Strain identifier
BacDive ID: 158186
Type strain:
Species: Leucothrix pacifica
Strain Designation: XH122
Strain history: X.-H. Zhang XH122.
NCBI tax ID(s): 1247513 (species)
General
@ref: 64782
BacDive-ID: 158186
DSM-Number: 25984
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Leucothrix pacifica XH122 is a mesophilic, Gram-negative bacterium that was isolated from surface seawater.
NCBI tax id
- NCBI tax id: 1247513
- Matching level: species
strain history
@ref | history |
---|---|
64782 | <- X.-H. Zhang, Ocean Univ. China, Dept. of Marine Biology, Qingdao, P. R. China; XH122 |
67770 | X.-H. Zhang XH122. |
doi: 10.13145/bacdive158186.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Leucotrichaceae
- genus: Leucothrix
- species: Leucothrix pacifica
- full scientific name: Leucothrix pacifica Zhang et al. 2015
@ref: 64782
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Thiotrichaceae
genus: Leucothrix
species: Leucothrix pacifica
full scientific name: Leucothrix pacifica Zhang et al. 2015
strain designation: XH122
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.997
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69480 | no | 99.896 |
69481 | no | 100 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | latitude | longitude |
---|---|---|---|---|---|
64782 | surface seawater | South Pacific Gyre | Southwest Pacific Ocean | -45.9667 | -163.183 |
67770 | Surface seawater from the South Pacific Gyre (163° 11' S 45° 58' E) |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_105060.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_473;96_20019;97_35394;98_52157;99_105060&stattab=map
- Last taxonomy: Leucothrix pacifica
- 16S sequence: JQ082190
- Sequence Identity:
- Total samples: 792
- soil counts: 4
- aquatic counts: 660
- animal counts: 123
- plant counts: 5
Safety information
risk assessment
- @ref: 64782
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
64782 | Leucothrix pacifica strain XH122 16S ribosomal RNA gene, partial sequence | JX501256 | 1445 | ena | 1247513 |
67770 | Leucothrix sp. U1371-101227-XH122 16S ribosomal RNA gene, partial sequence | JQ082190 | 1447 | ena | 1171542 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Leucothrix pacifica strain JCM 18388 | 1247513.4 | wgs | patric | 1247513 |
66792 | Leucothrix pacifica JCM 18388 | 2889727904 | draft | img | 1247513 |
67770 | Leucothrix pacifica JCM 18388 | GCA_003172875 | scaffold | ncbi | 1247513 |
GC content
- @ref: 64782
- GC-content: 46.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 89.342 | no |
gram-positive | no | 98.219 | no |
anaerobic | no | 97.942 | no |
aerobic | yes | 89.52 | no |
halophile | no | 62.722 | no |
spore-forming | no | 95.117 | no |
thermophile | no | 99.065 | no |
glucose-util | yes | 90.132 | no |
flagellated | no | 88.281 | no |
glucose-ferment | no | 86.051 | no |
External links
@ref: 64782
culture collection no.: DSM 25984, JCM 18388
straininfo link
- @ref: 111017
- straininfo: 405777
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25896354 | Leucothrix pacifica sp. nov., isolated from seawater, and emended description of the genus Leucothrix. | Zhang Z, Gao X, Wang L, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.000270 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pacific Ocean, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thiotrichaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
Phylogeny | 30516460 | Leucothrix arctica sp. nov., isolated from Arctic seawater. | Baek K, Choi A, Lee YM, Lee HK, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003072 | 2018 | Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thiotrichaceae/*classification/genetics, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 31486761 | Leucothrix sargassi sp. nov., isolated from a marine alga [Sargassum natans (L.) Gaillon]. | Liu T, Zhang Y, Zhang X, Zhou L, Meng C, Zhou C, Jing C, Zhu W, Wang Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003694 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sargassum/*microbiology, Sequence Analysis, DNA, Thiotrichaceae/*classification/isolation & purification, Ubiquinone/chemistry | Transcriptome |
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 | |||
64782 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25984 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25984) | |||
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/ | ||||
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 | |||
111017 | 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-ID405777.1 |