Strain identifier
BacDive ID: 131316
Type strain: 
Species: Hydrobacter penzbergensis
Strain Designation: EM 4
Strain history: <- H. Haug, Roche Diagnostics GmbH, Penzberg, Germany, EM4 <- W. Eder, Roche Diagnostics GmbH
NCBI tax ID(s): 1235997 (species)
version 8.1 (current version)
General
@ref: 22543
BacDive-ID: 131316
DSM-Number: 25353
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Hydrobacter penzbergensis EM 4 is a mesophilic, Gram-negative bacterium that was isolated from purified water system.
NCBI tax id
- NCBI tax id: 1235997
- Matching level: species
strain history
- @ref: 22543
- history: <- H. Haug, Roche Diagnostics GmbH, Penzberg, Germany, EM4 <- W. Eder, Roche Diagnostics GmbH
doi: 10.13145/bacdive131316.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Chitinophagia
- order: Chitinophagales
- family: Chitinophagaceae
- genus: Hydrobacter
- species: Hydrobacter penzbergensis
- full scientific name: Hydrobacter penzbergensis Eder et al. 2015
@ref: 22543
domain: Bacteria
phylum: Bacteroidetes
class: Chitinophagia
order: Sphingobacteriales
family: Chitinophagaceae
genus: Hydrobacter
species: Hydrobacter penzbergensis
full scientific name: Hydrobacter penzbergensis Eder et al. 2015
strain designation: EM 4
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
colony morphology
- @ref: 62815
- incubation period: 2 days
Culture and growth conditions
culture medium
- @ref: 22543
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 62815 | positive | growth | 30 | mesophilic |
| 22543 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.987 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 22543 | purified water system | Penzberg, Roche Diagnostics GmbH | Germany | DEU | Europe | |
| 62815 | Water system | Penzberg | Germany | DEU | Europe | 2010 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
taxonmaps
- @ref: 69479
- File name: preview.99_44433.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_1179;97_1383;98_32245;99_44433&stattab=map
- Last taxonomy: Sediminibacterium magnilacihabitans
- 16S sequence: JQ717375
- Sequence Identity:
- Total samples: 14083
- soil counts: 2579
- aquatic counts: 2659
- animal counts: 7557
- plant counts: 1288
Safety information
risk assessment
- @ref: 22543
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22543
- description: Hydrobacter penzbergensis strain EM 4 16S ribosomal RNA gene, partial sequence
- accession: JQ717375
- length: 1348
- database: ena
- NCBI tax ID: 1235997
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hydrobacter penzbergensis DSM 25353 | GCA_900106985 | contig | ncbi | 1235997 |
| 66792 | Hydrobacter penzbergensis strain DSM 25353 | 1235997.3 | wgs | patric | 1235997 |
| 66792 | Hydrobacter penzbergensis DSM 25353 | 2693429880 | draft | img | 1235997 |
GC content
- @ref: 22543
- GC-content: 44.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 96.408 | no |
| gram-positive | no | 96.713 | no |
| anaerobic | no | 99.56 | no |
| aerobic | yes | 93.707 | no |
| halophile | no | 96.883 | no |
| spore-forming | no | 94.673 | no |
| thermophile | no | 93.243 | no |
| glucose-util | yes | 87.286 | no |
| flagellated | no | 98.533 | no |
| glucose-ferment | no | 88.016 | no |
External links
@ref: 22543
culture collection no.: DSM 25353, CCUG 62278
straininfo link
- @ref: 89757
- straininfo: 405176
literature
- topic: Phylogeny
- Pubmed-ID: 25563914
- title: Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water.
- authors: Eder W, Peplies J, Wanner G, Fruhling A, Verbarg S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000040
- year: 2015
- mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 22543 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25353 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25353) | |||
| 62815 | Curators of the CCUG | https://www.ccug.se/strain?id=62278 | Culture Collection University of Gothenburg (CCUG) (CCUG 62278) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89757 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID405176.1 |