Strain identifier
BacDive ID: 14262
Type strain: 
Species: Rhizorhabdus histidinilytica
Strain Designation: UM2
Strain history: <- CCM <- R. Lal, Department of Zoology, Univ. of Delhi; UM2
NCBI tax ID(s): 439228 (species)
version 8.1 (current version)
General
@ref: 17806
BacDive-ID: 14262
DSM-Number: 24951
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Rhizorhabdus histidinilytica UM2 is an aerobe, Gram-negative, motile bacterium that was isolated from contaminated soil from hexachlorocyclohexane dump site.
NCBI tax id
- NCBI tax id: 439228
- Matching level: species
strain history
- @ref: 17806
- history: <- CCM <- R. Lal, Department of Zoology, Univ. of Delhi; UM2
doi: 10.13145/bacdive14262.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Rhizorhabdus
- species: Rhizorhabdus histidinilytica
- full scientific name: Rhizorhabdus histidinilytica (Nigam et al. 2010) Hördt et al. 2020
synonyms
- @ref: 20215
- synonym: Sphingomonas histidinilytica
@ref: 17806
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas histidinilytica
full scientific name: Sphingomonas histidinilytica Nigam et al. 2010
strain designation: UM2
type strain: yes
Morphology
cell morphology
- @ref: 29228
- gram stain: negative
- cell length: 1.4 µm
- cell width: 0.4 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29228
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 29228 | positive | growth | 04-40 | |
| 29228 | positive | optimum | 28 | mesophilic |
culture pH
- @ref: 29228
- ability: positive
- type: optimum
- pH: 7.5
Physiology and metabolism
oxygen tolerance
- @ref: 29228
- oxygen tolerance: aerobe
spore formation
- @ref: 29228
- spore formation: no
halophily
- @ref: 29228
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 1.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29228 | 22599 | arabinose | + | carbon source |
| 29228 | 27570 | histidine | + | carbon source |
| 29228 | 37684 | mannose | + | carbon source |
| 29228 | 28053 | melibiose | + | carbon source |
| 29228 | 18257 | ornithine | + | carbon source |
| 29228 | 26271 | proline | + | carbon source |
| 29228 | 17822 | serine | + | carbon source |
| 29228 | 16296 | D-tryptophan | + | carbon source |
| 29228 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 29228
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 17806
- sample type: contaminated soil from hexachlorocyclohexane dump site
- geographic location: Uttar Pradesh, Lucknow, Ummari village
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_1380.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_798;97_929;98_1089;99_1380&stattab=map
- Last taxonomy: Sphingomonas
- 16S sequence: EF530202
- Sequence Identity:
- Total samples: 656
- soil counts: 335
- aquatic counts: 171
- animal counts: 94
- plant counts: 56
Safety information
risk assessment
- @ref: 17806
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17806
- description: Sphingomonas histidinilytica strain UM2 16S ribosomal RNA gene, partial sequence
- accession: EF530202
- length: 1394
- database: ena
- NCBI tax ID: 439228
Genome sequences
- @ref: 66792
- description: Rhizorhabdus histidinilytica UM2
- accession: GCA_900167915
- assembly level: contig
- database: ncbi
- NCBI tax ID: 439228
GC content
- @ref: 29228
- GC-content: 66.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 84.62 | yes |
| flagellated | no | 89.746 | no |
| gram-positive | no | 96.035 | no |
| anaerobic | no | 99.061 | yes |
| aerobic | yes | 94.996 | yes |
| halophile | no | 95.806 | yes |
| spore-forming | no | 95.223 | yes |
| thermophile | no | 97.79 | yes |
| glucose-util | yes | 78.133 | no |
| glucose-ferment | no | 92.514 | no |
External links
@ref: 17806
culture collection no.: DSM 24951, CCM 7545, MTCC 9473
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17806 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24951) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24951 | |||
| 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 | |||
| 29228 | 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 | 25649 | 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) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta |