Name: Clostridium combesii A13D
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5421

Type strain:

Species: Clostridium combesii

Strain Designation: A13D

Culture col. no.: DSM 20696, ATCC 25545, JCM 9988, VPI 0136

Strain history: STAFF 1016 <-- ATCC 25545 <-- L. V. Holdeman VPI 0136 <-- A. Prévot A13D.

NCBI tax ID(s): 39481 (species)

SI-ID 38588

ATCC 25545, DSM 20696, JCM 9988

Section

Clostridium combesii A13D is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

motile
spore-forming
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	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium combesii**
	Full Scientific Name (LPSN)	Clostridium combesii (Prévot and Laplanche 1947) Bernard et al. 2018

	Synonym	"Cillobacterium* combesi"*
	Synonym	Eubacterium combesii

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	yes Confidence in %92.287

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9016]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #9016]

Culture medium growth

[Ref.: #9016]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9016]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #9016]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #9016]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #9016]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

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

[Ref.: #9016]	Sample type/isolated from	soil
[Ref.: #9016]	Country	Africa
[Ref.: #9016]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	African soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence NR_042951 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	3962
Soil Samples	4923
Animal Samples	31978
Plant Samples	1109
Total Samples	41972

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

[Ref.: #9016]

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.: #9016]	Clostridium combesii strain ATCC 25545 16S ribosomal RNA, partial sequence	NR_042951	1434	GenBank	39481 tax ID
[Ref.: #20218]	Eubacterium combesii 16S ribosomal RNA gene, partial sequence	AY533380	1434	ENA	39481 tax ID	*
[Ref.: #20218]	Eubacterium combesii 16S ribosomal RNA gene, complete sequence	L34614	1481	ENA	39481 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Clostridium combesii DSM 20696	GCA_002749945	scaffold	GenBank	39481 tax ID
[Ref.: #66792]	[Eubacterium] combesii strain DSM 20696	39481.3	wgs	PATRIC	39481 tax ID	*
[Ref.: #66792]	Clostridium combesii DSM 20696	2916602691	draft	JGI IMG/M	39481 tax ID	*

[Ref.: #9016]

GC-content

28.1 mol%

sequence analysis

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 combesii DSM 20696 NCBI: GCA_002749945.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Eubacterium] combesii strain DSM 20696 PATRIC: 39481.3
[Ref.: #69480]	gram-positive	yes	91.027	no
[Ref.: #69480]	anaerobic	yes	97.513	no
[Ref.: #69480]	halophile	no	82.126	no
[Ref.: #69480]	spore-forming	yes	91.042	no
[Ref.: #69480]	glucose-util	yes	87.54	no
[Ref.: #69480]	aerobic	no	98.028	no
[Ref.: #69480]	motile	yes	83.35	no
[Ref.: #69480]	flagellated	no	53.046	no
[Ref.: #69480]	thermophile	no	96.115	no
[Ref.: #69480]	glucose-ferment	yes	68.917	no

Availability in culture collections External links

[Ref.: #9016]

Culture collection no.

DSM 20696, ATCC 25545, JCM 9988, VPI 0136

[Ref.: #74910]

SI-ID 38588

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion.	Dobritsa AP, Kutumbaka KK, Samadpour M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002942	2018	*

References

#9016

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20696

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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 )

#74910

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-ID38588.1 )

* These data were automatically processed and therefore are not curated

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Clostridium combesii DSM 20696

[Eubacterium] combesii strain DSM 20696

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