Strain identifier

BacDive ID: 16806

Type strain: Yes

Species: Carboxydothermus hydrogenoformans

Strain Designation: Z-2901

Strain history: <- G. A. Zavarzin, Institute of Microbiology, Russ. Academy of Sciences, Moscow, Russia; Z-2901

NCBI tax ID(s): 129958 (species)

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General

@ref: 2417

BacDive-ID: 16806

DSM-Number: 6008

keywords: genome sequence, Bacteria, anaerobe, thermophilic

description: Carboxydothermus hydrogenoformans Z-2901 is an anaerobe, thermophilic bacterium that was isolated from hot spring.

NCBI tax id

  • NCBI tax id: 129958
  • Matching level: species

strain history

  • @ref: 2417
  • history: <- G. A. Zavarzin, Institute of Microbiology, Russ. Academy of Sciences, Moscow, Russia; Z-2901

doi: 10.13145/bacdive16806.20230509.8.1

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 hydrogenoformans
  • full scientific name: Carboxydothermus hydrogenoformans Svetlichny et al. 1991

@ref: 2417

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Thermoanaerobacteraceae

genus: Carboxydothermus

species: Carboxydothermus hydrogenoformans

full scientific name: Carboxydothermus hydrogenoformans Svetlichny et al. 1991

strain designation: Z-2901

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2417CARBOXYDOTHERMUS MEDIUM (HETEROTROPH) (DSMZ Medium 508)yeshttps://mediadive.dsmz.de/medium/508Name: 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
2417CARBOXYDOTHERMUS MEDIUM (DSMZ Medium 507)yeshttps://mediadive.dsmz.de/medium/507Name: 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: 2417
  • growth: positive
  • type: growth
  • temperature: 65
  • range: thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 2417
  • oxygen tolerance: anaerobe

compound production

  • @ref: 2417
  • compound: H2

Isolation, sampling and environmental information

isolation

  • @ref: 2417
  • sample type: hot spring
  • geographic location: Kunashir Island, Kuril Islands
  • country: USSR
  • origin.country: RUS
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 2417
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Carboxydothermus hydrogenoformans Z-2901GCA_000012865completencbi246194
66792Carboxydothermus hydrogenoformans Z-2901246194.6completepatric246194
66792Carboxydothermus hydrogenoformans Z-2901637000060completeimg246194

GC content

  • @ref: 2417
  • GC-content: 39.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes82.588no
flagellatedno96.304no
gram-positiveno82.897no
anaerobicyes99.552yes
halophileno94.778no
spore-formingyes80.924no
thermophileyes100no
glucose-utilyes82.979no
aerobicno97.586yes
glucose-fermentno81.965no

External links

@ref: 2417

culture collection no.: DSM 6008, ATCC BAA 161

straininfo link

  • @ref: 85819
  • straininfo: 48038

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16133342Carbon monoxide conversion by thermophilic sulfate-reducing bacteria in pure culture and in co-culture with Carboxydothermus hydrogenoformans.Parshina SN, Kijlstra S, Henstra AM, Sipma J, Plugge CM, Stams AJAppl Microbiol Biotechnol10.1007/s00253-004-1878-x2005Carbon Monoxide/*metabolism, Coculture Techniques, Gram-Positive Bacteria/*metabolism, Sulfates/*metabolism, Sulfur-Reducing Bacteria/*metabolism, Time Factors
Genetics16311624Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JAPLoS Genet10.1371/journal.pgen.00100652005Base Sequence, Carbon Monoxide/*chemistry, Genes, Bacterial, *Genome, Bacterial, Genomics, Hot Temperature, Models, Biological, Molecular Sequence Data, Oxidative Stress, Peptococcaceae/*genetics, Sequence Analysis, DNAStress
Phylogeny17012560Reclassification of Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov., and emended description of the genus Carboxydothermus.Slobodkin AI, Sokolova TG, Lysenko AM, Wiegel JInt J Syst Evol Microbiol10.1099/ijs.0.64503-02006Carbon Monoxide/metabolism, DNA, Bacterial/analysis, Ferric Compounds/metabolism, Genes, rRNA, Nucleic Acid Hybridization, Oxidation-Reduction, Peptococcaceae/*classification/genetics/metabolism/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Enzymology22005738Characterization of a thermostable methylaspartate ammonia lyase from Carboxydothermus hydrogenoformans.Raj H, Puthan Veetil V, Szymanski W, Dekker FJ, Quax WJ, Feringa BL, Janssen DB, Poelarends GJAppl Microbiol Biotechnol10.1007/s00253-011-3615-62011Ammonia-Lyases/genetics/*metabolism, Chromatography, Affinity, Cloning, Molecular, Enzyme Activators/metabolism, Enzyme Stability, Escherichia coli/genetics, Gene Expression, Gram-Positive Bacteria/chemistry/*enzymology/genetics, Hydrogen-Ion Concentration, Magnesium/metabolism, Molecular Weight, Potassium/metabolism, Protein Multimerization, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Substrate Specificity, TemperatureMetabolism
24822064Elementary Flux Mode Analysis of Acetyl-CoA Pathway in Carboxydothermus hydrogenoformans Z-2901.Chinnasamy Perumal R, Selvaraj A, Ramesh Kumar GAdv Bioinformatics10.1155/2014/9280382014

Reference

@idauthorscataloguedoi/urltitle
2417Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6008)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6008
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
85819Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48038.1StrainInfo: A central database for resolving microbial strain identifiers