We are hiring!

Strain identifier

BacDive ID: 131316

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7.1 (current version):
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 7.1 (current version)

General

@ref: 22543

BacDive-ID: 131316

DSM-Number: 25353

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Hydrobacter penzbergensis EM 4 is a mesophilic bacterium that was isolated from purified water system.

NCBI tax id

  • NCBI tax id: 1235997
  • Matching level: species

strain history: <- H. Haug, Roche Diagnostics GmbH, Penzberg, Germany, EM4 <- W. Eder, Roche Diagnostics GmbH

doi: 10.13145/bacdive131316.20221219.7.1

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: 99.192

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

@refgrowthtypetemperaturerange
62815positivegrowth30mesophilic
22543positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 96.525

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.24

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
22543purified water systemPenzberg, Roche Diagnostics GmbHGermanyDEUEurope
62815Water systemPenzbergGermanyDEUEurope2010

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hydrobacter penzbergensis DSM 25353GCA_900106985contigncbi1235997
66792Hydrobacter penzbergensis strain DSM 253531235997.3wgspatric1235997
66792Hydrobacter penzbergensis DSM 253532693429880draftimg1235997

GC content

  • @ref: 22543
  • GC-content: 44.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 22543

culture collection no.: DSM 25353, CCUG 62278

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

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22543Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25353Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25353)
62815Curators of the CCUGhttps://www.ccug.se/strain?id=62278Culture Collection University of Gothenburg (CCUG) (CCUG 62278)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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