Archive BacDiveID:10.13145/bacdive2788.20230509.8.1

Strain identifier

BacDive ID: 2788

Type strain:

Species: Clostridium fimetarium

Strain Designation: Z-2189

Strain history: CIP <- 1997, DSM <- O.R. Kotsyurbenko: strain Z-2189

NCBI tax ID(s): 1121311 (strain), 99656 (species)

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

General

@ref: 3505

BacDive-ID: 2788

DSM-Number: 9179

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, Gram-positive

description: Clostridium fimetarium Z-2189 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from cattle manure.

NCBI tax id

NCBI tax id	Matching level
1121311	strain
99656	species

strain history

@ref	history
3505	<- O. R. Kotsyurbenko, Z-2189
119350	CIP <- 1997, DSM <- O.R. Kotsyurbenko: strain Z-2189

doi: 10.13145/bacdive2788.20230509.8.1

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 fimetarium
full scientific name: Clostridium fimetarium Kotsyurbenko et al. 1997

@ref: 3505

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium fimetarium

full scientific name: Clostridium fimetarium Kotsyurbenko et al. 1997

strain designation: Z-2189

type strain: yes

Morphology

cell morphology

@ref	gram stain	confidence	cell shape	motility
69480	positive	100
119350	positive		rod-shaped	no

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
3505	CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500)	yes	https://mediadive.dsmz.de/medium/500	Name: CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500) Composition: D-Glucose 4.97512 g/l NaHCO3 2.98507 g/l NaCl 2.23881 g/l Yeast extract 0.995025 g/l NH4Cl 0.497512 g/l MgSO4 x 7 H2O 0.497512 g/l K2HPO4 0.348259 g/l Na2S x 9 H2O 0.298507 g/l L-Cysteine HCl x H2O 0.298507 g/l CaCl2 x 2 H2O 0.248756 g/l KH2PO4 0.228856 g/l HCl 0.00248756 g/l FeSO4 x 7 H2O 0.00199005 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l Sodium resazurin 0.000497512 g/l CoCl2 x 6 H2O 0.000189055 g/l MnCl2 x 4 H2O 9.95025e-05 g/l Pyridoxine hydrochloride 9.95025e-05 g/l ZnCl2 6.96517e-05 g/l p-Aminobenzoic acid 4.97512e-05 g/l (DL)-alpha-Lipoic acid 4.97512e-05 g/l Calcium D-(+)-pantothenate 4.97512e-05 g/l Nicotinic acid 4.97512e-05 g/l Riboflavin 4.97512e-05 g/l Thiamine HCl 4.97512e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l Folic acid 1.99005e-05 g/l Biotin 1.99005e-05 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l Vitamin B12 9.95025e-07 g/l Distilled water
36600	MEDIUM 424 - for Clostridium fimetarium	yes		Sodium hydrogen carbonate (3.000 g);Distilled water make up to (990.000 ml);Sodium chloride (2.250 g);Iron (II) sulphate heptahydrate (2.000 g);Magnesium sulphate heptahydrate (0.500 g);Calcium chloride dihydrate (0.250 g);Yeast extract (1.000 g);Potassiu
119350	CIP Medium 424	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=424

culture temp

@ref	growth	type	temperature	range
3505	positive	growth	20	psychrophilic
36600	positive	growth	20	psychrophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
3505	anaerobe
69480	anaerobe	99.549

spore formation

@ref: 69481
spore formation: yes
confidence: 100

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent
3505	cattle manure	Russia	RUS
119350	Cattle manure	Russian Federation	RUS	Europe

isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

taxonmaps

@ref: 69479
File name: preview.99_112284.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_31241;97_39512;98_76120;99_112284&stattab=map
Last taxonomy: [Clostridium] fimetarium subclade
16S sequence: AF126687
Sequence Identity:
Total samples: 3877
soil counts: 643
aquatic counts: 727
animal counts: 2428
plant counts: 79

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
3505	1	Risk group (German classification)
119350	2	Risk group (French classification)

Sequence information

16S sequences

@ref: 3505
description: Clostridium fimetarium 16S ribosomal RNA gene, partial sequence
accession: AF126687
length: 1497
database: ena
NCBI tax ID: 99656

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	[Clostridium] fimetarium DSM 9179	GCA_900111235	contig	ncbi	99656
66792	[Clostridium] fimetarium strain DSM 9179	99656.3	wgs	patric	99656
66792	Lachnoclostridium fimetarium DSM 9179	2675903166	draft	img	99656

GC content

@ref: 3505
GC-content: 35.6
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	74.667	no
flagellated	yes	52.271	no
gram-positive	yes	82.094	no
anaerobic	yes	97.983	no
halophile	no	95.351	no
spore-forming	yes	80.96	no
thermophile	no	99.13	yes
glucose-util	yes	89.818	no
aerobic	no	97.463	no
glucose-ferment	yes	71.136	no

External links

@ref: 3505

culture collection no.: DSM 9179, CIP 105360

straininfo link

@ref: 72315
straininfo: 48590

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
3505	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9179)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-9179
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
36600	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/17371
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)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
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
72315	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID48590.1	StrainInfo: A central database for resolving microbial strain identifiers
119350	Curators of the CIP	Collection of Institut Pasteur (CIP 105360)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105360