Strain identifier

BacDive ID: 2472

Type strain: Yes

Species: Thiorhodococcus mannitoliphagus

Strain Designation: WS

Strain history: <- J. F. Imhoff, IFM-GEOMAR, Kiel, Germany; WS <- V. Gorlenko, Winogradski Inst. Microbiol., RAS, Moscow, Russia

NCBI tax ID(s): 329406 (species)

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

@ref: 7465

BacDive-ID: 2472

DSM-Number: 18266

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, coccus-shaped

description: Thiorhodococcus mannitoliphagus WS is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from microbial mat communities of an estuary of the Nilma river.

NCBI tax id

  • NCBI tax id: 329406
  • Matching level: species

strain history

  • @ref: 7465
  • history: <- J. F. Imhoff, IFM-GEOMAR, Kiel, Germany; WS <- V. Gorlenko, Winogradski Inst. Microbiol., RAS, Moscow, Russia

doi: 10.13145/bacdive2472.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Chromatiales
  • family: Chromatiaceae
  • genus: Thiorhodococcus
  • species: Thiorhodococcus mannitoliphagus
  • full scientific name: Thiorhodococcus mannitoliphagus Rabold et al. 2006

@ref: 7465

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Thiorhodococcus

species: Thiorhodococcus mannitoliphagus

full scientific name: Thiorhodococcus mannitoliphagus Rabold et al. 2006

strain designation: WS

type strain: yes

Morphology

cell morphology

  • @ref: 31657
  • gram stain: negative
  • cell width: 1.85 µm
  • cell shape: coccus-shaped
  • motility: yes

pigmentation

  • @ref: 31657
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7465
  • name: THIORHODOCOCCUS MEDIUM II (DSMZ Medium 28b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/28b
  • composition: Name: THIORHODOCOCCUS MEDIUM II (DSMZ Medium 28b) Composition: NaCl 15.0 g/l MgCl2 x 6 H2O 2.5 g/l NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l Na2S2O3 x 5 H2O 0.5 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l Ammonium chloride 0.349999 g/l Dextrose 0.25 g/l Pyruvic acid sodium salt 0.25 g/l Ammonium acetate 0.25 g/l Yeast extract 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7465positivegrowth25-30mesophilic
31657positivegrowth25-30mesophilic
31657positiveoptimum25-30mesophilic

culture pH

@refabilitytypepH
31657positivegrowth7-7.5
31657positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31657
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 31657
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31657NaClpositivegrowth0.5-2 %
31657NaClpositiveoptimum0.5-2 %

observation

  • @ref: 31657
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3165730089acetate+carbon source
3165728757fructose+carbon source
3165717234glucose+carbon source
3165724996lactate+carbon source
3165725115malate+carbon source
3165729864mannitol+carbon source
3165717272propionate+carbon source
3165715361pyruvate+carbon source
3165730031succinate+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 7465
  • sample type: microbial mat communities of an estuary of the Nilma river
  • geographic location: White Sea coast
  • country: Russia
  • origin.country: RUS
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Estuary
#Environmental#Aquatic#River (Creek)
#Environmental#Microbial community#Microbial mat

taxonmaps

  • @ref: 69479
  • File name: preview.99_181117.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_50712;97_65310;98_118109;99_181117&stattab=map
  • Last taxonomy: Thiorhodococcus mannitoliphagus subclade
  • 16S sequence: AJ971090
  • Sequence Identity:
  • Total samples: 36
  • soil counts: 4
  • aquatic counts: 30
  • animal counts: 2

Safety information

risk assessment

  • @ref: 7465
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7465
  • description: Thiorhodococcus mannitoliphagus partial 16S rRNA gene, type strain WST
  • accession: AJ971090
  • length: 1404
  • database: ena
  • NCBI tax ID: 329406

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiorhodococcus mannitoliphagus DSM 18266GCA_010915725contigncbi329406
66792Thiorhodococcus mannitoliphagus strain DSM 18266329406.4wgspatric329406

GC content

  • @ref: 7465
  • GC-content: 61.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.645yes
anaerobicyes96.495yes
halophileno87.185no
spore-formingno90.758no
glucose-utilyes81.86yes
motileyes90.114yes
flagellatedyes53.508no
aerobicno95.966yes
thermophileno97.718yes
glucose-fermentno79.908no

External links

@ref: 7465

culture collection no.: DSM 18266, ATCC BAA 1228, VKM B-2393

straininfo link

  • @ref: 72014
  • straininfo: 297346

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902035
  • title: Thiorhodococcus mannitoliphagus sp. nov., a purple sulfur bacterium from the White Sea.
  • authors: Rabold S, Gorlenko VM, Imhoff JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63981-0
  • year: 2006
  • mesh: Bacteriochlorophylls/analysis, Base Composition, Carotenoids/analysis, Culture Media, DNA, Bacterial/genetics, Gammaproteobacteria/chemistry/*classification/isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Oceans and Seas, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Russia, Sequence Homology, Nucleic Acid, Sodium Chloride, Species Specificity, Sulfides/metabolism, Sulfur/metabolism, *Water Microbiology
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7465Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18266)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18266
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
31657Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2793828776041
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)
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
72014Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297346.1StrainInfo: A central database for resolving microbial strain identifiers