Strain identifier
BacDive ID: 131475
Type strain:
Species: Lewinella xylanilytica
Strain Designation: 13-9-B8
Strain history: <- Kee-Sun Shin, KRIBB
NCBI tax ID(s): 1514080 (species)
General
@ref: 22702
BacDive-ID: 131475
DSM-Number: 29526
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped
description: Lewinella xylanilytica 13-9-B8 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from coastal seawater.
NCBI tax id
- NCBI tax id: 1514080
- Matching level: species
strain history
@ref | history |
---|---|
22702 | <- H.-R. Sung, KRIBB; 13-9-B8 |
67771 | <- Kee-Sun Shin, KRIBB |
doi: 10.13145/bacdive131475.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Saprospiria
- order: Saprospirales
- family: Lewinellaceae
- genus: Lewinella
- species: Lewinella xylanilytica
- full scientific name: Lewinella xylanilytica Sung et al. 2015
synonyms
- @ref: 20215
- synonym: Neolewinella xylanilytica
@ref: 22702
domain: Bacteria
phylum: Bacteroidetes
class: Saprospiria
order: Sphingobacteriales
family: Lewinellaceae
genus: Lewinella
species: Lewinella xylanilytica
full scientific name: Lewinella xylanilytica Sung et al. 2015
strain designation: 13-9-B8
type strain: yes
Morphology
cell morphology
@ref | cell shape | motility | gram stain | confidence |
---|---|---|---|---|
67771 | rod-shaped | no | ||
67771 | negative | |||
69480 | no | 94.65 | ||
69480 | negative | 99.998 |
Culture and growth conditions
culture medium
- @ref: 22702
- 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 |
---|---|---|---|---|
22702 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.988 |
observation
- @ref: 67771
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | + | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22702 | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
22702 | coastal seawater | Marado, Jeju Island | Republic of Korea | KOR | Asia |
67771 | From Seawater | Jeju Island | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_41933.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_489;96_19415;97_24096;98_30481;99_41933&stattab=map
- Last taxonomy: Lewinella xylanilytica subclade
- 16S sequence: KJ573521
- Sequence Identity:
- Total samples: 313
- soil counts: 53
- aquatic counts: 192
- animal counts: 57
- plant counts: 11
Safety information
risk assessment
- @ref: 22702
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22702
- description: Lewinella xylanilytica strain 13-9-B8 16S ribosomal RNA gene, partial sequence
- accession: KJ573521
- length: 1462
- database: ena
- NCBI tax ID: 1514080
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Neolewinella xylanilytica DSM 29526 | GCA_002934605 | scaffold | ncbi | 1514080 |
66792 | Lewinella xylanilytica strain DSM 29526 | 1514080.3 | wgs | patric | 1514080 |
66792 | Lewinella xylanilytica DSM 29526 | 2734482073 | draft | img | 1514080 |
GC content
@ref | GC-content | method |
---|---|---|
22702 | 59.1 | high performance liquid chromatography (HPLC) |
67771 | 59.1 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 95.158 | yes |
gram-positive | no | 96.925 | yes |
anaerobic | no | 99.306 | yes |
aerobic | yes | 89.847 | no |
halophile | no | 76.619 | no |
spore-forming | no | 94.115 | no |
glucose-util | yes | 88.147 | no |
thermophile | no | 98.819 | yes |
motile | no | 88.692 | yes |
glucose-ferment | no | 88.257 | yes |
External links
@ref: 22702
culture collection no.: DSM 29526, KCTC 32663
straininfo link
- @ref: 89892
- straininfo: 402767
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26297220 | Lewinella xylanilytica sp. nov., a member of the family Saprospiraceae isolated from coastal seawater. | Sung HR, Lee JM, Kim M, Shin KS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000435 | 2015 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 28875904 | Lewinella maritima sp. nov., and Lewinella lacunae sp. nov., novel bacteria from marine environments. | Kang H, Kim H, Joung Y, Joh K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002176 | 2017 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | 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 | |
22702 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29526 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29526) | |
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 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
68368 | Automatically annotated from API 20E | |||
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 | |
89892 | 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-ID402767.1 |