Strain identifier
BacDive ID: 132960
Type strain:
Species: Actibacterium naphthalenivorans
Strain Designation: NS6
Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; NS6.
NCBI tax ID(s): 1614693 (species)
General
@ref: 24748
BacDive-ID: 132960
DSM-Number: 105040
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Actibacterium naphthalenivorans NS6 is a mesophilic, Gram-negative bacterium that was isolated from sea-tidal-flat sediment, crude-oil contaminated.
NCBI tax id
- NCBI tax id: 1614693
- Matching level: species
strain history
@ref | history |
---|---|
24748 | <- JCM <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; NS6 |
67770 | C. O. Jeon; Chung-Ang Univ., South Korea; NS6. |
doi: 10.13145/bacdive132960.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Actibacterium
- species: Actibacterium naphthalenivorans
- full scientific name: Actibacterium naphthalenivorans (Jeong et al. 2015) Hördt et al. 2020
synonyms
- @ref: 20215
- synonym: Confluentimicrobium naphthalenivorans
@ref: 24748
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Actibacterium
species: Actibacterium naphthalenivorans
full scientific name: Actibacterium naphthalenivorans (Jeong et al. 2015) Hördt et al. 2020
strain designation: NS6
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 24748
- 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 |
---|---|---|---|---|
24748 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 96 |
69480 | no | 99.978 |
observation
- @ref: 67770
- observation: quinones: Q-10
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24748 | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
24748 | sea-tidal-flat sediment, crude-oil contaminated | Yeosu coastel area | Republic of Korea | KOR | Asia | 34.8092 | 127.724 |
67770 | Sea-tidal-flat sediment | South Sea | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | #Oil (Fuel) |
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
#Environmental | #Terrestrial | #Tidal flat |
taxonmaps
- @ref: 69479
- File name: preview.99_517.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_330;97_368;98_420;99_517&stattab=map
- Last taxonomy: Actibacterium naphthalenivorans subclade
- 16S sequence: KP272155
- Sequence Identity:
- Total samples: 3295
- soil counts: 100
- aquatic counts: 3015
- animal counts: 171
- plant counts: 9
Safety information
risk assessment
- @ref: 24748
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24748
- description: Confluentimicrobium naphthalenivorans strain NS6 16S ribosomal RNA gene, partial sequence
- accession: KP272155
- length: 1453
- database: ena
- NCBI tax ID: 1614693
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actibacterium naphthalenivorans DSM 105040 | GCA_014196965 | contig | ncbi | 1614693 |
66792 | Confluentimicrobium naphthalenivorans strain DSM 105040 | 1614693.4 | wgs | patric | 1614693 |
66792 | Actibacterium naphthalenivorans DSM 105040 | 2830026743 | draft | img | 1614693 |
GC content
@ref | GC-content | method |
---|---|---|
24748 | 64.5 | |
67770 | 64.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 96 | no |
motile | yes | 54.798 | no |
gram-positive | no | 97.647 | no |
anaerobic | no | 97.31 | no |
aerobic | yes | 78.894 | no |
halophile | yes | 53.97 | no |
spore-forming | no | 95.563 | no |
thermophile | no | 95.168 | yes |
glucose-util | yes | 82.637 | yes |
flagellated | no | 86.643 | no |
glucose-ferment | no | 91.058 | yes |
External links
@ref: 24748
culture collection no.: DSM 105040, JCM 30828, KCTC 18418
straininfo link
- @ref: 91237
- straininfo: 396553
literature
- topic: Phylogeny
- Pubmed-ID: 26311461
- title: Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015.
- authors: Jeong HI, Jin HM, Jeon CO
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000561
- year: 2015
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Naphthalenes/*metabolism, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
- topic2: 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 | |
24748 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105040 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105040) | |
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 | |
91237 | 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-ID396553.1 |