Strain identifier
BacDive ID: 3828
Type strain: 
Species: Larkinella arboricola
Strain Designation: Z-0532, Z0532
Strain history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow; Z0532 <- I. S. Kulichevskaya
NCBI tax ID(s): 643671 (species)
version 8.1 (current version)
General
@ref: 15990
BacDive-ID: 3828
DSM-Number: 21851
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Larkinella arboricola Z-0532 is a Gram-negative bacterium that was isolated from decaying wood.
NCBI tax id
- NCBI tax id: 643671
- Matching level: species
strain history
- @ref: 15990
- history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow; Z0532 <- I. S. Kulichevskaya
doi: 10.13145/bacdive3828.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Larkinella
- species: Larkinella arboricola
- full scientific name: Larkinella arboricola Kulichevskaya et al. 2010
@ref: 15990
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Larkinella
species: Larkinella arboricola
full scientific name: Larkinella arboricola Kulichevskaya et al. 2010
strain designation: Z-0532, Z0532
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.997
Culture and growth conditions
culture medium
- @ref: 15990
- name: LARKINELLA ARBORICOLA MEDIUM (DSMZ Medium 1327)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1327
- composition: Name: LARKINELLA ARBORICOLA MEDIUM (DSMZ Medium 1327) Composition: Agar 15.0 g/l N-Acetylglucosamine 1.0 g/l MgSO4 x 7 H2O 0.594 g/l Glucose 0.5 g/l Nitrilotriacetic acid 0.2 g/l Peptone 0.1 g/l KH2PO4 0.1 g/l Yeast extract 0.1 g/l Casamino acids 0.1 g/l CaCl2 x 2 H2O 0.0667 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water
culture temp
- @ref: 15990
- growth: positive
- type: growth
- temperature: 22-28
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.918 |
Isolation, sampling and environmental information
isolation
- @ref: 15990
- sample type: decaying wood
- geographic location: Moscow region
- country: Russia
- origin.country: RUS
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Decomposing plant |
| #Host Body Product | #Plant | #Timber |
| #Host | #Plants | #Tree |
Safety information
risk assessment
- @ref: 15990
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15990
- description: Larkinella arboricola partial 16S rRNA gene, type strain Z0532T
- accession: FN391025
- length: 1437
- database: ena
- NCBI tax ID: 643671
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Larkinella arboricola DSM 21851 | GCA_003259745 | scaffold | ncbi | 643671 |
| 66792 | Larkinella arboricola strain DSM 21851 | 643671.4 | wgs | patric | 643671 |
| 66792 | Larkinella arboricola DSM 21851 | 2593339304 | draft | img | 643671 |
GC content
- @ref: 15990
- GC-content: 52.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 93.003 | no |
| flagellated | no | 97.22 | no |
| gram-positive | no | 96.852 | no |
| anaerobic | no | 99.48 | no |
| aerobic | yes | 92.706 | no |
| halophile | no | 96.004 | no |
| spore-forming | no | 94.331 | no |
| glucose-util | yes | 85.845 | no |
| thermophile | no | 98.86 | no |
| glucose-ferment | no | 84.13 | no |
External links
@ref: 15990
culture collection no.: DSM 21851, VKM B-2528
straininfo link
- @ref: 73339
- straininfo: 398361
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 28417190 | Larkinella harenae sp. nov., Isolated from Korean Beach Soil. | Park SJ, Lee JJ, Lee SY, Lee DS, Kim MK, Ten LN, Jung HY | Curr Microbiol | 10.1007/s00284-017-1246-6 | 2017 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Phylogeny, Republic of Korea, *Soil Microbiology | Metabolism |
| Phylogeny | 28879840 | Larkinella ripae sp. nov., isolated from seashore soil. | Lee YH, Lee JJ, Lee SY, Lee DS, Kim MK, Ten LN, Jung HY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002188 | 2017 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 29019013 | Larkinella terrae sp. nov., isolated from soil on Jeju Island, South Korea. | Ten LN, Jeon J, Park SJ, Park S, Lee SY, Kim MK, Jung HY | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0955-y | 2017 | Base Composition, Cytophagaceae/chemistry/*classification/genetics/isolation & purification, *Islands, Metabolomics/methods, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology | Phenotype |
| Phylogeny | 29299846 | Larkinella roseus sp. nov., a species of the family Cytophagaceae isolated from beach soil. | Lee JB, Hong S, Lee SY, Park SJ, Park KI, Choi SG, Kim MK, Ten LN, Jung HY | J Microbiol | 10.1007/s12275-018-7476-x | 2018 | Base Composition, Cytophagaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phosphatidylethanolamines/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
| Phylogeny | 29300161 | Larkinella knui sp. nov., isolated from soil. | Jeon J, Ten LN, Lee JJ, Lee SY, Park S, Cho YJ, Kim MK, Jung HY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002550 | 2018 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15990 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21851) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21851 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 73339 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398361.1 | StrainInfo: A central database for resolving microbial strain identifiers |