Strain identifier
BacDive ID: 17597
Type strain: 
Species: Xanthomonas sp.
Strain history: IAM 12308 <-- R. J. Roberts; Cold Sprig Habor Lab., USA <-- ATCC 13461 ("Xanthomonas holcicola") <-- W. H. Burkholder; XH3.
NCBI tax ID(s): 29446 (species)
version 8.1 (current version)
General
@ref: 1481
BacDive-ID: 17597
DSM-Number: 3851
keywords: genome sequence, Bacteria, mesophilic, motile
description: Xanthomonas sp. DSM 3851 is a mesophilic, motile bacterium that was isolated from Holcussp..
NCBI tax id
- NCBI tax id: 29446
- Matching level: species
strain history
| @ref | history |
|---|---|
| 1481 | <- ATCC <- W.H. Burkholder XH3 (Xanthomonas holcicola) |
| 67770 | IAM 12308 <-- R. J. Roberts; Cold Sprig Habor Lab., USA <-- ATCC 13461 ("Xanthomonas holcicola") <-- W. H. Burkholder; XH3. |
doi: 10.13145/bacdive17597.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Xanthomonas
- species: Xanthomonas sp.
- full scientific name: Xanthomonas Dowson 1939 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Phytomonas
@ref: 1481
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Xanthomonas
species: Xanthomonas sp.
full scientific name: Xanthomonas sp.
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.014 | |
| 69480 | 99.993 | negative |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 1481 | GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) | yes | https://mediadive.dsmz.de/medium/54 | Name: GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) Composition: CaCO3 20.0 g/l Glucose 20.0 g/l Agar 17.0 g/l Yeast extract 10.0 g/l Distilled water |
| 1481 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1481 | positive | growth | 26 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
compound production
- @ref: 1481
- compound: restriction endonuclease XhoI
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 1481 | Holcussp. | Holcus | ||||
| 67770 | Leaf of Holcus sp. | Holcus sp. | Texas | USA | USA | North America |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Xanthomonas vasicola NCPPB 989 | GCA_000772795 | scaffold | ncbi | 56459 |
| 66792 | Xanthomonas vasicola NCPPB 989 | 56459.26 | wgs | patric | 56459 |
| 66792 | Xanthomonas vasicola NCPPB 989 | 2645727931 | draft | img | 56459 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 82.702 | no |
| flagellated | no | 88.921 | no |
| gram-positive | no | 98.216 | no |
| anaerobic | no | 98.933 | no |
| aerobic | yes | 92.523 | no |
| halophile | no | 95.146 | no |
| spore-forming | no | 95.638 | no |
| thermophile | no | 99.195 | yes |
| glucose-util | yes | 93.75 | no |
| glucose-ferment | no | 89.333 | no |
External links
@ref: 1481
culture collection no.: DSM 3851, ATCC 13461, NCPPB 989, JCM 20467, CCM 1447, IAM 12308, ICMP 451, ICPB XH3, LMG 7416, VKM B-618
straininfo link
- @ref: 86592
- straininfo: 13888
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 1481 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3851) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3851 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 86592 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13888.1 | StrainInfo: A central database for resolving microbial strain identifiers |