Strain identifier
BacDive ID: 384
Type strain: 
Species: Advenella mimigardefordensis
Strain Designation: DPN7
Strain history: <- J. H. Wübbeler, Univ. Münster, Germany; DPN7 <- J. H. Wübbeler;
NCBI tax ID(s): 302406 (species)
version 9.3 (current version)
General
@ref: 6801
BacDive-ID: 384
DSM-Number: 17166
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, ovoid-shaped
description: Advenella mimigardefordensis DPN7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from matured compost after the sieving process from the compost plant Coerde.
NCBI tax id
- NCBI tax id: 302406
- Matching level: species
strain history
- @ref: 6801
- history: <- J. H. Wübbeler, Univ. Münster, Germany; DPN7 <- J. H. Wübbeler;
doi: 10.13145/bacdive384.20250331.9.3
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 mimigardefordensis
- full scientific name: Advenella mimigardefordensis (Wübbeler et al. 2006) Gibello et al. 2009
synonyms
- @ref: 20215
- synonym: Tetrathiobacter mimigardefordensis
@ref: 6801
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Advenella
species: Advenella mimigardefordensis
full scientific name: Advenella mimigardefordensis (Wübbeler et al. 2006) Gibello et al. 2009
strain designation: DPN7
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31724 | negative | 1.5-2 µm | 1.5 µm | ovoid-shaped | yes | |
| 125438 | negative | 96.216 | ||||
| 125439 | negative | 95.4 |
pigmentation
- @ref: 31724
- production: yes
Culture and growth conditions
culture medium
- @ref: 6801
- 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 |
|---|---|---|---|
| 6801 | positive | growth | 28 |
| 31724 | positive | growth | 15-40 |
| 31724 | positive | optimum | 30-37 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 31724 | aerobe | |
| 125439 | aerobe | 96.4 |
spore formation
- @ref: 31724
- spore formation: no
observation
- @ref: 31724
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31724 | 17128 | adipate | + | carbon source |
| 31724 | 22599 | arabinose | + | carbon source |
| 31724 | 16947 | citrate | + | carbon source |
| 31724 | 25115 | malate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31724 | catalase | + | 1.11.1.6 |
| 31724 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 6801
- sample type: matured compost after the sieving process from the compost plant Coerde
- geographic location: Münster
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Engineered
- Cat2: #Biodegradation
- Cat3: #Composting
taxonmaps
- @ref: 69479
- File name: preview.99_6020.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1003;97_1169;98_1397;99_6020&stattab=map
- Last taxonomy: Advenella mimigardefordensis
- 16S sequence: AY880023
- Sequence Identity:
- Total samples: 640
- soil counts: 227
- aquatic counts: 111
- animal counts: 194
- plant counts: 108
Safety information
risk assessment
- @ref: 6801
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6801
- description: Advenella mimigardefordensis DPN7 16S ribosomal RNA gene, partial sequence
- accession: AY880023
- length: 1502
- database: nuccore
- NCBI tax ID: 1247726
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Advenella mimigardefordensis DPN7 | GCA_000521505 | complete | ncbi | 1247726 |
| 66792 | Advenella mimigardefordensis DPN7 | 1247726.3 | complete | patric | 1247726 |
| 66792 | Advenella mimigardefordensis DPN7 | 1247726.11 | plasmid | patric | 1247726 |
| 66792 | Advenella mimigardefordensis DPN7 | 2548877156 | complete | img | 1247726 |
GC content
- @ref: 6801
- GC-content: 55.1
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 96.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 95.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 81.5 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 84 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.216 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 99.125 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.594 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.51 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 99 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 51.195 | no |
External links
@ref: 6801
culture collection no.: DSM 17166, LMG 22922
straininfo link
- @ref: 70064
- straininfo: 133642
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16738107 | Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3'-dithiodipropionic acid. | Wubbeler JH, Lutke-Eversloh T, Van Trappen S, Vandamme P, Steinbuchel A | Int J Syst Evol Microbiol | 10.1099/ijs.0.64126-0 | 2006 | Alcaligenaceae/*classification/isolation & purification, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, Disulfides/metabolism, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Enzymology |
| Metabolism | 18456849 | Novel pathway for catabolism of the organic sulfur compound 3,3'-dithiodipropionic acid via 3-mercaptopropionic acid and 3-Sulfinopropionic acid to propionyl-coenzyme A by the aerobic bacterium Tetrathiobacter mimigardefordensis strain DPN7. | Wubbeler JH, Bruland N, Kretschmer K, Steinbuchel A | Appl Environ Microbiol | 10.1128/AEM.00422-08 | 2008 | 3-Mercaptopropionic Acid/metabolism, Acyl Coenzyme A/*metabolism, Aerobiosis, Alcaligenaceae/enzymology/genetics/growth & development/*metabolism, Molecular Sequence Data, Organic Chemicals/*metabolism, Propionates/chemistry/*metabolism, Sequence Analysis, DNA, Sulfur Compounds/chemistry/*metabolism | Enzymology |
| 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 | 24436068 | Description of Pelistega indica sp. nov., isolated from human gut. | Prakash O, Munot H, Nimonkar Y, Sharma M, Kumbhare S, Shouche YS | Int J Syst Evol Microbiol | 10.1099/ijs.0.059782-0 | 2014 | Alcaligenaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Gastrointestinal Tract/microbiology, Humans, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Pathogenicity |
| 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 |
|---|---|---|---|---|---|---|
| 6801 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17166) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17166 | |||
| 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 | |||
| 31724 | 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 | 28000 | 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 | |||
| 70064 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID133642.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |