Archive BacDiveID:10.13145/bacdive17980.20230509.8.1

Strain identifier

BacDive ID: 17980

Type strain:

Species: Carboxydocella sporoproducens

Strain Designation: Kar

Strain history: <- T. V. Slepova, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Kar <- T. V. Slepova {2004}

NCBI tax ID(s): 1121270 (strain), 285110 (species)

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

General

@ref: 6386

BacDive-ID: 17980

DSM-Number: 16521

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

description: Carboxydocella sporoproducens Kar is an anaerobe, spore-forming, thermophilic bacterium that was isolated from hot spring of Karymskoe Lake.

NCBI tax id

NCBI tax id	Matching level
1121270	strain
285110	species

strain history

@ref: 6386
history: <- T. V. Slepova, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Kar <- T. V. Slepova {2004}

doi: 10.13145/bacdive17980.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Carboxydocellaceae
genus: Carboxydocella
species: Carboxydocella sporoproducens
full scientific name: Carboxydocella sporoproducens Slepova et al. 2006

@ref: 6386

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridia, not assigned to family

genus: Carboxydocella

species: Carboxydocella sporoproducens

full scientific name: Carboxydocella sporoproducens Slepova et al. 2006

strain designation: Kar

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31646	positive	01-06 µm	0.5 µm	rod-shaped	yes
69480					yes	90.097
69480	positive					99.999

pigmentation

@ref: 31646
production: yes

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
6386	CARBOXYDOTHERMUS MEDIUM (HETEROTROPH) (DSMZ Medium 508)	yes	https://mediadive.dsmz.de/medium/508	Name: CARBOXYDOTHERMUS MEDIUM (HETEROTROPH) (DSMZ Medium 508) Composition: Na-pyruvate 2.47036 g/l Na2CO3 0.988142 g/l MgCl2 x 6 H2O 0.513834 g/l NH4Cl 0.326087 g/l KH2PO4 0.326087 g/l KCl 0.326087 g/l Na2S x 9 H2O 0.296443 g/l CaCl2 x 2 H2O 0.286561 g/l Yeast extract 0.0494071 g/l Na2-EDTA 0.00494071 g/l H3BO3 0.00296443 g/l FeSO4 x 7 H2O 0.00197628 g/l CoCl2 x 6 H2O 0.00197628 g/l ZnSO4 x 7 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l Na2MoO4 x 2 H2O 0.000296443 g/l MnCl2 x 4 H2O 0.000296443 g/l Pyridoxine hydrochloride 0.000296443 g/l Thiamine-HCl x 2 H2O 0.000197628 g/l NiCl2 x 6 H2O 0.000197628 g/l Nicotinic acid 0.000197628 g/l Vitamin B12 9.88142e-05 g/l CuCl2 x 2 H2O 9.88142e-05 g/l Calcium pantothenate 9.88142e-05 g/l p-Aminobenzoic acid 7.90514e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Thiamine HCl 4.94071e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l D-(+)-biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l Biotin 1.97628e-05 g/l Distilled water
6386	CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507)	yes	https://mediadive.dsmz.de/medium/507	Name: CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507) Composition: NaHCO3 0.998004 g/l Na2S x 9 H2O 0.698603 g/l MgCl2 x 6 H2O 0.518962 g/l NH4Cl 0.329341 g/l KH2PO4 0.329341 g/l KCl 0.329341 g/l CaCl2 x 2 H2O 0.289421 g/l Yeast extract 0.0499002 g/l Na2-EDTA x 2 H2O 0.00518962 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Riboflavin 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
6386	positive	growth	60	thermophilic
31646	positive	growth	50-70	thermophilic
31646	positive	optimum	60	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH
31646	positive	growth	06-08
31646	positive	optimum	06-08

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6386	anaerobe
31646	anaerobe
69480	anaerobe	99.659

spore formation

@ref	spore formation	confidence
31646	yes
69481	yes	100
69480	yes	99.999

observation

@ref: 31646
observation: aggregates in chains

Isolation, sampling and environmental information

isolation

@ref: 6386
sample type: hot spring of Karymskoe Lake
geographic location: Kamchatka Peninsula
country: Russia
origin.country: RUS
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_82468.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15882;96_34535;97_43806;98_57284;99_82468&stattab=map
Last taxonomy: Carboxydocella
16S sequence: AY673988
Sequence Identity:
Total samples: 1
animal counts: 1

Safety information

risk assessment

@ref: 6386
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6386
description: Carboxydocella sporoproducens strain Kar 16S ribosomal RNA gene, partial sequence
accession: AY673988
length: 1418
database: ena
NCBI tax ID: 285110

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Carboxydocella sporoproducens DSM 16521	GCA_900167165	contig	ncbi	1121270
66792	Carboxydocella sporoproducens DSM 16521 strain DSM 16521	1121270.4	wgs	patric	1121270
66792	Carboxydocella sporoproducens DSM 16521	2568526009	draft	img	1121270

GC content

@ref: 6386
GC-content: 49.5

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	88.637	yes
flagellated	no	83.231	no
gram-positive	no	85.936	no
anaerobic	yes	99.125	no
aerobic	no	96.744	yes
halophile	no	94.323	no
spore-forming	yes	90.507	no
thermophile	yes	99.614	yes
glucose-util	yes	75.805	no
glucose-ferment	no	79.521	no

External links

@ref: 6386

culture collection no.: DSM 16521, VKM B-2358

straininfo link

@ref: 86967
straininfo: 290963

literature

topic: Phylogeny
Pubmed-ID: 16585697
title: Carboxydocella sporoproducens sp. nov., a novel anaerobic CO-utilizing/H2-producing thermophilic bacterium from a Kamchatka hot spring.
authors: Slepova TV, Sokolova TG, Lysenko AM, Tourova TP, Kolganova TV, Kamzolkina OV, Karpov GA, Bonch-Osmolovskaya EA
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.63961-0
year: 2006
mesh: Bacteria, Anaerobic/*classification/genetics/isolation & purification/metabolism, Carbon Monoxide/*metabolism, Gram-Positive Rods/*classification/genetics/isolation & purification/metabolism, Hot Springs/*microbiology, Hot Temperature, Hydrogen/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Russia
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
6386	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16521)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16521
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
31646	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	27929	28776041
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		33211880	Nucleic Acids Res. 49: D498-D508 2020
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
86967	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID290963.1	StrainInfo: A central database for resolving microbial strain identifiers