Strain identifier

BacDive ID: 16791

Type strain: Yes

Species: Carboxydibrachium pacificum

Strain Designation: JM

Strain history: <- T. G. Sokolova, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; JM

NCBI tax ID(s): 109807 (subspecies)

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General

@ref: 4781

BacDive-ID: 16791

DSM-Number: 12653

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

description: Carboxydibrachium pacificum JM is an anaerobe, spore-forming, thermophilic bacterium that was isolated from hydrothermal vent sample.

NCBI tax id

  • NCBI tax id: 109807
  • Matching level: subspecies

strain history

  • @ref: 4781
  • history: <- T. G. Sokolova, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; JM

doi: 10.13145/bacdive16791.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Thermoanaerobacterales
  • family: Thermoanaerobacteraceae
  • genus: Carboxydibrachium
  • species: Carboxydibrachium pacificum
  • full scientific name: Carboxydibrachium pacificum corrig. Sokolova et al. 2001

  • synonyms

    @refsynonym
    20215Carboxydobrachium pacificum
    20215Caldanaerobacter subterraneus subsp. pacificus

@ref: 4781

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermoanaerobacteraceae

genus: Carboxydibrachium

species: Carboxydibrachium pacificum

full scientific name: Carboxydibrachium pacificum Sokolova et al. 2001

strain designation: JM

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes93.223
6948099.531positive

Culture and growth conditions

culture medium

  • @ref: 4781
  • name: CARCBOXYDOBRACHIUM PACIFICUM MEDIUM (DSMZ Medium 902)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/902
  • composition: Name: CARCBOXYDIBRACHIUM MEDIUM (DSMZ Medium 902) Composition: NaCl 19.9601 g/l MgSO4 x 7 H2O 3.89222 g/l Na-pyruvate 2.49501 g/l KCl 0.698603 g/l NaHCO3 0.499002 g/l L-Cysteine HCl x H2O 0.449102 g/l Na2S x 9 H2O 0.449102 g/l CaCl2 x 2 H2O 0.399202 g/l NH4Cl 0.299401 g/l Na2HPO4 0.149701 g/l Yeast extract 0.0499002 g/l Na2SiO3 0.0299401 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 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

@refgrowthtypetemperaturerangeconfidence
4781positivegrowth70thermophilic
69480thermophilic99.999

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4781anaerobe
69480anaerobe99.589

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 98.05

Isolation, sampling and environmental information

isolation

  • @ref: 4781
  • sample type: hydrothermal vent sample
  • geographic location: Pacific, Okinawa Trough
  • country: Japan
  • origin.country: JPN
  • continent: Asia
  • latitude: 27.55
  • longitude: 126.933

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 4781
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4781
  • description: Carboxydibrachium pacificum DSM 12653 16S ribosomal RNA gene, partial sequence
  • accession: AF174484
  • length: 1486
  • database: ena
  • NCBI tax ID: 391606

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldanaerobacter subterraneus subsp. pacificus DSM 12653GCA_000156275contigncbi391606
66792Carboxydibrachium pacificum DSM 12653391606.3wgspatric391606
66792Caldanaerobacter subterraneus pacificus JM, DSM 12653647533123draftimg391606

GC content

  • @ref: 4781
  • GC-content: 33
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno69no
gram-positiveno80.414no
anaerobicyes99.111yes
halophileno97.905no
spore-formingyes67.585no
glucose-utilyes86.611no
aerobicno97.89yes
motileyes80.337no
flagellatedno86.553no
thermophileyes99.999yes
glucose-fermentyes52.588no

External links

@ref: 4781

culture collection no.: DSM 12653, ATCC BAA 271

straininfo link

  • @ref: 85807
  • straininfo: 49335

literature

  • topic: Phylogeny
  • Pubmed-ID: 15023962
  • title: Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies.
  • authors: Fardeau ML, Salinas MB, L'Haridon S, Jeanthon C, Verhe F, Cayol JL, Patel BKC, Garcia JL, Ollivier B
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02711-0
  • year: 2004
  • mesh: Anaerobiosis, Australia, Bacteria, Anaerobic/*classification/isolation & purification, Base Composition, Base Sequence, Clostridium/*classification/genetics/isolation & purification, DNA Primers, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fossil Fuels/*microbiology, France, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitle
4781Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12653)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12653
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)
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
85807Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49335.1StrainInfo: A central database for resolving microbial strain identifiers