Strain identifier
BacDive ID: 158174
Type strain: 
Species: Zhongshania aliphaticivorans
Strain Designation: SM-2
Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; SM-2.
NCBI tax ID(s): 1470434 (species)
version 9.1 (current version)
General
@ref: 64767
BacDive-ID: 158174
DSM-Number: 107354
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Zhongshania aliphaticivorans SM-2 is a Gram-negative bacterium that was isolated from tidal flat.
NCBI tax id
- NCBI tax id: 1470434
- Matching level: species
strain history
| @ref | history |
|---|---|
| 64767 | <- JCM <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea |
| 67770 | C. O. Jeon; Chung-Ang Univ., South Korea; SM-2. |
doi: 10.13145/bacdive158174.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Cellvibrionales
- family: Spongiibacteraceae
- genus: Zhongshania
- species: Zhongshania aliphaticivorans
- full scientific name: Zhongshania aliphaticivorans Lo et al. 2014
@ref: 64767
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Spongiibacteraceae
genus: Zhongshania
species: Zhongshania aliphaticivorans
full scientific name: Zhongshania aliphaticivorans Lo et al. 2014
strain designation: SM-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 93
Culture and growth conditions
culture medium
- @ref: 64767
- 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 |
|---|---|---|---|
| 64767 | positive | growth | 28 |
| 67770 | positive | growth | 25 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | - | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | - | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68369 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 64767 | + | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 64767 | tidal flat | Danjin Bay | Republic of Korea | KOR | Asia |
| 67770 | Sea-tidal flat of Danjin bay in South Korea |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Tidal flat
taxonmaps
- @ref: 69479
- File name: preview.99_3871.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_305;96_1986;97_2387;98_2948;99_3871&stattab=map
- Last taxonomy: Zhongshania
- 16S sequence: KF982857
- Sequence Identity:
- Total samples: 4397
- soil counts: 107
- aquatic counts: 3986
- animal counts: 283
- plant counts: 21
Safety information
risk assessment
- @ref: 64767
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64767
- description: Zhongshania aliphaticivorans strain SM-2 16S ribosomal RNA gene, partial sequence
- accession: KF982857
- length: 1403
- database: nuccore
- NCBI tax ID: 1470434
Genome sequences
- @ref: 66792
- description: Zhongshania aliphaticivorans SM-2
- accession: GCA_001586255
- assembly level: complete
- database: ncbi
- NCBI tax ID: 1470434
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 93 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.624 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.256 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.799 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.052 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 64.032 | no |
External links
@ref: 64767
culture collection no.: DSM 107354, JCM 30138, KACC 18120
straininfo link
- @ref: 111005
- straininfo: 403472
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25122615 | Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov. | Lo N, Kang HJ, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.068593-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Hydrocarbons/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
| Genetics | 27034022 | Complete genome of Zhongshania aliphaticivorans SM-2(T), an aliphatic hydrocarbon-degrading bacterium isolated from tidal flat sediment. | Jia B, Jeong HI, Kim KH, Jeon CO | J Biotechnol | 10.1016/j.jbiotec.2016.03.039 | 2016 | Bacteria/*genetics/*isolation & purification, Biodegradation, Environmental, *Genome, Bacterial, Geologic Sediments/*microbiology, Hydrocarbons/*metabolism | Enzymology |
| Phylogeny | 30570482 | Zhongshania marina sp. nov., isolated from deep-sea water. | On YG, Oh JS, Roh DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003195 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 35982281 | Zhongshania aquimaris sp. nov., isolated from seawater. | Weerawongwiwat V, Kim JH, Lee JS, Yoon JH, Sukhoom A, Kim W | Arch Microbiol | 10.1007/s00203-022-03184-2 | 2022 | Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 64767 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-107354 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107354) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 68369 | Automatically annotated from API 20NE | |||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 111005 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID403472.1 |