Strain identifier

BacDive ID: 10428

Type strain: Yes

Species: Caminibacter mediatlanticus

Strain Designation: TB-2

Strain history: C. Vetriani TB-2.

NCBI tax ID(s): 391592 (strain), 291048 (species)

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General

@ref: 6556

BacDive-ID: 10428

DSM-Number: 16658

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped

description: Caminibacter mediatlanticus TB-2 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from walls of an active deep-sea hydrothermal vent chimney.

NCBI tax id

NCBI tax idMatching level
391592strain
291048species

strain history

@refhistory
6556<- C. Vetriani, Rutgers, State Univ. New Jersey, New Brunswick, USA; TB-2 <- J. W. Voordeckers {2003}
67770C. Vetriani TB-2.

doi: 10.13145/bacdive10428.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Nautiliales
  • family: Nautiliaceae
  • genus: Caminibacter
  • species: Caminibacter mediatlanticus
  • full scientific name: Caminibacter mediatlanticus Voordeckers et al. 2005

@ref: 6556

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Nautiliales

family: Nautiliaceae

genus: Caminibacter

species: Caminibacter mediatlanticus

full scientific name: Caminibacter mediatlanticus Voordeckers et al. 2005

strain designation: TB-2

type strain: yes

Morphology

cell morphology

  • @ref: 31378
  • gram stain: negative
  • cell length: 1.5 µm
  • cell width: 0.75 µm
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 6556
  • name: CAMINIBACTER MEDIATLANTICUS MEDIUM (DSMZ Medium 792b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/792b
  • composition: Name: CAMINIBACTER MEDIATLANTICUS MEDIUM (DSMZ Medium 792b) Composition: MgCl2 x 6 H2O 2.72547 g/l KNO3 0.99108 g/l KH2PO4 0.49554 g/l KCl 0.327056 g/l Na2S x 9 H2O 0.148662 g/l NaBr 0.049554 g/l MgSO4 x 7 H2O 0.0297324 g/l NaCl 0.0099108 g/l SrCl2 x 6 H2O 0.00693757 g/l MnSO4 x H2O 0.0049554 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00277502 g/l CoCl2 x 6 H2O 0.00178394 g/l ZnSO4 x 7 H2O 0.00178394 g/l FeSO4 x 7 H2O 0.00099108 g/l CaCl2 x 2 H2O 0.00099108 g/l Sodium resazurin 0.00049554 g/l AlK(SO4)2 x 12 H2O 0.000178394 g/l Na2SeO4 9.9108e-05 g/l Na2WO4 x 2 H2O 9.9108e-05 g/l H3BO3 9.9108e-05 g/l CuSO4 x 5 H2O 9.9108e-05 g/l Na2MoO4 x 2 H2O 9.9108e-05 g/l KI 4.9554e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6556positivegrowth55thermophilic
31378positivegrowth45-70thermophilic
31378positiveoptimum55thermophilic
67770positivegrowth55thermophilic

culture pH

@refabilitytypepH
31378positivegrowth4.5-7.5
31378positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6556anaerobe
31378anaerobe

spore formation

  • @ref: 31378
  • spore formation: no

metabolite production

  • @ref: 31378
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

  • @ref: 31378
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrylatitudelongitude
6556walls of an active deep-sea hydrothermal vent chimneyMid-Atlantic RidgeInternational waters36.2333-33.9
67770Deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2253.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_250;96_1214;97_1440;98_1758;99_2253&stattab=map
  • Last taxonomy: Caminibacter mediatlanticus subclade
  • 16S sequence: AY691430
  • Sequence Identity:
  • Total samples: 827
  • soil counts: 52
  • aquatic counts: 495
  • animal counts: 265
  • plant counts: 15

Safety information

risk assessment

  • @ref: 6556
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6556
  • description: Caminibacter mediatlanticus 16S ribosomal RNA gene, partial sequence
  • accession: AY691430
  • length: 1358
  • database: ena
  • NCBI tax ID: 391592

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caminibacter mediatlanticus TB-2GCA_005843985completencbi391592
66792Caminibacter mediatlanticus TB-2391592.5wgspatric391592
66792Caminibacter mediatlanticus TB-2640963039draftimg391592
67770Caminibacter mediatlanticus TB-2GCA_000170735contigncbi391592

GC content

  • @ref: 6556
  • GC-content: 25.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.329yes
flagellatedno77.779no
gram-positiveno99.061yes
anaerobicyes97.009yes
aerobicno97.915yes
halophileno82.767no
spore-formingno94.446yes
glucose-utilno80.05no
thermophileyes98.6no
glucose-fermentno87.089no

External links

@ref: 6556

culture collection no.: DSM 16658, JCM 12641

straininfo link

  • @ref: 79710
  • straininfo: 137999

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774661Caminibacter mediatlanticus sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge.Voordeckers JW, Starovoytov V, Vetriani CInt J Syst Evol Microbiol10.1099/ijs.0.63430-02005Atlantic Ocean, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Epsilonproteobacteria/*classification/genetics/isolation & purification/physiology, Hot Temperature, Molecular Sequence Data, Nitrates/*metabolism, Phylogeny, Quaternary Ammonium Compounds/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAStress
Genetics22180817Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent.Giovannelli D, Ferriera S, Johnson J, Kravitz S, Perez-Rodriguez I, Ricci J, O'Brien C, Voordeckers JW, Bini E, Vetriani CStand Genomic Sci10.4056/sigs.20948592011

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6556Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16658)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16658
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
31378Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2769128776041
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
79710Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137999.1StrainInfo: A central database for resolving microbial strain identifiers