Archive BacDiveID:10.13145/bacdive2831.20230509.8.1

Strain identifier

BacDive ID: 2831

Type strain:

Species: Clostridium lundense

Strain Designation: R1

Strain history: <- D. G. Cirne, Lund University, Department of Biotechnology, Lund, Sweden; R1 <- D. G. Cirne {2001}

NCBI tax ID(s): 1410653 (strain), 319475 (species)

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

General

@ref: 6709

BacDive-ID: 2831

DSM-Number: 17049

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

description: Clostridium lundense R1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from cow rumen fluid.

NCBI tax id

NCBI tax id	Matching level
1410653	strain
319475	species

strain history

@ref: 6709
history: <- D. G. Cirne, Lund University, Department of Biotechnology, Lund, Sweden; R1 <- D. G. Cirne {2001}

doi: 10.13145/bacdive2831.20230509.8.1

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 lundense
full scientific name: Clostridium lundense Cirne et al. 2006

@ref: 6709

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium lundense

full scientific name: Clostridium lundense Cirne et al. 2006

strain designation: R1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31519	positive	2.8-4.5 µm	0.56 µm	rod-shaped	no
69480					yes	91.777
69480	positive					100

pigmentation

@ref: 31519
production: yes

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
6709	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	yes	https://mediadive.dsmz.de/medium/110	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
6709	PY + X MEDIUM (DSMZ Medium 104b)	yes	https://mediadive.dsmz.de/medium/104b	Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
6709	positive	growth	37	mesophilic
31519	positive	growth	25-47
31519	positive	optimum	37	mesophilic
58865	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH	PH range
31519	positive	growth	5-8.5	alkaliphile
31519	positive	optimum	5.5-7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6709	anaerobe
31519	anaerobe
58865	anaerobe
69480	anaerobe	98.65

spore formation

@ref	spore formation	confidence
31519	yes
69481	yes	100
69480	yes	100

halophily

@ref: 31519
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-3 %

observation

@ref: 31519
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31519	33942	ribose	+	carbon source
31519	4853	esculin	+	hydrolysis

metabolite production

@ref: 31519
Chebi-ID: 35581
metabolite: indole
production: yes

metabolite tests

@ref: 31519
Chebi-ID: 35581
metabolite: indole
indole test: +

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date
6709	cow rumen fluid	Lund	Sweden	SWE	Europe
58865	Bovine rumen fluid	Lund	Sweden	SWE	Europe	2000-12-01

isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body Product	#Fluids	#Rumen fluid

Safety information

risk assessment

@ref: 6709
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6709
description: Clostridium lundense strain DSM 17049 16S ribosomal RNA gene, partial sequence
accession: AY858804
length: 1439
database: ena
NCBI tax ID: 319475

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Clostridium lundense DSM 17049	GCA_000619945	scaffold	ncbi	1410653
66792	Clostridium lundense DSM 17049	1410653.3	wgs	patric	1410653
66792	Clostridium lundense DSM 17049	2558860132	draft	img	1410653

GC content

@ref: 6709
GC-content: 31.2

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	76.4	yes
flagellated	no	61.144	yes
gram-positive	yes	59.142	no
anaerobic	yes	99.062	yes
halophile	no	92.269	no
spore-forming	yes	95.249	yes
thermophile	no	96.714	no
glucose-util	yes	87.387	no
aerobic	no	97.05	yes
glucose-ferment	yes	51.959	no

External links

@ref: 6709

culture collection no.: DSM 17049, CCUG 50446

straininfo link

@ref: 72355
straininfo: 286031

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	16514039	Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen.	Cirne DG, Delgado OD, Marichamy S, Mattiasson B	Int J Syst Evol Microbiol	10.1099/ijs.0.63730-0	2006	Animals, Cattle/microbiology, Clostridium/classification/genetics/isolation & purification/physiology, DNA, Ribosomal/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNA	Phenotype
Phylogeny	26597830	Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor.	Yin Q, Tao Y, Zhu X, Zhou Y, He X, Cheng L, Huang Y, Li D	Int J Syst Evol Microbiol	10.1099/ijsem.0.000787	2015		Biotechnology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
6709	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17049)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17049
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
31519	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	27814	28776041
58865	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 50446)	https://www.ccug.se/strain?id=50446
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)
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
72355	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID286031.1	StrainInfo: A central database for resolving microbial strain identifiers