Strain identifier
BacDive ID: 13867
Type strain: 
Species: Parvibaculum lavamentivorans
Strain Designation: DS-1
Strain history: <- DSM <- D. Schleheck and K. Denger, Univ. Konstanz
NCBI tax ID(s): 256618 (species)
version 9.1 (current version)
General
@ref: 4875
BacDive-ID: 13867
DSM-Number: 13023
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Parvibaculum lavamentivorans DS-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from activated sludge of industrial sewage plant.
NCBI tax id
- NCBI tax id: 256618
- Matching level: species
strain history
| @ref | history |
|---|---|
| 4875 | <- D. Schleheck and K. Denger, Univ. Konstanz |
| 67771 | <- DSM <- D. Schleheck and K. Denger, Univ. Konstanz |
doi: 10.13145/bacdive13867.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Parvibaculaceae
- genus: Parvibaculum
- species: Parvibaculum lavamentivorans
- full scientific name: Parvibaculum lavamentivorans Schleheck et al. 2004
@ref: 4875
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Parvibaculaceae
genus: Parvibaculum
species: Parvibaculum lavamentivorans
full scientific name: Parvibaculum lavamentivorans Schleheck et al. 2004
strain designation: DS-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 30169 | negative | rod-shaped | no | |
| 67771 | negative | |||
| 69480 | negative | 98.828 |
Culture and growth conditions
culture medium
- @ref: 4875
- name: TWEEN 80-AGAR (DSMZ Medium 884)
- growth: yes
- link: https://mediadive.dsmz.de/medium/884
- composition: Name: TWEEN 80-AGAR (DSMZ Medium 884) Composition: Agar 15.0 g/l Tween 80 10.0 g/l Peptone 9.99999 g/l NaCl 5.0 g/l CaCl2 x 2 H2O 0.0999999 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 4875 | positive | growth | 30 |
| 67771 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 30169 | aerobe |
| 67771 | aerobe |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30169 | 30089 | acetate | + | carbon source |
| 30169 | 16236 | ethanol | + | carbon source |
| 30169 | 15361 | pyruvate | + | carbon source |
| 30169 | 30031 | succinate | + | carbon source |
| 30169 | 53424 | tween 20 | + | carbon source |
| 30169 | 53426 | tween 80 | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30169 | catalase | + | 1.11.1.6 |
| 30169 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 4875 | activated sludge of industrial sewage plant | Ludwigshafen | Germany | DEU | Europe |
| 67771 | From activated sludge of industrial sewage plant | Germany | DEU | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | |
| #Engineered | #Waste | #Activated sludge |
| #Engineered | #Waste | #Water treatment plant |
Safety information
risk assessment
- @ref: 4875
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4875
- description: Parvibaculum lavamentivorans 16S ribosomal RNA gene, complete sequence
- accession: AY387398
- length: 1451
- database: nuccore
- NCBI tax ID: 402881
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Parvibaculum lavamentivorans DS-1 | GCA_000017565 | complete | ncbi | 402881 |
| 66792 | Parvibaculum lavamentivorans DS-1 | 402881.8 | complete | patric | 402881 |
| 66792 | Parvibaculum lavamentivorans DS-1 | 640753040 | complete | img | 402881 |
GC content
- @ref: 4875
- GC-content: 64
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.828 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 87.375 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.132 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.489 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.707 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 57.014 | no |
External links
@ref: 4875
culture collection no.: DSM 13023, KCTC 22775, NCIMB 13966
straininfo link
- @ref: 83043
- straininfo: 49388
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 15240283 | Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria. | Schleheck D, Knepper TP, Fischer K, Cook AM | Appl Environ Microbiol | 10.1128/AEM.70.7.4053-4063.2004 | 2004 | Bacteria/growth & development/*metabolism, Benzenesulfonates/*metabolism, Biodegradation, Environmental, Oxygenases/metabolism, Spectrophotometry, Ultraviolet, Surface-Active Agents/*metabolism | |
| Phylogeny | 15388700 | Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. | Schleheck D, Tindall BJ, Rossello-Mora R, Cook AM | Int J Syst Evol Microbiol | 10.1099/ijs.0.03020-0 | 2004 | Acetic Acid/metabolism, Alkanesulfonic Acids/*metabolism, Alphaproteobacteria/*classification/cytology/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, Biofilms/growth & development, Cardiolipins/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA/genetics, Molecular Sequence Data, Movement, Octanes/metabolism, Phosphatidylcholines/analysis, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Surface-Active Agents/metabolism, Water Microbiology | Metabolism |
| Metabolism | 16075201 | Omega-oxygenation of the alkyl sidechain of linear alkylbenzenesulfonate (LAS) surfactant in Parvibaculum lavamentivorans(T). | Schleheck D, Cook AM | Arch Microbiol | 10.1007/s00203-005-0002-7 | 2005 | Acetates/metabolism, Alkanesulfonic Acids/*metabolism, Alphaproteobacteria/growth & development/*metabolism, Biodegradation, Environmental, Oxidation-Reduction, Oxygen/*metabolism, Oxygenases/metabolism, Surface-Active Agents/*metabolism | |
| Metabolism | 17557839 | Parvibaculum lavamentivorans DS-1T degrades centrally substituted congeners of commercial linear alkylbenzenesulfonate to sulfophenyl carboxylates and sulfophenyl dicarboxylates. | Schleheck D, Knepper TP, Eichhorn P, Cook AM | Appl Environ Microbiol | 10.1128/AEM.00632-07 | 2007 | Alkanesulfonic Acids/*metabolism, Alphaproteobacteria/growth & development/*metabolism, Bacteriological Techniques, Biodegradation, Environmental, Biotechnology, Carboxylic Acids/*metabolism, Chromatography, High Pressure Liquid, Spectrometry, Mass, Electrospray Ionization, Surface-Active Agents/metabolism | Biotechnology |
| Phylogeny | 20228216 | Parvibaculum indicum sp. nov., isolated from deep-sea water. | Lai Q, Wang L, Liu Y, Yuan J, Sun F, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.021899-0 | 2010 | Alphaproteobacteria/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
| Phylogeny | 22268074 | Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise. | Rosario-Passapera R, Keddis R, Wong R, Lutz RA, Starovoytov V, Vetriani C | Int J Syst Evol Microbiol | 10.1099/ijs.0.039594-0 | 2012 | Alkanes/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phyllobacteriaceae/*classification/genetics/isolation & purification/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Metabolism |
| Genetics | 22675581 | Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)). | Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, Han J, Woyke T, Goodwin L, Pennacchio L, Nolan M, Cook AM, Kjelleberg S, Thomas T | Stand Genomic Sci | 10.4056/sigs.2215005 | 2011 | ||
| Metabolism | 25805343 | An efficient high-throughput screening assay for rapid directed evolution of halohydrin dehalogenase for preparation of beta-substituted alcohols. | Wan NW, Liu ZQ, Xue F, Huang K, Tang LJ, Zheng YG | Appl Microbiol Biotechnol | 10.1007/s00253-015-6527-z | 2015 | Alcohols/*metabolism, Alphaproteobacteria/enzymology/genetics, Amino Acid Substitution, Azides/metabolism, Colorimetry/*methods, Directed Molecular Evolution/*methods, High-Throughput Screening Assays/*methods, Hydrolases/genetics/*metabolism, Mutant Proteins/genetics/metabolism, Mutation, Missense | Enzymology |
| Metabolism | 26359084 | An enzymatic method for determination of azide and cyanide in aqueous phase. | Wan NW, Liu ZQ, Xue F, Zheng YG | J Biotechnol | 10.1016/j.jbiotec.2015.09.001 | 2015 | Alphaproteobacteria/enzymology, Azides/*analysis/chemistry/metabolism, Bacterial Proteins/metabolism, Chromatography, Gas/*methods, Cyanides/*analysis/chemistry/metabolism, Enzyme Stability, Hydrogen-Ion Concentration, Hydrolases/*metabolism, Temperature | Enzymology |
| Enzymology | 35101610 | Exploration and structure-based engineering of alkenal double bond reductases catalyzing the CalphaCbeta double bond reduction of coniferaldehyde. | Kamimura N, Watanabe S, Sugimoto K, Senda M, Araki T, Yu HY, Hishiyama S, Kajita S, Senda T, Masai E | N Biotechnol | 10.1016/j.nbt.2022.01.007 | 2022 | Acrolein/analogs & derivatives, *Lignin/chemistry, *Oxidoreductases/genetics/metabolism, Substrate Specificity | Biotechnology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 4875 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13023) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13023 | |||
| 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 | |||
| 30169 | 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 | 26518 | 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) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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) | |||
| 83043 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49388.1 | StrainInfo: A central database for resolving microbial strain identifiers |