Thermoclostridium caenicola (DSM 19027, NBRC 102590, EBR 596)

Name: Thermoclostridium caenicola (DSM 19027, NBRC 102590, EBR 596)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2854

Type strain

Culture col. no. DSM 19027 NBRC 102590 EBR 596

NCBI tax ID(s) 1121300 659425

Special Collections DSMZ Literature strains

History DSMZ <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR596 <- H. Shiratori {2005}

Links

Thermoclostridium caenicola DSM 19027 is an anaerobe, spore-forming, Gram-negative bacterium that was isolated from methanogenic sludge of a cellulose-degrading bioreactor.

spore-forming Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408015

NBRC 102590,DSM 19027

@ref 20215

Last LPSN update 2026-05-29 08:25:34

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Thermoclostridium

Species Thermoclostridium caenicola

Full scientific name Thermoclostridium caenicola (Shiratori et al. 2009) Zhang et al. 2018

Synonyms (1)

Clostridium caenicola

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29002	negative	3.1 µm	0.5 µm	rod-shaped

Pigmentation

29002

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7847	THERMOCLOSTRIDIUM CAENICOLA MEDIUM (DSMZ Medium 640a)		Medium recipe at MediaDive	Name: THERMOCLOSTRIDIUM CAENICOLA MEDIUM (DSMZ Medium 640a) Composition: NaHCO3 2.0 g/l Trypticase peptone 2.0 g/l K2HPO4 1.5 g/l Cellobiose 1.0 g/l Yeast extract 1.0 g/l NH4Cl 0.9 g/l NaCl 0.9 g/l KH2PO4 0.75 g/l L-Cysteine HCl x H2O 0.5 g/l MgCl2 x 6 H2O 0.4 g/l HCl 0.0025 g/l FeCl3 x 6 H2O 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7847	positive	growth	55
29002	positive	growth	50-70
29002	positive	optimum	60

Culture pH

@ref	Ability	Type	PH
29002	positive	optimum	6.5
29002	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7847	anaerobe
29002	anaerobe
125438	anaerobe	94.885
125439	facultative anaerobe	96.999

Spore formation

29002

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29002	NaCl	positive	growth	0-1.5 %
29002	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29002	22599 ChEBI	arabinose	+	carbon source
29002	17057 ChEBI	cellobiose	+	carbon source
29002	4853 ChEBI	esculin	+	hydrolysis
29002	17234 ChEBI	glucose	+	carbon source
29002	17306 ChEBI	maltose	+	carbon source
29002	29864 ChEBI	mannitol	+	carbon source
29002	17814 ChEBI	salicin	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	-
#Engineered	#Bioreactor	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7847	methanogenic sludge of a cellulose-degrading bioreactor	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB221372 (>99% sequence identity) for Thermoclostridium caenicola subclade from Microbeatlas

Aquatic Samples	428
Soil Samples	549
Animal Samples	256
Plant Samples	253
Total Samples	1486

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7847	1	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
66792	IMG-taxon 2700988698 annotated assembly for Thermoclostridium caenicola DSM 19027	scaffold	GCA_900142095	659425.3	2700988698	659425	53.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7847	Clostridium caenicola gene for 16S rRNA, partial sequence	AB221372	1565		659425

GC content

7847

GC-content (mol%)51.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2700988698 annotated assembly for Thermoclostridium caenicola DSM 19027
NCBI: GCA_900142095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.00	no
125439	gram_stain	BacteriaNetⓘ	variable	63.24	no
125439	motility	BacteriaNetⓘ	yes	62.63	no
125439	spore_formation	BacteriaNetⓘ	yes	63.76	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermoclostridium caenicola DSM 19027
NCBI: GCA_900142095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.54	yes
125438	anaerobic	anaerobicⓘ	yes	94.89	yes
125438	aerobic	aerobicⓘ	no	99.27	no
125438	spore-forming	spore-formingⓘ	yes	78.65	yes
125438	thermophilic	thermophileⓘ	no	58.64	no
125438	flagellated	motile2+ⓘ	yes	77.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge.	Shiratori H, Sasaya K, Ohiwa H, Ikeno H, Ayame S, Kataoka N, Miya A, Beppu T, Ueda K	Int J Syst Evol Microbiol	10.1099/ijs.0.003483-0	2009

References

#7847	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19027
#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 )
#25435	IJSEM 1764 2009 ( DOI 10.1099/ijs.0.003483-0 , PubMed 19542130 )
#29002	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 #25435
#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) .
#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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Thermoclostridium caenicola (DSM 19027, NBRC 102590, EBR 596)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900142095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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