Strain identifier
BacDive ID: 2883
Type strain: 
Species: Thalassotalea agarivorans
Strain history: W. Y. Shieh TMA1.
NCBI tax ID(s): 349064 (species)
version 8.1 (current version)
General
@ref: 8257
BacDive-ID: 2883
DSM-Number: 19706
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Thalassotalea agarivorans DSM 19706 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from shallow coastel water.
NCBI tax id
- NCBI tax id: 349064
- Matching level: species
strain history
| @ref | history |
|---|---|
| 8257 | <- BCRC <- W. Y. Shieh, Natl. Taiwan Univ., Inst. Oceanography, Taipei; TMA1 |
| 67770 | W. Y. Shieh TMA1. |
doi: 10.13145/bacdive2883.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Colwelliaceae
- genus: Thalassotalea
- species: Thalassotalea agarivorans
- full scientific name: Thalassotalea agarivorans (Jean et al. 2006) Zhang et al. 2014
synonyms
- @ref: 20215
- synonym: Thalassomonas agarivorans
@ref: 8257
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Colwelliaceae
genus: Thalassotalea
species: Thalassotalea agarivorans
full scientific name: Thalassotalea agarivorans (Jean et al. 2006) Zhang et al. 2014
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31726 | negative | 1.4-2.2 µm | 0.4-0.7 µm | rod-shaped | no | |
| 69480 | negative | 99.807 |
pigmentation
- @ref: 31726
- production: yes
Culture and growth conditions
culture medium
- @ref: 8257
- 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 |
|---|---|---|---|---|
| 8257 | positive | growth | 28 | mesophilic |
| 31726 | positive | growth | 15-37 | |
| 31726 | positive | optimum | 25 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31726 | positive | growth | 07-09 | alkaliphile |
| 31726 | positive | optimum | 07-09 |
Physiology and metabolism
oxygen tolerance
- @ref: 31726
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31726 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.969 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31726 | NaCl | positive | growth | 01-05 % |
| 31726 | NaCl | positive | optimum | 3 % |
observation
- @ref: 31726
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31726 | 4853 | esculin | + | hydrolysis |
| 31726 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 31726
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31726 | catalase | + | 1.11.1.6 |
| 31726 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 8257 | shallow coastel water | south-west coast, Tainan, An-Ping Harbour | Taiwan | TWN | Asia |
| 67770 | Seawater sample collected in a shallow-water region of An-Ping Harbour | Taiwan | TWN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_68086.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_82;96_12366;97_33729;98_43385;99_68086&stattab=map
- Last taxonomy: Thalassotalea agarivorans subclade
- 16S sequence: DQ212914
- Sequence Identity:
- Total samples: 583
- soil counts: 5
- aquatic counts: 546
- animal counts: 27
- plant counts: 5
Safety information
risk assessment
- @ref: 8257
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8257
- description: Thalassomonas agarivorans strain TMA1 16S ribosomal RNA gene, partial sequence
- accession: DQ212914
- length: 1465
- database: ena
- NCBI tax ID: 349064
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thalassotalea agarivorans strain DSM 19706 | 349064.5 | wgs | patric | 349064 |
| 66792 | Thalassotalea agarivorans DSM 19706 | 2599185215 | draft | img | 349064 |
| 67770 | Thalassotalea agarivorans DSM 19706 | GCA_900111755 | scaffold | ncbi | 349064 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8257 | 41.0 | |
| 31726 | 41 | |
| 67770 | 41 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.426 | no |
| anaerobic | no | 99.459 | yes |
| halophile | yes | 78.695 | no |
| spore-forming | no | 98.381 | no |
| glucose-util | yes | 90.011 | no |
| motile | no | 88.538 | yes |
| flagellated | no | 92.234 | yes |
| aerobic | yes | 89.466 | yes |
| thermophile | no | 98.501 | no |
| glucose-ferment | no | 73.55 | no |
External links
@ref: 8257
culture collection no.: DSM 19706, BCRC 17492, JCM 13379, TMA 1
straininfo link
- @ref: 72406
- straininfo: 297356
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16738099 | Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas. | Jean WD, Shieh WY, Liu TY | Int J Syst Evol Microbiol | 10.1099/ijs.0.64130-0 | 2006 | Bacteria, Anaerobic/classification/growth & development/isolation & purification, Fatty Acids/analysis, Flagella/physiology, Gammaproteobacteria/*classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Taiwan, Water Microbiology | Enzymology |
| Phylogeny | 21131503 | Thalassomonas agariperforans sp. nov., an agarolytic bacterium isolated from marine sand. | Park S, Choi WC, Oh TK, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.027821-0 | 2010 | Agar/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolism | Metabolism |
| Enzymology | 24206167 | Characterization and overexpression of a novel beta-agarase from Thalassomonas agarivorans. | Liang SS, Chen YP, Chen YH, Chiu SH, Liaw LL | J Appl Microbiol | 10.1111/jam.12389 | 2013 | Amino Acid Sequence, Cloning, Molecular, Disaccharides/metabolism, Escherichia coli/genetics, Gammaproteobacteria/*enzymology/genetics, Glycoside Hydrolases/chemistry/*genetics/metabolism, Hydrolysis, Recombinant Proteins/metabolism | Metabolism |
| Phylogeny | 24421274 | Description of Thalassotalea piscium gen. nov., sp. nov., isolated from flounder (Paralichthys olivaceus), reclassification of four species of the genus Thalassomonas as members of the genus Thalassotalea gen. nov. and emended description of the genus Thalassomonas. | Zhang Y, Tang K, Shi X, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.055913-0 | 2014 | Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flounder/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Gills/microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 8257 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19706) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19706 | ||||
| 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 | ||||
| 31726 | 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 | 28002 | 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 | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 72406 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297356.1 | StrainInfo: A central database for resolving microbial strain identifiers |