Name: Verrucomicrobium spinosum DSM 4136
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17210

Type strain:

Species: Verrucomicrobium spinosum

Culture col. no.: DSM 4136, ATCC 43997, IFAM 1439, JCM 18804

Strain history: DSM 4136 <-- H. Schlesner IFAM 1439.

NCBI tax ID(s): 240016 (strain), 2736 (species)

SI-ID 42166

ATCC 43997, DSM 4136

Other strains from Verrucomicrobium spinosum

V. spinosum CCUG 46164

Section

Verrucomicrobium spinosum DSM 4136 is a mesophilic, Gram-negative bacterium that was isolated from fresh water from lake.

Gram-negative
mesophilic
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	*Verrucomicrobiota*
	Class	*Verrucomicrobiia*
	Order	*Verrucomicrobiales*
	Family	*Verrucomicrobiaceae*
	Genus	*Verrucomicrobium*
	Species	**Verrucomicrobium spinosum**
	Full Scientific Name (LPSN)	Verrucomicrobium spinosum Schlesner 1988

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.981

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1598]

Culture medium

M13 VERRUCOMICROBIUM MEDIUM (DSMZ Medium 607)

[Ref.: #1598]

Culture medium growth

[Ref.: #1598]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1598]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1598]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #1598]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %95
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.971

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

[Ref.: #1598]	Sample type/isolated from	fresh water from lake
[Ref.: #1598]	Geographic location (country and/or sea, region)	Holstein, Vollstedter See
[Ref.: #1598]	Country	Germany
[Ref.: #1598]	Country ISO 3 Code	DEU
[Ref.: #1598]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Surface water of an eutrophic lake (Vollstedter See
[Ref.: #67770]	Geographic location (country and/or sea, region)	Holstein
[Ref.: #67770]	Country	Germany
[Ref.: #67770]	Country ISO 3 Code	DEU
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X90515 (>99% sequence identity) for Verrucomicrobium spinosum subclade from Microbeatlas

Aquatic Samples	4307
Soil Samples	10809
Animal Samples	3476
Plant Samples	3518
Total Samples	22110

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

[Ref.: #1598]

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.: #20218]	V.spinosum DNA for 16S ribosomal RNA gene	X90515	1492	ENA	240016 tax ID	*
[Ref.: #20218]	V.spinosum partial 16S rRNA (part 1)	X59721	285	ENA	240016 tax ID	*
[Ref.: #20218]	V.spinosum 16S partial rRNA (part 2)	X59722	229	ENA	240016 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Verrucomicrobium spinosum DSM 4136 = JCM 18804	GCA_000172155	complete	GenBank	240016 tax ID
[Ref.: #67770]	Verrucomicrobium spinosum DSM 4136 = JCM 18804	GCA_001313125	contig	GenBank	240016 tax ID
[Ref.: #66792]	Verrucomicrobium spinosum DSM 4136	240016.6	wgs	PATRIC	240016 tax ID	*
[Ref.: #66792]	Verrucomicrobium spinosum DSM 4136 = JCM 18804	240016.10	wgs	PATRIC	240016 tax ID	*
[Ref.: #66792]	Verrucomicrobium spinosum DSM 4136	641736179	complete	JGI IMG/M	240016 tax ID	*
[Ref.: #66792]	Verrucomicrobium spinosum JCM 18804	2734481932	draft	JGI IMG/M	240016 tax ID	*

[Ref.: #67770]

GC-content

58.4-58.8 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Verrucomicrobium spinosum DSM 4136 = JCM 18804 DSM 4136 NCBI: GCA_000172155.1
[Ref.: #69481]	spore-forming	no	95	no

Availability in culture collections External links

[Ref.: #1598]

Culture collection no.

DSM 4136, ATCC 43997, IFAM 1439, JCM 18804

[Ref.: #86209]

SI-ID 42166

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae.	Szuroczki S, Abbaszade G, Szabo A, Boka K, Schumann P, Toth E	Int J Syst Evol Microbiol	10.1099/ijsem.0.004025	2020	*
Enzymology	Identification and Partial Characterization of a Novel UDP-N-Acetylenolpyruvoylglucosamine Reductase/UDP-N-Acetylmuramate:l-Alanine Ligase Fusion Enzyme from Verrucomicrobium spinosum DSM 4136(T).	Naqvi KF, Patin D, Wheatley MS, Savka MA, Dobson RC, Gan HM, Barreteau H, Blanot D, Mengin-Lecreulx D, Hudson AO	Front Microbiol	10.3389/fmicb.2016.00362	2016	*
Enzymology	Biochemical characterization of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate ligase (MurE) from Verrucomicrobium spinosum DSM 4136(T.).	McGroty SE, Pattaniyil DT, Patin D, Blanot D, Ravichandran AC, Suzuki H, Dobson RC, Savka MA, Hudson AO	PLoS One	10.1371/journal.pone.0066458	2013	*
Phylogeny	Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class Verrucomicrobiae.	Otsuka S, Ueda H, Suenaga T, Uchino Y, Hamada M, Yokota A, Senoo K	Int J Syst Evol Microbiol	10.1099/ijs.0.041848-0	2012	*
Phylogeny	Random transposon mutagenesis of Verrucomicrobium spinosum DSM 4136(T).	Domman DB, Steven BT, Ward NL	Arch Microbiol	10.1007/s00203-010-0666-5	2010	*

References

#1598

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4136

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86209

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-ID42166.1 )

* These data were automatically processed and therefore are not curated

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Verrucomicrobium spinosum DSM 4136 = JCM 18804 DSM 4136

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