Strain identifier
BacDive ID: 2903
Type strain: 
Species: Acidovorax caeni
Strain Designation: R-24608
Strain history: <- K. Heylen, Ghent University, Belgium
NCBI tax ID(s): 343013 (species)
version 8.1 (current version)
General
@ref: 8047
BacDive-ID: 2903
DSM-Number: 19327
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Acidovorax caeni R-24608 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.
NCBI tax id
- NCBI tax id: 343013
- Matching level: species
strain history
- @ref: 8047
- history: <- K. Heylen, Ghent University, Belgium
doi: 10.13145/bacdive2903.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Acidovorax
- species: Acidovorax caeni
- full scientific name: Acidovorax caeni Heylen et al. 2008
synonyms
- @ref: 20215
- synonym: Paenacidovorax caeni
@ref: 8047
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Acidovorax
species: Acidovorax caeni
full scientific name: Acidovorax caeni Heylen et al. 2008
strain designation: R-24608
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32368 | negative | 1.8 µm | 0.9 µm | rod-shaped | yes | |
| 69480 | yes | 97.825 | ||||
| 69480 | negative | 100 |
pigmentation
- @ref: 32368
- production: yes
Culture and growth conditions
culture medium
- @ref: 8047
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: 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 |
|---|---|---|---|---|
| 8047 | positive | growth | 28 | mesophilic |
| 32368 | positive | growth | 15-37 |
culture pH
- @ref: 32368
- ability: positive
- type: growth
- pH: 5.5-10.5
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 32368
- oxygen tolerance: facultative aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32368 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.998 |
halophily
- @ref: 32368
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0.5-2 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32368 | 16449 | alanine | + | carbon source |
| 32368 | 28644 | 2-oxopentanoate | + | carbon source |
| 32368 | 35391 | aspartate | + | carbon source |
| 32368 | 15740 | formate | + | carbon source |
| 32368 | 29987 | glutamate | + | carbon source |
| 32368 | 17754 | glycerol | + | carbon source |
| 32368 | 28087 | glycogen | + | carbon source |
| 32368 | 24996 | lactate | + | carbon source |
| 32368 | 25017 | leucine | + | carbon source |
| 32368 | 25115 | malate | + | carbon source |
| 32368 | 51850 | methyl pyruvate | + | carbon source |
| 32368 | 26271 | proline | + | carbon source |
| 32368 | 17272 | propionate | + | carbon source |
| 32368 | 17822 | serine | + | carbon source |
| 32368 | 30031 | succinate | + | carbon source |
| 32368 | 26986 | threonine | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32368 | catalase | + | 1.11.1.6 |
| 32368 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8047
- sample type: activated sludge
- geographic location: Ghent
- country: Belgium
- origin.country: BEL
- continent: Europe
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_1965.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_1537;99_1965&stattab=map
- Last taxonomy: Acidovorax caeni subclade
- 16S sequence: AM084006
- Sequence Identity:
- Total samples: 36303
- soil counts: 3656
- aquatic counts: 18053
- animal counts: 10287
- plant counts: 4307
Safety information
risk assessment
- @ref: 8047
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8047
- description: Acidovorax caeni 16S rRNA gene, type strain R-24608T
- accession: AM084006
- length: 1518
- database: ena
- NCBI tax ID: 343013
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenacidovorax caeni R-24608 | GCA_900116825 | contig | ncbi | 343013 |
| 66792 | Paenacidovorax caeni R-24608 | GCA_001298675 | contig | ncbi | 343013 |
| 66792 | Acidovorax caeni strain R-24608 | 343013.6 | wgs | patric | 343013 |
| 66792 | Acidovorax caeni R-24608 | 2740892283 | draft | img | 343013 |
| 66792 | Acidovorax caeni DSM 19327 | 2634166357 | draft | img | 343013 |
GC content
- @ref: 32368
- GC-content: 65.7
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.818 | no |
| anaerobic | no | 96.513 | no |
| halophile | no | 96.32 | no |
| spore-forming | no | 94.48 | yes |
| glucose-util | no | 81.533 | no |
| motile | yes | 89.904 | yes |
| flagellated | yes | 73.602 | no |
| thermophile | no | 98.908 | yes |
| aerobic | yes | 93.999 | no |
| glucose-ferment | no | 90.389 | no |
External links
@ref: 8047
culture collection no.: DSM 19327, LMG 24103
straininfo link
- @ref: 72426
- straininfo: 132460
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18175686 | Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge. | Heylen K, Lebbe L, De Vos P | Int J Syst Evol Microbiol | 10.1099/ijs.0.65387-0 | 2008 | Bacterial Proteins/analysis, Bacterial Typing Techniques, Belgium, Comamonadaceae/*classification/*genetics/isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, *Genetic Variation, Molecular Sequence Data, Nitrates/*metabolism, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Repetitive Sequences, Nucleic Acid/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity, Waste Disposal, Fluid/methods | Genetics |
| Phylogeny | 25212224 | Comamonas humi sp. nov., isolated from soil. | Hatayama K | Int J Syst Evol Microbiol | 10.1099/ijs.0.067439-0 | 2014 | Bacterial Typing Techniques, Base Composition, Comamonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
| Genetics | 26586902 | First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327). | Ehsani E, Jauregui R, Geffers R, Jarek M, Boon N, Pieper DH, Vilchez-Vargas R | Genome Announc | 10.1128/genomeA.01378-15 | 2015 | Phylogeny | |
| Phylogeny | 28068215 | Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring. | Khan IU, Hussain F, Tian Y, Habib N, Xian WD, Jiang Z, Amin A, Yuan CG, Zhou EM, Zhi XY, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001777 | 2017 | Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 29616893 | Acidovorax kalamii sp. nov., isolated from a water sample of the river Ganges. | Pal D, Kaur N, Sudan SK, Bisht B, Krishnamurthi S, Mayilraj S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002736 | 2018 | Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, India, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA | Transcriptome |
| Phylogeny | 29627890 | Acidovorax monticola sp. nov., isolated from soil. | Chaudhary DK, Kim J | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1083-z | 2018 | Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, Forests, Metabolomics/methods, Molecular Typing, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology | Phenotype |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 8047 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19327) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19327 | ||||
| 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 | ||||
| 32368 | 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 | 28596 | 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 | ||
| 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 | ||||
| 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 | ||||
| 72426 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID132460.1 | StrainInfo: A central database for resolving microbial strain identifiers |