Strain identifier
BacDive ID: 466
Type strain: 
Species: Microbulbifer thermotolerans
Strain history: M. Miyazaki JAMB A94.
NCBI tax ID(s): 252514 (species)
version 8.1 (current version)
General
@ref: 7959
BacDive-ID: 466
DSM-Number: 19189
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, thermophilic, Gram-negative, motile, rod-shaped
description: Microbulbifer thermotolerans DSM 19189 is a facultative anaerobe, thermophilic, Gram-negative bacterium that was isolated from deep-sea sediment.
NCBI tax id
- NCBI tax id: 252514
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7959 | <- M. Miyazaki, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; JAMB A94 |
| 67770 | M. Miyazaki JAMB A94. |
doi: 10.13145/bacdive466.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Cellvibrionales
- family: Microbulbiferaceae
- genus: Microbulbifer
- species: Microbulbifer thermotolerans
- full scientific name: Microbulbifer thermotolerans Miyazaki et al. 2008
@ref: 7959
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Microbulbiferaceae
genus: Microbulbifer
species: Microbulbifer thermotolerans
full scientific name: Microbulbifer thermotolerans Miyazaki et al. 2008
type strain: yes
Morphology
cell morphology
- @ref: 32443
- gram stain: negative
- cell length: 4 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 7959
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7959 | positive | growth | 42 | thermophilic |
| 32443 | positive | growth | 40-49 | thermophilic |
| 32443 | positive | optimum | 46 | thermophilic |
| 67770 | positive | growth | 42 | thermophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32443 | positive | growth | 5.5-9 | alkaliphile |
| 32443 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32443
- oxygen tolerance: facultative anaerobe
compound production
- @ref: 67770
- compound: Thermostable beta-agarase
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32443 | NaCl | positive | growth | <7 % |
| 32443 | NaCl | positive | optimum | 1.5 % |
observation
- @ref: 67770
- observation: quinones: Q-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32443 | 17057 | cellobiose | + | carbon source |
| 32443 | 28757 | fructose | + | carbon source |
| 32443 | 17234 | glucose | + | carbon source |
| 32443 | 17306 | maltose | + | carbon source |
| 32443 | 29864 | mannitol | + | carbon source |
| 32443 | 27082 | trehalose | + | carbon source |
| 32443 | 18222 | xylose | + | carbon source |
| 32443 | 4853 | esculin | + | hydrolysis |
| 32443 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32443 | catalase | + | 1.11.1.6 |
| 32443 | gelatinase | + | |
| 32443 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7959 | deep-sea sediment | Suruga Bay | Japan | JPN | Asia |
| 67770 | Sediment in Suruga Bay, at a depth of 2,406 m | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_5977.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_2852;97_3507;98_4439;99_5977&stattab=map
- Last taxonomy: Microbulbifer thermotolerans subclade
- 16S sequence: AB124836
- Sequence Identity:
- Total samples: 942
- soil counts: 88
- aquatic counts: 708
- animal counts: 116
- plant counts: 30
Safety information
risk assessment
- @ref: 7959
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7959
- description: Microbulbifer thermotolerans gene for 16S rRNA, partial sequence, strain: JAMB A94
- accession: AB124836
- length: 1490
- database: ena
- NCBI tax ID: 252514
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microbulbifer thermotolerans DSM 19189 | GCA_900112305 | scaffold | ncbi | 252514 |
| 66792 | Microbulbifer thermotolerans strain DSM 19189 | 252514.11 | wgs | patric | 252514 |
| 66792 | Microbulbifer thermotolerans DSM 19189 | 2599185213 | draft | img | 252514 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7959 | 56.2 | |
| 67770 | 56.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 78.718 | no |
| flagellated | no | 50 | no |
| gram-positive | no | 98.951 | no |
| anaerobic | no | 98.593 | no |
| aerobic | yes | 77.845 | yes |
| halophile | no | 53.78 | no |
| spore-forming | no | 94.262 | no |
| glucose-ferment | no | 87.265 | no |
| thermophile | no | 90.597 | yes |
| glucose-util | yes | 87.428 | yes |
External links
@ref: 7959
culture collection no.: DSM 19189, JCM 14709, JAMB A94
straininfo link
- @ref: 70145
- straininfo: 399804
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18450701 | Microbulbifer agarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov., agar-degrading bacteria isolated from deep-sea sediment. | Miyazaki M, Nogi Y, Ohta Y, Hatada Y, Fujiwara Y, Ito S, Horikoshi K | Int J Syst Evol Microbiol | 10.1099/ijs.0.65507-0 | 2008 | Agar/metabolism, Alteromonadaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 21669928 | Simiduia areninigrae sp. nov., an agarolytic bacterium isolated from sea sand. | Kim BC, Poo H, Lee KH, Kim MN, Park DS, Oh HW, Lee JM, Shin KS | Int J Syst Evol Microbiol | 10.1099/ijs.0.031153-0 | 2011 | Agar/metabolism, Alteromonadaceae/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Glycoside Hydrolases/*genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Silicon Dioxide, Ubiquinone/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 7959 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19189) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19189 | ||||
| 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 | ||||
| 32443 | 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 | 28665 | 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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 | ||||
| 70145 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399804.1 | StrainInfo: A central database for resolving microbial strain identifiers |