Strain identifier

BacDive ID: 17803

Type strain: Yes

Species: Caldicoprobacter oshimai

Strain Designation: JW/HY-331

Strain history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/HY-331 <- H. Yokoyama

NCBI tax ID(s): 1304880 (strain), 551788 (species)

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General

@ref: 15872

BacDive-ID: 17803

DSM-Number: 21659

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

description: Caldicoprobacter oshimai JW/HY-331 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sheep feces.

NCBI tax id

NCBI tax idMatching level
1304880strain
551788species

strain history

  • @ref: 15872
  • history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/HY-331 <- H. Yokoyama

doi: 10.13145/bacdive17803.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Caldicoprobacteraceae
  • genus: Caldicoprobacter
  • species: Caldicoprobacter oshimai
  • full scientific name: Caldicoprobacter oshimai Yokoyama et al. 2010

@ref: 15872

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Caldicoprobacteraceae

genus: Caldicoprobacter

species: Caldicoprobacter oshimai

full scientific name: Caldicoprobacter oshimai Yokoyama et al. 2010

strain designation: JW/HY-331

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29349positive9 µm0.45 µmrod-shapedno
69480positive99.72

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21659_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21659_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21659_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21659_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 15872
  • name: CALDICOPROBACTER MEDIUM (DSMZ Medium 1233)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1233
  • composition: Name: CALDICOPROBACTER MEDIUM (DSMZ Medium 1233) Composition: Yeast extract 4.96524 g/l D-Glucose 4.96524 g/l HEPES 4.76663 g/l Tryptone 2.48262 g/l L-Cysteine HCl x H2O 0.993049 g/l NaCl 0.496524 g/l KCl 0.19861 g/l MgCl2 x 6 H2O 0.178749 g/l NH4Cl 0.0993049 g/l Na2HPO4 x 7 H2O 0.0536246 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00397219 g/l CaCl2 x 2 H2O 0.0019861 g/l MnCl2 x 4 H2O 0.000993049 g/l Sodium resazurin 0.000496524 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
15872positivegrowth70thermophilic
29349positivegrowth44-77thermophilic
29349positiveoptimum70thermophilic
69480thermophilic99.999

culture pH

@refabilitytypepHPH range
29349positivegrowth5.9-8.6alkaliphile
29349positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
15872anaerobe
69480anaerobe99.998

spore formation

@refspore formationconfidence
29349yes
69481yes100

halophily

  • @ref: 29349
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2934917057cellobiose+carbon source
2934928757fructose+carbon source
2934928260galactose+carbon source
2934917234glucose+carbon source
2934917716lactose+carbon source
2934937684mannose+carbon source
2934916634raffinose+carbon source
2934918222xylose+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 15872
  • sample type: sheep feces
  • geographic location: farm at Univ. of Georgia
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_28926.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3079;96_14245;97_17365;98_21577;99_28926&stattab=map
  • Last taxonomy: Caldicoprobacter
  • 16S sequence: AB450762
  • Sequence Identity:
  • Total samples: 1261
  • soil counts: 174
  • aquatic counts: 123
  • animal counts: 903
  • plant counts: 61

Safety information

risk assessment

  • @ref: 15872
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15872
  • description: Caldicoprobacter oshimai gene for 16S rRNA, partial sequence
  • accession: AB450762
  • length: 1471
  • database: ena
  • NCBI tax ID: 551788

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldicoprobacter oshimai DSM 216591304880.3wgspatric1304880
66792Caldicoprobacter oshimai DSM 216592540341239draftimg1304880

GC content

@refGC-contentmethod
1587245.6
1587245.4high performance liquid chromatography (HPLC)
2934945.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno55.846yes
gram-positiveyes87.106yes
anaerobicyes98.22yes
halophileno94.964no
spore-formingyes82.723yes
thermophileyes100yes
glucose-utilyes93.629yes
aerobicno97.976yes
flagellatedno94.195yes
glucose-fermentyes60.277no

External links

@ref: 15872

culture collection no.: DSM 21659, ATCC BAA 1711

straininfo link

  • @ref: 86795
  • straininfo: 400242

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648349Caldicoprobacter oshimai gen. nov., sp. nov., an anaerobic, xylanolytic, extremely thermophilic bacterium isolated from sheep faeces, and proposal of Caldicoprobacteraceae fam. nov.Yokoyama H, Wagner ID, Wiegel JInt J Syst Evol Microbiol10.1099/ijs.0.011379-02009Anaerobiosis, Animals, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Feces/*microbiology, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sheep, Xylose/metabolismMetabolism
Metabolism21357455Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov.Morotomi M, Nagai F, Watanabe YInt J Syst Evol Microbiol10.1099/ijs.0.026989-02011Acetic Acid/metabolism, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Butyrates/metabolism, Carbohydrates/analysis, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/metabolism, Feces/*microbiology, Fermentation, Glucose/metabolism, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Humans, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sucrose/metabolism, Urease/metabolismPhylogeny
Phylogeny23041645Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.Bouanane-Darenfed A, Ben Hania W, Hacene H, Cayol JL, Ollivier B, Fardeau MLInt J Syst Evol Microbiol10.1099/ijs.0.043497-02012Algeria, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xylans/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15872Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21659)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21659
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
29349Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2576128776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86795Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400242.1StrainInfo: A central database for resolving microbial strain identifiers