Strain identifier
BacDive ID: 130146
Type strain:
Species: Verticiella sediminum
Strain Designation: XH089
Strain history: CIP <- 2019, JCM <- X.-H. Zhang and X. Fan, Ocean Univ. China, Qingdao, P. R. China: strain XH089
NCBI tax ID(s): 1247510 (species)
General
@ref: 21444
BacDive-ID: 130146
DSM-Number: 27279
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Verticiella sediminum XH089 is a mesophilic, motile bacterium that was isolated from deep subseafloor sediment.
NCBI tax id
- NCBI tax id: 1247510
- Matching level: species
strain history
@ref | history |
---|---|
21444 | <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; XH089 |
67770 | X.-H. Zhang and X. Fan XH089. |
122538 | CIP <- 2019, JCM <- X.-H. Zhang and X. Fan, Ocean Univ. China, Qingdao, P. R. China: strain XH089 |
doi: 10.13145/bacdive130146.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Alcaligenaceae
- genus: Verticiella
- species: Verticiella sediminum
- full scientific name: Verticiella sediminum (Zhang et al. 2014) Vandamme 2016
synonyms
@ref synonym 20215 Verticia sediminum 20215 Achromobacter sediminum
@ref: 21444
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Verticiella
species: Verticiella sediminum
full scientific name: Verticiella sediminum (Zhang et al. 2014) Vandamme 2016
strain designation: XH089
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 92.032 | ||
69480 | 99.999 | negative | ||
122538 | yes | negative | rod-shaped |
colony morphology
- @ref: 21444
- incubation period: 2-3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
21444 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
122538 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21444 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.997 |
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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21444 | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + | + | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | latitude | longitude | country | isolation date |
---|---|---|---|---|---|---|
21444 | deep subseafloor sediment | South Pacific Gyre at station U1370 (41°51' S 153°06' W) at a depth of 18.1–18.2 m below the sea floor | -41.85 | -153.1 | ||
67770 | Deep-sea sediment at a depth of 18.1-18.2 m below the sea floor in the South Pacific Gyre (41° 51' S 153° 06' W) | -41.85 | -153.1 | |||
122538 | Environment, Deep-sea sediment | Pacific Ocean | 2010-10-09 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
21444 | 1 | Risk group (German classification) |
122538 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
21444 | Achromobacter sediminum strain XH089 16S ribosomal RNA gene, partial sequence | KC986352 | 1454 | ena | 1247510 |
67770 | Achromobacter sediminum strain XH089 16S ribosomal RNA gene, partial sequence | JX501254 | 1433 | ena | 1247510 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Verticiella sediminum strain DSM 27279 | 1247510.3 | wgs | patric | 1247510 |
66792 | Verticiella sediminum DSM 27279 | 2886867506 | draft | img | 1247510 |
67770 | Verticiella sediminum DSM 27279 | GCA_007558815 | contig | ncbi | 1247510 |
GC content
- @ref: 21444
- GC-content: 66.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 82.681 | no |
gram-positive | no | 97.825 | no |
anaerobic | no | 98.577 | no |
aerobic | yes | 90.542 | no |
halophile | no | 84.233 | no |
spore-forming | no | 93.803 | no |
thermophile | no | 98.462 | yes |
glucose-util | no | 78.437 | yes |
flagellated | no | 69.604 | no |
glucose-ferment | no | 92.666 | yes |
External links
@ref: 21444
culture collection no.: DSM 27279, JCM 19223, CIP 111718
straininfo link
- @ref: 88700
- straininfo: 402940
literature
- topic: Phylogeny
- Pubmed-ID: 24711589
- title: Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre.
- authors: Zhang Z, Fan X, Gao X, Zhang XH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.062265-0
- year: 2014
- mesh: Achromobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
- topic2: Genetics
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
21444 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27279 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27279) | |||
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 | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
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 | |||
88700 | 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-ID402940.1 | |||
122538 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111718 | Collection of Institut Pasteur (CIP 111718) |