopic image

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Intellectual property rights:

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electron microscopic image

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Intellectual property rights:

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electron microscopic image

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15872]

Culture medium

CALDICOPROBACTER MEDIUM (DSMZ Medium 1233)

[Ref.: #15872]

Culture medium growth

[Ref.: #15872]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15872]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15872]	growth	70 °C
[Ref.: #29349]	growth	44-77 °C
[Ref.: #29349]	optimum	70 °C

[Ref.: #15872]	Temperature range	thermophilic
[Ref.: #29349]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

	pH	Kind of pH		pH
[Ref.: #29349]			optimum	7.2
[Ref.: #29349]			growth	5.9-8.6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #15872]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #29349]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29349]		NaCl		growth	0-2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29349]	cellobiose ChEBI	+	carbon source
[Ref.: #29349]	fructose ChEBI	+	carbon source
[Ref.: #29349]	galactose ChEBI	+	carbon source
[Ref.: #29349]	glucose ChEBI	+	carbon source
[Ref.: #29349]	lactose ChEBI	+	carbon source
[Ref.: #29349]	mannose ChEBI	+	carbon source
[Ref.: #29349]	raffinose ChEBI	+	carbon source
[Ref.: #29349]	xylose ChEBI	+	carbon source

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

[Ref.: #15872]	Sample type/isolated from	sheep feces
[Ref.: #15872]	Geographic location (country and/or sea, region)	farm at Univ. of Georgia
[Ref.: #15872]	Country	USA
[Ref.: #15872]	Country ISO 3 Code	USA
[Ref.: #15872]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Caprinae (Sheep/Goat)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB450762 (>99% sequence identity) for Caldicoprobacter from Microbeatlas

Aquatic Samples	123
Soil Samples	174
Animal Samples	903
Plant Samples	61
Total Samples	1261

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

[Ref.: #15872]

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.: #15872]	Caldicoprobacter oshimai gene for 16S rRNA, partial sequence	AB450762	1471	ENA	551788 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caldicoprobacter oshimai DSM 21659	1304880.3	wgs	PATRIC	1304880 tax ID	*
[Ref.: #66792]	Caldicoprobacter oshimai DSM 21659	2540341239	draft	JGI IMG/M	1304880 tax ID	*

[Ref.: #15872]	GC-content	45.6 mol%
[Ref.: #15872]	GC-content	45.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29349]	GC-content	45.4 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: Caldicoprobacter oshimai DSM 21659 PATRIC: 1304880.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Caldicoprobacter oshimai DSM 21659 PATRIC: 1304880.3
[Ref.: #69480]	motile	no	55.846	yes
[Ref.: #69480]	gram-positive	yes	87.106	yes
[Ref.: #69480]	anaerobic	yes	98.22	yes
[Ref.: #69480]	halophile	no	94.964	no
[Ref.: #69480]	spore-forming	yes	82.723	yes
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-util	yes	93.629	yes
[Ref.: #69480]	aerobic	no	97.976	yes
[Ref.: #69480]	flagellated	no	94.195	yes
[Ref.: #69480]	glucose-ferment	yes	60.277	no

Availability in culture collections External links

[Ref.: #15872]

Culture collection no.

DSM 21659, ATCC BAA-1711

[Ref.: #86795]

SI-ID 400242

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.	Bouanane-Darenfed A, Ben Hania W, Hacene H, Cayol JL, Ollivier B, Fardeau ML	Int J Syst Evol Microbiol	10.1099/ijs.0.043497-0	2012	*
Metabolism	Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov.	Morotomi M, Nagai F, Watanabe Y	Int J Syst Evol Microbiol	10.1099/ijs.0.026989-0	2011	*
Phylogeny	Caldicoprobacter oshimai gen. nov., sp. nov., an anaerobic, xylanolytic, extremely thermophilic bacterium isolated from sheep faeces, and proposal of Caldicoprobacteraceae fam. nov.	Yokoyama H, Wagner ID, Wiegel J	Int J Syst Evol Microbiol	10.1099/ijs.0.011379-0	2009	*

References

#15872

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21659

#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 )

#29349

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 #25761 (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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#86795

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-ID400242.1 )

#25761

IJSEM 67 2010 ( DOI 10.1099/ijs.0.011379-0 , PubMed 19648349 )

* These data were automatically processed and therefore are not curated

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Caldicoprobacter oshimai DSM 21659

Caldicoprobacter oshimai DSM 21659

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