Strain identifier
BacDive ID: 12609
Type strain: 
Species: Xylanimonas ulmi
Strain Designation: XIL08
Strain history: CECT 5731 <-- E. Velázquez XIL08.
NCBI tax ID(s): 228973 (species)
version 8.1 (current version)
General
@ref: 6652
BacDive-ID: 12609
DSM-Number: 16932
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Xylanimonas ulmi XIL08 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from decayed wood .
NCBI tax id
- NCBI tax id: 228973
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6652 | <- M. Trujillo <- R. Rivas; XIL08 |
| 67770 | CECT 5731 <-- E. Velázquez XIL08. |
doi: 10.13145/bacdive12609.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Promicromonosporaceae
- genus: Xylanimonas
- species: Xylanimonas ulmi
- full scientific name: Xylanimonas ulmi (Rivas et al. 2004) Heo et al. 2020
synonyms
- @ref: 20215
- synonym: Xylanibacterium ulmi
@ref: 6652
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Promicromonosporaceae
genus: Xylanimonas
species: Xylanimonas ulmi
full scientific name: Xylanimonas ulmi (Rivas et al. 2004) Heo et al. 2020
strain designation: XIL08
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29998 | positive | 0.9 µm | 0.3 µm | rod-shaped | no | |
| 69480 | positive | 100 |
pigmentation
- @ref: 29998
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 6652 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
| 6652 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6652 | positive | growth | 28 | mesophilic |
| 29998 | positive | growth | 25-28 | mesophilic |
| 29998 | positive | optimum | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 29998
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
- @ref: 29998
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29998 | no | |
| 69481 | no | 92 |
| 69480 | no | 99.93 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-8(H4)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29998 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
| 29998 | 30089 | acetate | + | carbon source |
| 29998 | 22599 | arabinose | + | carbon source |
| 29998 | 17057 | cellobiose | + | carbon source |
| 29998 | 28757 | fructose | + | carbon source |
| 29998 | 28260 | galactose | + | carbon source |
| 29998 | 17754 | glycerol | + | carbon source |
| 29998 | 37684 | mannose | + | carbon source |
| 29998 | 506227 | N-acetylglucosamine | + | carbon source |
| 29998 | 33942 | ribose | + | carbon source |
| 29998 | 17992 | sucrose | + | carbon source |
| 29998 | 27082 | trehalose | + | carbon source |
| 29998 | 17151 | xylitol | + | carbon source |
| 29998 | 18222 | xylose | + | carbon source |
| 29998 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29998 | gelatinase | + | |
| 29998 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 6652 | decayed wood (Ulmus nigra) | Ulmus nigra | Salamanca | Spain | ESP | Europe |
| 67770 | Decayed wood of an elm tree | Spain | ESP | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Decomposing plant |
| #Host | #Plants | #Tree |
| #Host Body Product | #Plant | #Timber |
Safety information
risk assessment
- @ref: 6652
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6652
- description: Xylanibacterium ulmi 16S ribosomal RNA gene, complete sequence
- accession: AY273185
- length: 1513
- database: ena
- NCBI tax ID: 228973
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Xylanibacterium ulmi strain DSM 16932 | 228973.3 | wgs | patric | 228973 |
| 66792 | Xylanibacterium ulmi DSM 16932 | 2806310544 | draft | img | 228973 |
| 67770 | Xylanibacterium ulmi DSM 16932 | GCA_004216535 | contig | ncbi | 228973 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6652 | 72.3 | |
| 67770 | 72 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 92 | no |
| motile | no | 88.5 | yes |
| gram-positive | yes | 89.886 | yes |
| anaerobic | no | 96.642 | no |
| aerobic | yes | 79.667 | yes |
| halophile | no | 95.592 | no |
| spore-forming | no | 91.213 | yes |
| glucose-util | yes | 84.749 | no |
| flagellated | no | 98.306 | no |
| thermophile | no | 98.894 | yes |
| glucose-ferment | no | 74.409 | no |
External links
@ref: 6652
culture collection no.: DSM 16932, CECT 5731, LMG 21721, JCM 14284, NBRC 106152, NCIMB 14264
straininfo link
- @ref: 81823
- straininfo: 89016
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15023975 | Xylanibacterium ulmi gen. nov., sp. nov., a novel xylanolytic member of the family Promicromonosporaceae. | Rivas R, Trujillo ME, Schumann P, Kroppenstedt RM, Sanchez M, Mateos PF, Martinez-Molina E, Velazquez E | Int J Syst Evol Microbiol | 10.1099/ijs.0.02808-0 | 2004 | Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Lipid Metabolism, Micrococcaceae/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Phylogeny, Xylans/metabolism | Metabolism |
| Phylogeny | 31976851 | Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas. | Heo J, Cho H, Hamada M, Kim JS, Hong SB, Kim SJ, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004001 | 2020 | Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6652 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16932) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16932 | ||||
| 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 | ||||
| 29998 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26363 | 28776041 | ||
| 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 81823 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID89016.1 | StrainInfo: A central database for resolving microbial strain identifiers |