Strain identifier
BacDive ID: 24676
Type strain: 
Species: Luteimonas abyssi
Strain Designation: XH031
Strain history: X.-H. Zhang and X. Fan XH031.
NCBI tax ID(s): 1247514 (species)
version 8.1 (current version)
General
@ref: 20637
BacDive-ID: 24676
DSM-Number: 25880
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Luteimonas abyssi XH031 is a mesophilic, motile bacterium that was isolated from ocean sediment.
NCBI tax id
- NCBI tax id: 1247514
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20637 | <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; XH031 |
| 67770 | X.-H. Zhang and X. Fan XH031. |
doi: 10.13145/bacdive24676.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Luteimonas
- species: Luteimonas abyssi
- full scientific name: Luteimonas abyssi Fan et al. 2014
@ref: 20637
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Lysobacteraceae, not assigned to order
family: Lysobacteraceae
genus: Luteimonas
species: Luteimonas abyssi
full scientific name: Luteimonas abyssi Fan et al. 2014
strain designation: XH031
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 91.29 | |
| 69480 | 99.996 | negative |
multimedia
- @ref: 20637
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25880.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 20637
- 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 |
|---|---|---|---|---|
| 20637 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 97 |
| 69480 | no | 99.995 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | latitude | longitude |
|---|---|---|---|---|
| 20637 | ocean sediment | South Pacific Gyre, station U1370 (41° 51' S 153° 06' W), 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 in the South Pacific Gyre (41° 51' S 153° 06' W) | -41.85 | -153.1 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_6824.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_2286;97_3378;98_5029;99_6824&stattab=map
- Last taxonomy: Luteimonas abyssi subclade
- 16S sequence: KC986351
- Sequence Identity:
- Total samples: 105
- soil counts: 20
- aquatic counts: 12
- animal counts: 60
- plant counts: 13
Safety information
risk assessment
- @ref: 20637
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20637
- description: Luteimonas abyssi strain XH031 16S ribosomal RNA gene, partial sequence
- accession: KC986351
- length: 1468
- database: ena
- NCBI tax ID: 1247514
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Luteimonas abyssi XH031 | 2775506892 | draft | img | 1247514 |
| 67770 | Luteimonas abyssi XH031 | GCA_001482195 | scaffold | ncbi | 1247514 |
GC content
- @ref: 20637
- GC-content: 70.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
- trait: spore-forming
- prediction: no
- confidence: 97
- training_data: no
External links
@ref: 20637
culture collection no.: DSM 25880, CGMCC 1.12611, JCM 19229
straininfo link
- @ref: 88514
- straininfo: 403743
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24170776 | Luteimonas abyssi sp. nov., isolated from deep-sea sediment. | Fan X, Yu T, Li Z, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.056010-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 26437920 | Luteimonas soli sp. nov., isolated from farmland soil. | Wang X, Yang HX, Zhang YK, Zhu SJ, Liu XW, Zhang H, Zhang CF, Zhao CR, Hu G, Hong Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000652 | 2015 | *Agriculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 26690083 | Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle. | Zhang L, Wang X, Yu M, Qiao Y, Zhang XH | BMC Genomics | 10.1186/s12864-015-2326-2 | 2015 | Adaptation, Biological, Bacterial Proteins/*genetics, *Genome, Bacterial, Geologic Sediments/microbiology, Molecular Sequence Annotation, Phylogeny, Sequence Analysis, DNA, Xanthomonadaceae/classification/*genetics/physiology | Genetics |
| Enzymology | 27241296 | LaaA, a novel high-active alkalophilic alpha-amylase from deep-sea bacterium Luteimonas abyssi XH031(T). | Song Q, Wang Y, Yin C, Zhang XH | Enzyme Microb Technol | 10.1016/j.enzmictec.2016.05.003 | 2016 | Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/*metabolism, Catalytic Domain/genetics, Cloning, Molecular, Escherichia coli/genetics/metabolism, Hydrogen-Ion Concentration, Industrial Microbiology, Kinetics, Mutagenesis, Site-Directed, Phylogeny, Protein Engineering, Recombinant Proteins/chemistry/genetics/metabolism, Seawater/microbiology, Sequence Homology, Amino Acid, Xanthomonadaceae/*enzymology/genetics/isolation & purification, alpha-Amylases/chemistry/genetics/*metabolism | Metabolism |
| Metabolism | 27342115 | Degradation properties of various macromolecules of cultivable psychrophilic bacteria from the deep-sea water of the South Pacific Gyre. | Zhang L, Wang Y, Liang J, Song Q, Zhang XH | Extremophiles | 10.1007/s00792-016-0856-4 | 2016 | Adaptation, Physiological, Bacterial Proteins/genetics/*metabolism, Carbohydrate Metabolism, *Cold Temperature, Glycoside Hydrolases/genetics/*metabolism, Hydrostatic Pressure, Lipase/genetics/*metabolism, Lipid Metabolism, *Microbiota, Pacific Ocean, Peptide Hydrolases/genetics/*metabolism, Proteolysis, Seawater/*microbiology | |
| Enzymology | 30054735 | Characterization of a novel cold-active xylanase from Luteimonas species. | Han Z, Shang-Guan F, Yang J | World J Microbiol Biotechnol | 10.1007/s11274-018-2505-9 | 2018 | Amino Acid Sequence, Bacterial Proteins/genetics, *Cold Temperature, DNA, Bacterial, Endo-1,4-beta Xylanases/chemistry/genetics/metabolism, Enzyme Assays, Enzyme Stability, Gene Expression Regulation, Bacterial, Genes, Bacterial/genetics, Hydrogen-Ion Concentration, Kinetics, Metals, Models, Molecular, Protein Conformation, Recombinant Proteins/chemistry/genetics/metabolism, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Sodium Chloride, Xanthomonadaceae/*enzymology/*genetics, Xylosidases/*chemistry/classification/*genetics/*metabolism | Metabolism |
| Phylogeny | 31833828 | Luteimonas yindakuii sp. nov. isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau. | Zhang S, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Li J, Huang Y, Zhang G, Zhu W, Huang Y, Tian Z, Zhou J, Dong K, Lei W, Ren Z, Wang S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003863 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taraxacum/*microbiology, Tibet, Vitamin K 2/analogs & derivatives/chemistry, Xanthomonadaceae/*classification/isolation & purification | 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 | |
| 20637 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25880 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25880) | |
| 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/ | ||
| 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 | |
| 88514 | 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-ID403743.1 |