Archive BacDiveID:10.13145/bacdive2606.20230509.8.1

Strain identifier

BacDive ID: 2606

Type strain:

Species: Clostridium kluyveri

Strain Designation: K1

Strain history: <- S. Schoberth, Universität Göttingen, Germany; K1 <- G. Gottschalk <- H. A. Barker, University of California, Berkeley, USA

NCBI tax ID(s): 431943 (strain), 1534 (species)

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

General

@ref: 276

BacDive-ID: 2606

DSM-Number: 555

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

description: Clostridium kluyveri K1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from mud.

NCBI tax id

NCBI tax id	Matching level
431943	strain
1534	species

strain history

@ref: 276
history: <- S. Schoberth, Universität Göttingen, Germany; K1 <- G. Gottschalk <- H. A. Barker, University of California, Berkeley, USA

doi: 10.13145/bacdive2606.20230509.8.1

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 kluyveri
full scientific name: Clostridium kluyveri Barker and Taha 1942 (Approved Lists 1980)

@ref: 276

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium kluyveri

full scientific name: Clostridium kluyveri Barker and Taha 1942

strain designation: K1

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

colony morphology

@ref: 276
incubation period: 1-2 days

Culture and growth conditions

culture medium

@ref: 276
name: CLOSTRIDIUM KLUYVERI MEDIUM (DSMZ Medium 52)
growth: yes
link: https://mediadive.dsmz.de/medium/52
composition: Name: CLOSTRIDIUM KLUYVERI MEDIUM (DSMZ Medium 52) Composition: K-acetate 10.0 g/l Yeast extract 1.0 g/l Na2CO3 1.0 g/l K2HPO4 0.31 g/l L-Cysteine HCl x H2O 0.25 g/l NH4Cl 0.25 g/l Na2S x 9 H2O 0.25 g/l KH2PO4 0.23 g/l MgSO4 x 7 H2O 0.2 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l NaOH 0.0005 g/l Pyridoxine hydrochloride 0.0003 g/l Thiamine-HCl x 2 H2O 0.0002 g/l Nicotinic acid 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Calcium pantothenate 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Vitamin B12 0.0001 g/l p-Aminobenzoic acid 8e-05 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 D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Ethanol absolute Distilled water

culture temp

@ref: 276
growth: positive
type: growth
temperature: 37
range: mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
276	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	yes	100
69480	yes	100

compound production

@ref	compound
276	acetaldehyde dehydrogenase
276	ß hydroxybutyryl-CoA dehydrogenase
276	diaphorase
276	phosphotransacetylase
276	vinylacetyl isomerase
276	flavin nucleotides, radioactive
276	enoate reductase

Isolation, sampling and environmental information

isolation

@ref: 276
sample type: mud

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Mud (Sludge)

Safety information

risk assessment

@ref: 276
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Clostridium kluyveri strain DSM 555 16S ribosomal RNA gene, partial sequence	DQ911271	320	ena	431943
20218	Clostridium kluyveri 16S ribosomal RNA	M59092	1460	ena	1534

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Clostridium kluyveri DSM 555	GCA_000016505	complete	ncbi	431943
66792	Clostridium kluyveri DSM 555	431943.20	plasmid	patric	431943
66792	Clostridium kluyveri DSM 555	431943.8	complete	patric	431943
66792	Clostridium kluyveri NBRC 12016	583346.15	plasmid	patric	583346
66792	Clostridium kluyveri NBRC 12016	583346.6	complete	patric	583346
66792	Clostridium kluyveri DSM 555	640753020	complete	img	431943

GC content

@ref: 276
GC-content: 29.8

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	82.417	no
flagellated	yes	64.272	no
gram-positive	yes	56.447	no
anaerobic	yes	98.504	yes
halophile	no	96.304	no
spore-forming	yes	98.025	no
thermophile	no	98.577	yes
glucose-util	yes	75.984	no
aerobic	no	96.435	yes
glucose-ferment	yes	50.692	no

External links

@ref: 276

culture collection no.: DSM 555, ATCC 12489, ATCC 8527, NCIMB 10680

straininfo link

@ref: 72137
straininfo: 34982

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	627401	Properties of two Clostridia strains acting as catalysts for the preparative stereospecific hydrogenation of 2-enoic acids and 2-alken-1-ols with hydrogen gas.	Bader J, Gunther H, Rambeck B, Simon H	Hoppe Seylers Z Physiol Chem	10.1515/bchm.1978.359.1.19	1978	Clostridium/isolation & purification, Fatty Acids, Unsaturated/metabolism, Fatty Alcohols/metabolism, Hydrogen/pharmacology, Hydrogenation, Stereoisomerism	Enzymology
Metabolism	7387331	Utilization of (E)-2-butenoate (crotonate) by Clostridium kluyveri and some other Clostridium species.	Bader J, Gunther H, Schleicher E, Simon H, Pohl S, Mannheim W	Arch Microbiol	10.1007/BF00403214	1980	Acetates/metabolism, Butyrates/metabolism, Carbohydrate Metabolism, Clostridium/growth & development/metabolism, Crotonates/*metabolism, Fermentation, Glucose/metabolism, Species Specificity	Phylogeny
Phylogeny	26420591	Clostridium luticellarii sp. nov., isolated from a mud cellar used for producing strong aromatic liquors.	Wang Q, Wang CD, Li CH, Li JG, Chen Q, Li YZ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000641	2015	Alcoholic Beverages, Bacterial Typing Techniques, Base Composition, China, Clostridium/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology	Genetics
	32540193	Ethanol:propionate ratio drives product selectivity in odd-chain elongation with Clostridium kluyveri and mixed communities.	Candry P, Ulcar B, Petrognani C, Rabaey K, Ganigue R	Bioresour Technol	10.1016/j.biortech.2020.123651	2020	Caproates, *Clostridium kluyveri, Ethanol, Fermentation, Propionates

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
276	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 555)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-555
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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
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
72137	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID34982.1	StrainInfo: A central database for resolving microbial strain identifiers