Archive BacDiveID:10.13145/bacdive2763.20230509.8.1

Strain identifier

BacDive ID: 2763

Type strain:

Species: Clostridium thermopalmarium

Strain Designation: BVP

Strain history: <- J.-L. Garcia <- B. Ollivier, BVP

NCBI tax ID(s): 1121340 (strain), 29373 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 2401

BacDive-ID: 2763

DSM-Number: 5974

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile

description: Clostridium thermopalmarium BVP is an anaerobe, spore-forming, thermophilic bacterium that was isolated from palm wine.

NCBI tax id

NCBI tax id	Matching level
1121340	strain
29373	species

strain history

@ref: 2401
history: <- J.-L. Garcia <- B. Ollivier, BVP

doi: 10.13145/bacdive2763.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Clostridiaceae
genus: Clostridium
species: Clostridium thermopalmarium
full scientific name: Clostridium thermopalmarium Soh et al. 1991

@ref: 2401

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium thermopalmarium

full scientific name: Clostridium thermopalmarium Soh et al. 1991

strain designation: BVP

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	95.102
69480		100	positive

Culture and growth conditions

culture medium

@ref: 2401
name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)
growth: yes
link: https://mediadive.dsmz.de/medium/520
composition: Name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520; with strain-specific modifications) Composition: Cellulose 9.97009 g/l (optional) Cellobiose 5.98205 g/l D-Glucose 4.98504 g/l K2HPO4 x 3 H2O 2.89133 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l KH2PO4 1.49551 g/l (NH4)2SO4 1.29611 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0747757 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l FeSO4 x 7 H2O 0.00124626 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

culture temp

@ref: 2401
growth: positive
type: growth
temperature: 55
range: thermophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
2401	anaerobe
69480	anaerobe	99.475

spore formation

@ref	spore formation	confidence
69481	yes	100
69480	yes	100

Isolation, sampling and environmental information

isolation

@ref: 2401
sample type: palm wine
country: Senegal
origin.country: SEN
continent: Africa

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Beverage
#Engineered	#Food production	#Fermented
#Host	#Plants	#Tree
#Host Body Product	#Plant	#Plant sap (Flux)

taxonmaps

@ref: 69479
File name: preview.99_25475.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_3674;97_15461;98_19150;99_25475&stattab=map
Last taxonomy: Clostridium
16S sequence: X72869
Sequence Identity:
Total samples: 2556
soil counts: 540
aquatic counts: 267
animal counts: 1451
plant counts: 298

Safety information

risk assessment

@ref: 2401
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 2401
description: C.thermopalmarium gene for 16S rRNA
accession: X72869
length: 1503
database: ena
NCBI tax ID: 29373

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Clostridium thermopalmarium DSM 5974	GCA_002995795	contig	ncbi	1121340
66792	Clostridium thermopalmarium DSM 5974	GCA_003097175	scaffold	ncbi	1121340
66792	Clostridium thermopalmarium DSM 5974	1121340.3	wgs	patric	1121340
66792	Clostridium thermopalmarium DSM 5974	1121340.4	wgs	patric	1121340
66792	Clostridium thermopalmarium DSM 5974	2599185222	draft	img	1121340

GC content

@ref: 2401
GC-content: 35.7
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
flagellated	yes	51.464	no
gram-positive	yes	66.365	no
anaerobic	yes	99.433	yes
halophile	no	80.712	no
spore-forming	yes	85.985	no
glucose-util	yes	86.308	no
aerobic	no	98.659	yes
thermophile	yes	55.582	yes
motile	yes	78.725	no
glucose-ferment	yes	55.531	no

External links

@ref: 2401

culture collection no.: DSM 5974, ATCC 51427

straininfo link

@ref: 72293
straininfo: 42978

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	11760953	Metabolism of cinnamic acids by some Clostridiales and emendation of the descriptions of Clostridium aerotolerans, Clostridium celerecrescens and Clostridium xylanolyticum.	Chamkha M, Garcia JL, Labat M	Int J Syst Evol Microbiol	10.1099/00207713-51-6-2105	2001	Bacterial Typing Techniques, Cinnamates/metabolism, Clostridium/classification/growth & development/*metabolism, Culture Media, Glucose/metabolism	Cultivation
Metabolism	20144864	Effect of key factors on hydrogen production from cellulose in a co-culture of Clostridium thermocellum and Clostridium thermopalmarium.	Geng A, He Y, Qian C, Yan X, Zhou Z	Bioresour Technol	10.1016/j.biortech.2010.01.042	2010	Base Sequence, Cellulose/metabolism, Clostridium/classification/metabolism, Coculture Techniques, Culture Media, DNA Primers, Hydrogen/*metabolism, Polymerase Chain Reaction, Species Specificity	Phylogeny
Genetics	29700158	First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974, a Butyrate-Producing Bacterium Isolated from Palm Wine.	Poehlein A, Hettwer E, Mohnike L, Daniel R	Genome Announc	10.1128/genomeA.00338-18	2018		Phylogeny
Phylogeny	30058994	Clostridium bovifaecis sp. nov., a novel acetogenic bacterium isolated from cow manure.	Zhu H, Fu B, Lu S, Liu H, Liu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.002928	2018	Animals, Bacterial Typing Techniques, Base Composition, Cattle/microbiology, Clostridium/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Manure/microbiology, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Transcriptome

Reference

@id	authors	catalogue	doi/url	title
2401	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5974)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-5974
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
72293	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID42978.1	StrainInfo: A central database for resolving microbial strain identifiers