Name: Verminephrobacter eiseniae EF01-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3022

Type strain:

Species: Verminephrobacter eiseniae

Strain Designation: EF01-2

Culture col. no.: DSM 19249, ATCC BAA-1489

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

NCBI tax ID(s): 364317 (species)

SI-ID 406744

DSM 19249

Special Collections

Other strains from Verminephrobacter eiseniae

Section

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

Gram-negative
rod-shaped
chemoorganotroph
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Verminephrobacter*
	Species	**Verminephrobacter eiseniae**
	Full Scientific Name (LPSN)	Verminephrobacter eiseniae Pinel et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #23093]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.346

[Ref.: #23093]	Cell length	1.3-1.7 µm

[Ref.: #23093]	Cell width	0.4-0.8 µm

[Ref.: #23093]	Cell shape	rod-shaped

[Ref.: #7908]

Incubation period

>14 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7908]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7908]

Culture medium growth

[Ref.: #7908]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7908]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7908]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23093]

Nutrition type

chemoorganotroph

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23093]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #23093]	acetate ChEBI	+	carbon source
[Ref.: #23093]	aconitate ChEBI	-	carbon source
[Ref.: #23093]	aspartate ChEBI	+	carbon source
[Ref.: #23093]	benzoate ChEBI	-	carbon source
[Ref.: #23093]	citrate ChEBI	-	carbon source
[Ref.: #23093]	D-fructose ChEBI	+	carbon source
[Ref.: #23093]	D-fucose ChEBI	+	carbon source
[Ref.: #23093]	D-glucose ChEBI	+	carbon source
[Ref.: #23093]	D-mannose ChEBI	+	carbon source
[Ref.: #23093]	D-ribose ChEBI	+	carbon source
[Ref.: #23093]	D-xylose ChEBI	+	carbon source
[Ref.: #23093]	fumarate ChEBI	-	carbon source
[Ref.: #23093]	galactose ChEBI	+	carbon source
[Ref.: #23093]	glutaric acid ChEBI	-	carbon source
[Ref.: #23093]	L-arabinose ChEBI	+	carbon source
[Ref.: #23093]	L-fucose ChEBI	+	carbon source
[Ref.: #23093]	L-histidine ChEBI	-	carbon source
[Ref.: #23093]	L-isoleucine ChEBI	+	carbon source
[Ref.: #23093]	L-rhamnose ChEBI	+	carbon source
[Ref.: #23093]	L-serine ChEBI	-	carbon source
[Ref.: #23093]	L-threonine ChEBI	-	carbon source
[Ref.: #23093]	L-valine ChEBI	-	carbon source
[Ref.: #23093]	lactate ChEBI	+	carbon source
[Ref.: #23093]	maleic acid ChEBI	-	carbon source
[Ref.: #23093]	nitrate ChEBI	-	reduction
[Ref.: #23093]	propionate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #23093]	catalase	-	1.11.1.6
[Ref.: #23093]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23093]	gelatinase	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7908]	Sample type/isolated from	nephridia of earthworm Eisenia foetida
[Ref.: #7908]	Host species	Eisenia foetida
[Ref.: #7908]	Geographic location (country and/or sea, region)	Seattle
[Ref.: #7908]	Country	USA
[Ref.: #7908]	Country ISO 3 Code	USA
[Ref.: #7908]	Continent	North America

[Ref.: #23093]	Sample type/isolated from	from platings of nephridial homogenates of the earthworm species Eisenia foetida onto complex media
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ327663 (>99% sequence identity) for Verminephrobacter eiseniae subclade from Microbeatlas

Aquatic Samples	22
Soil Samples	37
Animal Samples	15
Plant Samples	5
Total Samples	79

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7908]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7908]	Verminephrobacter eiseniae EF01-2 16S ribosomal RNA gene, partial sequence	DQ327663	1459	GenBank ENA	391735 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Verminephrobacter eiseniae EF01-2	GCA_000015565	complete	GenBank ENA	391735 tax ID	*
[Ref.: #66792]	Verminephrobacter eiseniae EF01-2	391735.16	plasmid	PATRIC	391735 tax ID	*
[Ref.: #66792]	Verminephrobacter eiseniae EF01-2	391735.7	complete	PATRIC	391735 tax ID	*
[Ref.: #66792]	Verminephrobacter eiseniae EF01-2	639633065	complete	JGI IMG/M	391735 tax ID	*

[Ref.: #23093]

GC-content

66.8-67.2 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Verminephrobacter eiseniae EF01-2 EF01-2 NCBI: GCA_000015565.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.346	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.618	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	77.539	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.032	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	89.278	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	80.115	no

Availability in culture collections External links

[Ref.: #7908]

Culture collection no.

DSM 19249, ATCC BAA-1489

[Ref.: #72544]

SI-ID 406744

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny).	Pinel N, Davidson SK, Stahl DA	Int J Syst Evol Microbiol	10.1099/ijs.0.65174-0	2008	*

References

#7908

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19249

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#23093

Nicolás Pinel,Seana K. Davidson,David A. Stahl: Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny). IJSEM 58: 2147 - 2157 2008 ( DOI 10.1099/ijs.0.65174-0 , PubMed 18768621 )

#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) .

#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 .

#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) .

#72544

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 . ( DOI 10.60712/SI-ID406744.1 )

* These data were automatically processed and therefore are not curated

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Verminephrobacter eiseniae EF01-2 EF01-2

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