Strain identifier

BacDive ID: 140656

Type strain: Yes

Species: Caldicellulosiruptor obsidiansis

Strain Designation: OB47

Strain history: J. G. Elkins OB47.

NCBI tax ID(s): 717609 (species)

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General

@ref: 43401

BacDive-ID: 140656

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, chemoorganoheterotroph, thermophilic, Gram-positive, rod-shaped, colony-forming

description: Caldicellulosiruptor obsidiansis OB47 is an obligate anaerobe, chemoorganoheterotroph, thermophilic bacterium that forms circular colonies and was isolated from Sample consisting of water, sediment and grass taken from a collection site at the edge of Obsidian Pool .

NCBI tax id

  • NCBI tax id: 717609
  • Matching level: species

strain history

  • @ref: 67770
  • history: J. G. Elkins OB47.

doi: 10.13145/bacdive140656.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Syntrophomonadaceae
  • genus: Caldicellulosiruptor
  • species: Caldicellulosiruptor obsidiansis
  • full scientific name: Caldicellulosiruptor obsidiansis Hamilton-Brehm et al. 2010

@ref: 43401

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermoanaerobacterales, not assigned to family

genus: Caldicellulosiruptor

species: Caldicellulosiruptor obsidiansis

strain designation: OB47

type strain: yes

Morphology

cell morphology

  • @ref: 43401
  • gram stain: positive
  • cell length: 2 µm
  • cell width: 0.2 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43401
  • colony color: opal
  • colony shape: circular
  • medium used: gelrite plate with 0.5%(w/v) cellobiose and yeast extract

Culture and growth conditions

culture medium

  • @ref: 43401
  • name: gelrite plate with 0.5%(w/v) cellobiose and yeast extract
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43401positiveoptimum78thermophilic
43401positivegrowth55-85hyperthermophilic
67770positivegrowth75thermophilic

culture pH

@refabilitytypepH
43401positivegrowth5-8
43401positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43401
  • oxygen tolerance: obligate anaerobe

nutrition type

  • @ref: 43401
  • type: chemoorganoheterotroph

spore formation

  • @ref: 43401
  • spore formation: no

halophily

  • @ref: 43401
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4340130089acetate-growth
4340127569arabinogalactan+growth
4340122599arabinose+growth
4340185146carboxymethylcellulose-growth
43401casein-growth
4340117057cellobiose+growth
4340162968cellulose+growth
4340162968cellulose+degradation
4340133403elemental sulfur-assimilation
4340128757fructose+growth
4340133984fucose-growth
4340128260galactose+growth
4340185248gellan gum-growth
4340117234glucose+growth
4340117754glycerol-growth
4340117716lactose+growth
434016457lignin-growth
4340117306maltose+growth
4340129864mannitol-growth
4340137684mannose+growth
4340117632nitrate-assimilation
4340117309pectin+growth
4340133942ribose-growth
4340130911sorbitol-growth
4340128017starch+growth
4340117992sucrose+growth
4340116189sulfate-assimilation
4340116094thiosulfate-assimilation
4340127082trehalose+growth
4340137166xylan+growth
4340118222xylose+growth
43401yeast extract (0.01 %, w/v)+growth

metabolite production

@refChebi-IDmetaboliteproduction
4340130089acetateyes
4340116526carbon dioxideyes
4340118276dihydrogenyes
4340124996lactateyes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43401Sample consisting of water, sediment and grass taken from a collection site at the edge of Obsidian Pool (66°C, pH 5)Yellowstone National ParkUSAUSANorth America
67770Obsidian PoolYellowstone National Park, WYUSAUSANorth America

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4699.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_153;96_509;97_587;98_675;99_4699&stattab=map
  • Last taxonomy: Caldicellulosiruptor obsidiansis subclade
  • 16S sequence: GQ338764
  • Sequence Identity:
  • Total samples: 8
  • aquatic counts: 7
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 67770
  • description: Caldicellulosiruptor obsidiansis strain OB47 16S ribosomal RNA gene, partial sequence
  • accession: GQ338764
  • length: 1466
  • database: ena
  • NCBI tax ID: 608506

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldicellulosiruptor obsidiansis OB47GCA_000145215completencbi608506
66792Caldicellulosiruptor obsidiansis OB47608506.3completepatric608506
66792Caldicellulosiruptor obsidiansis OB47648028013completeimg608506

GC content

@refGC-contentmethod
4340135.2sequence analysis
6777035

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes83.765no
flagellatedno85.389no
gram-positiveyes83.831yes
anaerobicyes99.467yes
aerobicno98.896no
halophileno97.263yes
spore-formingno74.844yes
thermophileyes100yes
glucose-utilyes88.08no
glucose-fermentyes51.66no

External links

@ref: 43401

culture collection no.: ATCC BAA 2073, JCM 16842

literature

  • topic: Genetics
  • Pubmed-ID: 20851897
  • title: Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T.
  • authors: Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE
  • journal: J Bacteriol
  • DOI: 10.1128/JB.00950-10
  • year: 2010
  • mesh: Anaerobiosis, Cellulose/metabolism, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Gram-Positive Bacteria/*genetics/metabolism, Hot Temperature, Hydrolases/genetics/metabolism, Molecular Sequence Data, Sequence Analysis, DNA
  • topic2: Metabolism

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43401Scott D. Hamilton-Brehm, Jennifer J. Mosher, Tatiana Vishnivetskaya, Mircea Podar, Sue Carroll, Steve Allman, Tommy J. Phelps, Martin Keller, and James G. ElkinsCaldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park10.1128/AEM.01903-09Appl. Environ. Microbiol. 76(4): 1014-1020 201020023107
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/