Archive BacDiveID:10.13145/bacdive16810.20230509.8.1

Strain identifier

BacDive ID: 16810

Type strain:

Species: Carboxydothermus pertinax

Strain Designation: Ug1

Strain history: <- Y. Yoneda, Kyoto Univ., Japan; Ug1 <- Y. Yoneda {2009}

NCBI tax ID(s): 870242 (species)

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

General

@ref: 17349

BacDive-ID: 16810

DSM-Number: 23698

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

description: Carboxydothermus pertinax Ug1 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from acidic hot spring.

NCBI tax id

NCBI tax id: 870242
Matching level: species

strain history

@ref: 17349
history: <- Y. Yoneda, Kyoto Univ., Japan; Ug1 <- Y. Yoneda {2009}

doi: 10.13145/bacdive16810.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Thermoanaerobacterales
family: Thermoanaerobacteraceae
genus: Carboxydothermus
species: Carboxydothermus pertinax
full scientific name: Carboxydothermus pertinax Yoneda et al. 2012

@ref: 17349

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Thermoanaerobacteraceae

genus: Carboxydothermus

species: Carboxydothermus pertinax

full scientific name: Carboxydothermus pertinax Yoneda et al. 2012

strain designation: Ug1

type strain: yes

Morphology

cell morphology

@ref	cell length	cell shape	motility	confidence	gram stain
30244	2 µm	rod-shaped	yes
69480			yes	92.826
69480				100	positive

Culture and growth conditions

culture medium

@ref: 17349
name: CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507)
growth: yes
link: https://mediadive.dsmz.de/medium/507
composition: Name: CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507; with strain-specific modifications) Composition: Na-pyruvate 1.99601 g/l NaHCO3 0.998004 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
17349	positive	growth	65	thermophilic
30244	positive	growth	50-73	thermophilic
30244	positive	optimum	65	thermophilic
69480				thermophilic	99.687

culture pH

@ref	ability	type	pH	PH range
30244	positive	growth	4.8-8.6	alkaliphile
30244	positive	optimum	6.25

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
17349	anaerobe
30244	anaerobe
69480	anaerobe	99.477

spore formation

@ref: 69480
spore formation: yes
confidence: 99.999

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
30244	16236	ethanol	+	carbon source
30244	28757	fructose	+	carbon source
30244	17234	glucose	+	carbon source
30244	17754	glycerol	+	carbon source
30244	24996	lactate	+	carbon source
30244	15361	pyruvate	+	carbon source
30244	30031	succinate	+	carbon source
30244	17992	sucrose	+	carbon source

Isolation, sampling and environmental information

isolation

@ref: 17349
sample type: acidic hot spring
geographic location: Kagoshima Prefecture, Ibusuki, Unagi-onsen
country: Japan
origin.country: JPN
continent: Asia
latitude: 31.2272
longitude: 130.612

isolation source categories

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

Safety information

risk assessment

@ref: 17349
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
17349	Carboxydothermus pertinax gene for 16S rRNA, partial sequence, clone: A	AB573431	1497	ena	870242
17349	Carboxydothermus pertinax gene for 16S rRNA, partial sequence, clone: B	AB573432	1497	ena	870242
17349	Carboxydothermus pertinax gene for 16S rRNA, partial sequence, clone: C	AB573433	1497	ena	870242
17349	Carboxydothermus pertinax gene for 16S rRNA, partial sequence, clone: D	AB573434	1497	ena	870242

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Carboxydothermus pertinax Ug1	GCA_001950255	scaffold	ncbi	870242
66792	Carboxydothermus pertinax Ug1	2832181228	draft	img	870242

GC content

@ref	GC-content	method
17349	42.2	high performance liquid chromatography (HPLC)
30244	42.2

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	84	no
flagellated	no	94.727	no
gram-positive	no	76.374	no
anaerobic	yes	99.399	no
halophile	no	96.139	no
spore-forming	yes	85.463	no
glucose-util	yes	87.902	yes
aerobic	no	97.552	no
thermophile	yes	100	no
motile	yes	82.485	no
glucose-ferment	no	79.834	no

External links

@ref: 17349

culture collection no.: DSM 23698, NBRC 107576

straininfo link

@ref: 85823
straininfo: 400955

literature

topic: Phylogeny
Pubmed-ID: 21908679
title: Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring.
authors: Yoneda Y, Yoshida T, Kawaichi S, Daifuku T, Takabe K, Sako Y
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.031583-0
year: 2011
mesh: Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbon Dioxide/metabolism, Carbon Monoxide/*metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flagella/physiology, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/metabolism, Hot Springs/*microbiology, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Iron/*metabolism, Japan, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/*metabolism, Temperature
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
17349	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23698)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23698
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
30244	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	26586	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)
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)
85823	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID400955.1	StrainInfo: A central database for resolving microbial strain identifiers