Strain identifier
BacDive ID: 2472
Type strain:
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)
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7465 | positive | growth | 25-30 | mesophilic |
31657 | positive | growth | 25-30 | mesophilic |
31657 | positive | optimum | 25-30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31657 | positive | growth | 7-7.5 |
31657 | positive | optimum | 7-7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31657
- oxygen tolerance: anaerobe
spore formation
- @ref: 31657
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31657 | NaCl | positive | growth | 0.5-2 % |
31657 | NaCl | positive | optimum | 0.5-2 % |
observation
- @ref: 31657
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31657 | 30089 | acetate | + | carbon source |
31657 | 28757 | fructose | + | carbon source |
31657 | 17234 | glucose | + | carbon source |
31657 | 24996 | lactate | + | carbon source |
31657 | 25115 | malate | + | carbon source |
31657 | 29864 | mannitol | + | carbon source |
31657 | 17272 | propionate | + | carbon source |
31657 | 15361 | pyruvate | + | carbon source |
31657 | 30031 | succinate | + | 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thiorhodococcus mannitoliphagus DSM 18266 | GCA_010915725 | contig | ncbi | 329406 |
66792 | Thiorhodococcus mannitoliphagus strain DSM 18266 | 329406.4 | wgs | patric | 329406 |
GC content
- @ref: 7465
- GC-content: 61.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.645 | yes |
anaerobic | yes | 96.495 | yes |
halophile | no | 87.185 | no |
spore-forming | no | 90.758 | no |
glucose-util | yes | 81.86 | yes |
motile | yes | 90.114 | yes |
flagellated | yes | 53.508 | no |
aerobic | no | 95.966 | yes |
thermophile | no | 97.718 | yes |
glucose-ferment | no | 79.908 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7465 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18266) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18266 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31657 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27938 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69479 | João 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 | |||
72014 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297346.1 | StrainInfo: A central database for resolving microbial strain identifiers |