Strain identifier

BacDive ID: 3022

Type strain: Yes

Species: Verminephrobacter eiseniae

Strain Designation: EF01-2

Strain history: <- N. Pinel, Univ. of Washington; EF01-2 <- S. K. Davidson

NCBI tax ID(s): 364317 (species)

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General

@ref: 7908

BacDive-ID: 3022

DSM-Number: 19249

keywords: genome sequence, 16S sequence, Bacteria, chemoorganotroph, mesophilic, Gram-negative, rod-shaped

description: Verminephrobacter eiseniae EF01-2 is a chemoorganotroph, mesophilic, Gram-negative bacterium that was isolated from nephridia of earthworm Eisenia foetida.

NCBI tax id

  • NCBI tax id: 364317
  • Matching level: species

strain history

  • @ref: 7908
  • history: <- N. Pinel, Univ. of Washington; EF01-2 <- S. K. Davidson

doi: 10.13145/bacdive3022.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Verminephrobacter
  • species: Verminephrobacter eiseniae
  • full scientific name: Verminephrobacter eiseniae Pinel et al. 2012

@ref: 7908

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Verminephrobacter

species: Verminephrobacter eiseniae

full scientific name: Verminephrobacter eiseniae Pinel et al. 2012

strain designation: EF01-2

type strain: yes

Morphology

cell morphology

  • @ref: 23093
  • gram stain: negative
  • cell length: 1.3-1.7 µm
  • cell width: 0.4-0.8 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 7908
  • incubation period: >14 days

Culture and growth conditions

culture medium

  • @ref: 7908
  • 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: 7908
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

nutrition type

  • @ref: 23093
  • type: chemoorganotroph

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2309322210aconitate-carbon source
2309316150benzoate-carbon source
2309316947citrate-carbon source
2309329806fumarate-carbon source
2309317859glutaric acid-carbon source
2309315971L-histidine-carbon source
2309317115L-serine-carbon source
2309316857L-threonine-carbon source
2309316414L-valine-carbon source
2309318300maleic acid-carbon source
2309317632nitrate-reduction
23093309162-oxoglutarate+carbon source
2309330089acetate+carbon source
2309335391aspartate+carbon source
2309315824D-fructose+carbon source
2309328847D-fucose+carbon source
2309317634D-glucose+carbon source
2309316024D-mannose+carbon source
2309316988D-ribose+carbon source
2309365327D-xylose+carbon source
2309324996lactate+carbon source
2309328260galactose+carbon source
2309330849L-arabinose+carbon source
2309318287L-fucose+carbon source
2309317191L-isoleucine+carbon source
2309362345L-rhamnose+carbon source
2309317272propionate+carbon source

enzymes

@refvalueactivityec
23093catalase-1.11.1.6
23093cytochrome oxidase+1.9.3.1
23093gelatinase-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
7908nephridia of earthworm Eisenia foetidaEisenia foetidaSeattleUSAUSANorth America
23093from platings of nephridial homogenates of the earthworm species Eisenia foetida onto complex media

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Host Body-Site#Urogenital tract#Nephridium
#Host#Invertebrates (Other)#Annelida
#Host Body-Site#Gastrointestinal tract
#Host Body-Site#Organ

taxonmaps

  • @ref: 69479
  • File name: preview.99_174667.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_2072;97_2497;98_3090;99_174667&stattab=map
  • Last taxonomy: Verminephrobacter eiseniae subclade
  • 16S sequence: DQ327663
  • Sequence Identity:
  • Total samples: 79
  • soil counts: 37
  • aquatic counts: 22
  • animal counts: 15
  • plant counts: 5

Safety information

risk assessment

  • @ref: 7908
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7908
  • description: Verminephrobacter eiseniae EF01-2 16S ribosomal RNA gene, partial sequence
  • accession: DQ327663
  • length: 1459
  • database: ena
  • NCBI tax ID: 391735

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Verminephrobacter eiseniae EF01-2GCA_000015565completencbi391735
66792Verminephrobacter eiseniae EF01-2391735.16plasmidpatric391735
66792Verminephrobacter eiseniae EF01-2391735.7completepatric391735
66792Verminephrobacter eiseniae EF01-2639633065completeimg391735

GC content

  • @ref: 23093
  • GC-content: 66.8-67.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes84.654no
flagellatedyes59.443no
gram-positiveno97.853no
anaerobicno99.067no
halophileno93.441no
spore-formingno93.015no
thermophileno84.937no
glucose-utilyes82.438yes
aerobicyes91.138no
glucose-fermentno85.467no

External links

@ref: 7908

culture collection no.: DSM 19249, ATCC BAA 1489

straininfo link

  • @ref: 72544
  • straininfo: 406744

literature

  • topic: Phylogeny
  • Pubmed-ID: 18768621
  • title: Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny).
  • authors: Pinel N, Davidson SK, Stahl DA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65174-0
  • year: 2008
  • mesh: Aerobiosis, Amino Acids/metabolism, Animals, Bacterial Typing Techniques, Base Composition, Biotin/metabolism, Catalase/metabolism, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oligochaeta/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Symbiosis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7908Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19249)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19249
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23093Nicolás Pinel,Seana K. Davidson,David A. Stahl10.1099/ijs.0.65174-0Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny)IJSEM 58: 2147-2157 200818768621
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
72544Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406744.1StrainInfo: A central database for resolving microbial strain identifiers