Name: Ruminiclostridium josui DSM 25723
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2840

Type strain:

Species: Ruminiclostridium josui

Culture col. no.: DSM 25723, FERM P-9684, JCM 17888, KCTC 15379

Strain history: K. Sakka <-- K. Ohmiya strain III.

NCBI tax ID(s): 1291050 (strain), 1499 (species)

SI-ID 399265

DSM 25723

Section

Ruminiclostridium josui DSM 25723 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from Thai compost.

motile
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	*Oscillospiraceae*
	Genus	*Ruminiclostridium*
	Species	**Ruminiclostridium josui**
	Full Scientific Name (LPSN)	Ruminiclostridium josui (Sukhumavasi et al. 1988) Zhang et al. 2018

Synonym

Clostridium josui

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	yes Confidence in %93.058

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18098]

Culture medium

ACETIVIBRIO MEDIUM (DSMZ Medium 122)

[Ref.: #18098]

Culture medium growth

[Ref.: #18098]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18098]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #18098]			growth	45 °C
[Ref.: #67770]			growth	45 °C

[Ref.: #18098]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #18098]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #69481]	Ability of spore formation	yes Confidence in %95
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.644

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

[Ref.: #18098]	Sample type/isolated from	Thai compost
[Ref.: #18098]	Country	Thailand
[Ref.: #18098]	Country ISO 3 Code	THA
[Ref.: #18098]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Compost
[Ref.: #67770]	Country	Thailand
[Ref.: #67770]	Country ISO 3 Code	THA
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Biodegradation

#Composting

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB011057 (>99% sequence identity) for Ruminiclostridium from Microbeatlas

Aquatic Samples	5182
Soil Samples	10142
Animal Samples	1933
Plant Samples	1390
Total Samples	18647

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

[Ref.: #18098]

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.: #18098]	Clostridium josui gene for 16S rRNA, partial sequence	AB011057	1565	ENA	1499 tax ID
[Ref.: #67770]	Clostridium josui gene for 16S ribosomal RNA, partial sequence, strain: JCM 17888	AB675738	1537	ENA	1291050 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]	Ruminiclostridium josui JCM 17888	GCA_001311015	contig	GenBank	1291050 tax ID
[Ref.: #67770]	Ruminiclostridium josui JCM 17888	GCA_000526495	contig	GenBank	1291050 tax ID
[Ref.: #66792]	[Clostridium] josui JCM 17888	1291050.6	wgs	PATRIC	1291050 tax ID	*
[Ref.: #66792]	Clostridium josui JCM 17888	1291050.4	wgs	PATRIC	1291050 tax ID	*
[Ref.: #66792]	Clostridium josui JCM 17888	2541046955	draft	JGI IMG/M	1291050 tax ID	*
[Ref.: #66792]	Ruminiclostridium josui JCM 17888	2728369667	draft	JGI IMG/M	1291050 tax ID	*

[Ref.: #18098]

GC-content

40 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 GenomeNet Sporulation v. 1 based on: [Clostridium] josui JCM 17888 PATRIC: 1291050.6
[Ref.: #69481]	spore-forming	yes	95	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Clostridium] josui JCM 17888 PATRIC: 1291050.6
[Ref.: #69480]	motile	yes	75.835	no
[Ref.: #69480]	gram-positive	yes	56.384	no
[Ref.: #69480]	anaerobic	yes	99.193	yes
[Ref.: #69480]	aerobic	no	98.514	yes
[Ref.: #69480]	halophile	no	96.794	no
[Ref.: #69480]	spore-forming	yes	95.908	no
[Ref.: #69480]	glucose-util	yes	85.211	no
[Ref.: #69480]	flagellated	no	61.001	no
[Ref.: #69480]	thermophile	yes	80.482	no
[Ref.: #69480]	glucose-ferment	yes	53.008	no

Availability in culture collections External links

[Ref.: #18098]

Culture collection no.

DSM 25723, FERM P-9684, JCM 17888, KCTC 15379

[Ref.: #72364]

SI-ID 399265

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Cloning, sequencing, and expression of the gene encoding a cell-bound multi-domain xylanase from Clostridium josui, and characterization of the translated product.	Feng JX, Karita S, Fujino E, Fujino T, Kimura T, Sakka K, Ohmiya K	Biosci Biotechnol Biochem	10.1271/bbb.64.2614	2000	*
Enzymology	Cloning of an endo-1,4-beta-D-glucanase gene from Clostridium josui and its expression in Escherichia coli.	Ohmiya K, Fujino T, Sukhumavasi J, Shimizu S	Appl Environ Microbiol	10.1128/aem.55.9.2399-2402.1989	1989	*

References

#18098

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25723

#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 )

#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;

#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 )

#72364

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-ID399265.1 )

* These data were automatically processed and therefore are not curated

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[Clostridium] josui JCM 17888

[Clostridium] josui JCM 17888

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