Clostridium combesii (DSM 20696, ATCC 25545, JCM 9988)

Name: Clostridium combesii (DSM 20696, ATCC 25545, JCM 9988)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5421

Type strain

Strain Designation A13D

Culture col. no. DSM 20696 ATCC 25545 JCM 9988 VPI 0136 A13D

NCBI tax ID(s) 39481

Special Collections DSMZ JCM

History <- ATCC <- L. Holdeman, VPI 0136 <- A. Prévot, A13D STAFF 1016 <-- ATCC 25545 <-- L. V. Holdeman VPI 0136 <-- A. Prévot A13D.

Links

Clostridium combesii A13D is an anaerobe bacterium that was isolated from soil.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 38588

ATCC 25545,DSM 20696,JCM 9988

@ref 20215

Last LPSN update 2026-02-09 11:18:57

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium combesii

Full scientific name Clostridium combesii (Prévot and Laplanche 1947) Bernard et al. 2018

Synonyms (3)

"Cillobacterium combesii"
"Cillobacterium combesi"
Eubacterium combesii

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9016	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9016	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
9016	anaerobe
125439	anaerobe	99

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Continent
9016	soil	Africa	Africa
67770	African soil

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9016	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM274994v1 assembly for Clostridium combesii DSM 20696	scaffold	GCA_002749945	39481.3	2916602691	39481	71.32

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Eubacterium combesii 16S ribosomal RNA gene, partial sequence	AY533380	1434	39481
20218	Eubacterium combesii 16S ribosomal RNA gene, complete sequence	L34614	1481	39481
9016	Clostridium combesii strain ATCC 25545 16S ribosomal RNA, partial sequence	NR_042951	1434	39481

GC content

@ref	GC-content (mol%)	Method
9016	28.1	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium combesii DSM 20696
NCBI: GCA_002749945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	85.00	no
125439	motility	BacteriaNetⓘ	yes	81.30	no
125439	gram_stain	BacteriaNetⓘ	positive	81.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Eubacterium] combesii strain DSM 20696
PATRIC: 39481.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	63.27	no
125438	anaerobic	anaerobicⓘ	yes	82.76	yes
125438	spore-forming	spore-formingⓘ	yes	68.58	no
125438	aerobic	aerobicⓘ	no	95.31	yes
125438	thermophilic	thermophileⓘ	no	90.85	yes
125438	flagellated	motile2+ⓘ	yes	77.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Deciphering the complex interplay between gut microbiota and crop residue breakdown in forager and hive bees (Apis mellifera L.).	Rudra Gouda MN, Kumaranag KM, Ramakrishnan B, Subramanian S.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100233	2024
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
Biotechnology	Clostridium caseinilyticum sp. nov., a close relative of Clostridium tepidum and Clostridium sporogenes, isolated from spoiled cheese and silage.	Shani N, Zago M, Berthoud H, Marzohl D, Michellod E, Gindro K, Giraffa G, Arias-Roth E.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006875	2025
Phylogeny	Clostridium neonatale sp. nov. linked to necrotizing enterocolitis in neonates and a clarification of species assignable to the genus Clostridium (Prazmowski 1880) emend. Lawson and Rainey 2016.	Bernard K, Burdz T, Wiebe D, Alfa M, Bernier AM.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002827	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 )
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Clostridium combesii (DSM 20696, ATCC 25545, JCM 9988)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002749945

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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