Strain identifier

BacDive ID: 17795

Type strain: Yes

Species: Rhodothermus profundi

Strain Designation: 2037 Souchothèque de Bretagne

Strain history: J.-L. Birrien PRI 2902.

NCBI tax ID(s): 633813 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16205

BacDive-ID: 17795

DSM-Number: 22212

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

description: Rhodothermus profundi 2037 Souchothèque de Bretagne is an aerobe, thermophilic, Gram-negative bacterium that was isolated from hydrothermal chimney material.

NCBI tax id

  • NCBI tax id: 633813
  • Matching level: species

strain history

@refhistory
16205<- J.-L. Birrien, IUEM, Univ. Brest, Plouzané, France; PRI 2902 <- V. T. Marteinsson
67770J.-L. Birrien PRI 2902.

doi: 10.13145/bacdive17795.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/rhodothermota
  • domain: Bacteria
  • phylum: Rhodothermota
  • class: Rhodothermia
  • order: Rhodothermales
  • family: Rhodothermaceae
  • genus: Rhodothermus
  • species: Rhodothermus profundi
  • full scientific name: Rhodothermus profundi Marteinsson et al. 2010

@ref: 16205

domain: Bacteria

phylum: Rhodothermaeota

class: Rhodothermia

order: Cytophagales

family: Rhodothermaceae

genus: Rhodothermus

species: Rhodothermus profundi

full scientific name: Rhodothermus profundi Marteinsson et al. 2010

strain designation: 2037 Souchothèque de Bretagne

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29418negative1.5-3.5 µm0.5 µmrod-shapedno
69480negative99.74

pigmentation

  • @ref: 29418
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16205
  • name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514a
  • composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 10.0 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
16205positivegrowth70thermophilic
29418positivegrowth55-80hyperthermophilic
29418positiveoptimum70thermophilic
67770positivegrowth70thermophilic
69480thermophilic98.658

culture pH

@refabilitytypepH
29418positivegrowth06-08
29418positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29418
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29418no
69480no99.935

halophily

@refsaltgrowthtested relationconcentration
29418NaClpositivegrowth01-05 %
29418NaClpositiveoptimum02-03 %

observation

@refobservation
29418aggregates in chains
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2941822653asparagine+carbon source
2941835391aspartate+carbon source
294185291gelatin+carbon source
2941829987glutamate+carbon source
2941815361pyruvate+carbon source

enzymes

  • @ref: 29418
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitude
16205hydrothermal chimney materialEast Pacific Rise, hydrothermal vent fields of Genesis (12.449844° N 103.56812° W) at a depth of 2634 m12.4498-103.568
67770Chimney collected from a deep-sea hydrothermal field at a depth of 2,634 m on the East Pacific Rise

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6891.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_302;96_1200;97_1415;98_1722;99_6891&stattab=map
  • Last taxonomy: Rhodothermus profundi
  • 16S sequence: FJ624399
  • Sequence Identity:
  • Total samples: 24
  • soil counts: 4
  • aquatic counts: 12
  • animal counts: 6
  • plant counts: 2

Safety information

risk assessment

  • @ref: 16205
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16205
  • description: Rhodothermus profundi strain PRI 2902 16S ribosomal RNA gene, partial sequence
  • accession: FJ624399
  • length: 1509
  • database: ena
  • NCBI tax ID: 633813

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodothermus profundi strain DSM 22212633813.3wgspatric633813
66792Rhodothermus profundi DSM 222122622736637draftimg633813
67770Rhodothermus profundi DSM 22212GCA_900142415scaffoldncbi633813

GC content

@refGC-contentmethod
1620560.9high performance liquid chromatography (HPLC)
2941860.9
6777060.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
gram-positiveno97.173no
anaerobicno96.954yes
halophileno54.766no
spore-formingno92.857yes
glucose-utilyes86.922no
thermophileyes99.736no
flagellatedno90.798yes
aerobicyes59.815no
motileyes64.708no
glucose-fermentno81.235no

External links

@ref: 16205

culture collection no.: DSM 22212, JCM 15944, PRI 2902

straininfo link

  • @ref: 86787
  • straininfo: 398419

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20061490Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean.Marteinsson VT, Bjornsdottir SH, Bienvenu N, Kristjansson JK, Birrien JLInt J Syst Evol Microbiol10.1099/ijs.0.012724-02010Amplified Fragment Length Polymorphism Analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodothermus/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny35072600Rhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island Surtsey.Bergsten P, Vannier P, Mougeolle A, Rigaud L, Marteinsson VTInt J Syst Evol Microbiol10.1099/ijsem.0.0052142022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Iceland, Islands, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodothermus/cytology/isolation & purification, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22212)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22212
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
29418Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2582528776041
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
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)
86787Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398419.1StrainInfo: A central database for resolving microbial strain identifiers