Strain identifier
BacDive ID: 383
Type strain: 
Species: Advenella kashmirensis
Strain Designation: WT001
Strain history: <- P. Roy <- W. Ghosh; WT001
NCBI tax ID(s): 310575 (species)
version 8.1 (current version)
General
@ref: 6757
BacDive-ID: 383
DSM-Number: 17095
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped
description: Advenella kashmirensis WT001 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from bulk soil of a temperate orchard.
NCBI tax id
- NCBI tax id: 310575
- Matching level: species
strain history
- @ref: 6757
- history: <- P. Roy <- W. Ghosh; WT001
doi: 10.13145/bacdive383.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Alcaligenaceae
- genus: Advenella
- species: Advenella kashmirensis
- full scientific name: Advenella kashmirensis (Ghosh et al. 2005) Gibello et al. 2009
synonyms
- @ref: 20215
- synonym: Tetrathiobacter kashmirensis
@ref: 6757
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Advenella
species: Advenella kashmirensis
full scientific name: Advenella kashmirensis (Ghosh et al. 2005) Gibello et al. 2009 emend. Shmareva et al. 2016
strain designation: WT001
type strain: yes
Morphology
cell morphology
- @ref: 31452
- gram stain: negative
- cell length: 1.4 µm
- cell width: 1.05 µm
- cell shape: coccus-shaped
- motility: no
pigmentation
- @ref: 31452
- production: yes
Culture and growth conditions
culture medium
- @ref: 6757
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: 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 |
|---|---|---|---|---|
| 6757 | positive | growth | 28 | mesophilic |
| 31452 | positive | growth | 10-42 | |
| 31452 | positive | optimum | 26 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31452 | positive | growth | 4.5-8.5 | alkaliphile |
| 31452 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 6757
- oxygen tolerance: aerobe
observation
- @ref: 31452
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31452 | 30089 | acetate | + | carbon source |
| 31452 | 22599 | arabinose | + | carbon source |
| 31452 | 29016 | arginine | + | carbon source |
| 31452 | 35391 | aspartate | + | carbon source |
| 31452 | 16947 | citrate | + | carbon source |
| 31452 | 28757 | fructose | + | carbon source |
| 31452 | 28260 | galactose | + | carbon source |
| 31452 | 17234 | glucose | + | carbon source |
| 31452 | 29987 | glutamate | + | carbon source |
| 31452 | 17716 | lactose | + | carbon source |
| 31452 | 25115 | malate | + | carbon source |
| 31452 | 17306 | maltose | + | carbon source |
| 31452 | 37684 | mannose | + | carbon source |
| 31452 | 30031 | succinate | + | carbon source |
| 31452 | 16296 | D-tryptophan | + | carbon source |
| 31452 | 18222 | xylose | + | carbon source |
| 31452 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31452 | catalase | + | 1.11.1.6 |
| 31452 | cytochrome oxidase | + | 1.9.3.1 |
| 31452 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 6757
- sample type: bulk soil of a temperate orchard
- geographic location: Srinagar, Jammu and Kashmir
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Grove (Orchard) |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_1770.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1003;97_1169;98_1397;99_1770&stattab=map
- Last taxonomy: Advenella
- 16S sequence: AJ864470
- Sequence Identity:
- Total samples: 2457
- soil counts: 822
- aquatic counts: 378
- animal counts: 766
- plant counts: 491
Safety information
risk assessment
- @ref: 6757
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6757
- description: Tetrathiobacter kashmirensis 16S rRNA gene, type strain WT001T
- accession: AJ864470
- length: 1467
- database: ena
- NCBI tax ID: 310575
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Advenella kashmirensis WT001 | GCA_000219915 | complete | ncbi | 1036672 |
| 66792 | Advenella kashmirensis WT001 | 1036672.3 | wgs | patric | 1036672 |
| 66792 | Advenella kashmirensis WT001 | 1036672.20 | plasmid | patric | 1036672 |
| 66792 | Advenella kashmirensis WT001 | 2515154053 | complete | img | 1036672 |
GC content
- @ref: 31452
- GC-content: 55.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 77.488 | no |
| flagellated | no | 96.208 | no |
| gram-positive | no | 98.119 | yes |
| anaerobic | no | 99.416 | no |
| aerobic | yes | 94.01 | yes |
| halophile | no | 77.461 | no |
| spore-forming | no | 96.751 | no |
| thermophile | no | 99.677 | no |
| glucose-util | yes | 54.65 | no |
| glucose-ferment | no | 89.789 | no |
External links
@ref: 6757
culture collection no.: DSM 17095, LMG 22965, MTCC 7002
straininfo link
- @ref: 70063
- straininfo: 135988
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16166666 | Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India. | Ghosh W, Bagchi A, Mandal S, Dam B, Roy P | Int J Syst Evol Microbiol | 10.1099/ijs.0.63595-0 | 2005 | Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification/physiology, Climate, Crops, Agricultural/growth & development, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, India, Malus/growth & development, Molecular Sequence Data, Oxidation-Reduction, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Tetrathionic Acid/*metabolism | Genetics |
| Phylogeny | 19567588 | Reclassification of the members of the genus Tetrathiobacter Ghosh et al. 2005 to the genus Advenella Coenye et al. 2005. | Gibello A, Vela AI, Martin M, Barra-Caracciolo A, Grenni P, Fernandez-Garayzabal JF | Int J Syst Evol Microbiol | 10.1099/ijs.0.007443-0 | 2009 | Alcaligenaceae/*classification/genetics, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 22307513 | Advenella faeciporci sp. nov., a nitrite-denitrifying bacterium isolated from nitrifying-denitrifying activated sludge collected from a laboratory-scale bioreactor treating piggery wastewater. | Matsuoka M, Park S, An SY, Miyahara M, Kim SW, Kamino K, Fushinobu S, Yokota A, Wakagi T, Shoun H | Int J Syst Evol Microbiol | 10.1099/ijs.0.037440-0 | 2012 | Alcaligenaceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Bioreactors, DNA, Bacterial/genetics, Denitrification, Fatty Acids/analysis, Molecular Sequence Data, Nitrification, Nitrites, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Swine, Waste Water/*microbiology | Genetics |
| Genetics | 23741407 | Genome implosion elicits host-confinement in Alcaligenaceae: evidence from the comparative genomics of Tetrathiobacter kashmirensis, a pathogen in the making. | Ghosh W, Alam M, Roy C, Pyne P, George A, Chakraborty R, Majumder S, Agarwal A, Chakraborty S, Majumdar S, Gupta SK | PLoS One | 10.1371/journal.pone.0064856 | 2013 | Alcaligenaceae/*genetics/pathogenicity, Bacterial Adhesion, Base Composition, Betaproteobacteria/genetics/pathogenicity, Biological Evolution, Cell Line, Gene Transfer, Horizontal, Genes, Bacterial, *Genome, Bacterial, Genomics, Hemolysis, *Host-Pathogen Interactions, Humans, Molecular Sequence Annotation, Open Reading Frames, Recombination, Genetic, Virulence Factors/genetics | Pathogenicity |
| Enzymology | 24317404 | Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. | Schurmann M, Demming RM, Krewing M, Rose J, Wubbeler JH, Steinbuchel A | J Bacteriol | 10.1128/JB.01265-13 | 2013 | Acyl Coenzyme A/metabolism, Acyl-CoA Dehydrogenases/genetics/*isolation & purification/*metabolism, Bacteria/*enzymology/genetics, Chromatography, Gel, Cloning, Molecular, Gene Expression, Kinetics, Oxidation-Reduction, Protein Multimerization, Recombinant Proteins/genetics/isolation & purification/metabolism, Spectrophotometry, Substrate Specificity | Metabolism |
| Enzymology | 24339214 | Optimization of a phenol extraction-based protein preparation method amenable to downstream 2DE and MALDI-MS based analysis of bacterial proteomes. | Alam M, Ghosh W | Proteomics | 10.1002/pmic.201300146 | 2014 | Acetone/chemistry, Bacteria/*chemistry, Bacterial Proteins/analysis/*isolation & purification, Chemical Precipitation, Electrophoresis, Gel, Two-Dimensional/*methods, Phenol/*chemistry, Proteome/analysis/*isolation & purification, Proteomics/methods, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods, Trichloroacetic Acid/chemistry | Proteome |
| Phylogeny | 25916151 | [Advenella kashmirensis subsp. methylica PK1, a facultative methylotroph from carex rhizosphere]. | Poroshina MN, Doronina NV, Kaparullina EN, Trotsenko IuA | Mikrobiologiia | 2015 | Alcaligenaceae/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition, Cyperus/microbiology, DNA, Bacterial/chemistry/*genetics, Fatty Acids/metabolism, Hydrogen-Ion Concentration, Metabolic Networks and Pathways, Methanol/metabolism, Methylobacterium/*classification/genetics/isolation & purification/*metabolism, Phospholipids/metabolism, *Phylogeny, RNA, Ribosomal, 16S/chemistry/*genetics, Rhizosphere, Sequence Analysis, DNA, Temperature, Turkey | Metabolism | |
| Phylogeny | 26620977 | Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples. | Wang H, Zhou S, Wang Y, Kong D, Guo X, Zhu J, Dong W, Ruan Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000811 | 2015 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6757 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17095) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17095 | |||
| 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 | |||
| 31452 | 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 | 27755 | 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 | |||
| 70063 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID135988.1 | StrainInfo: A central database for resolving microbial strain identifiers |