Strain identifier
BacDive ID: 17210
Type strain: 
Species: Verrucomicrobium spinosum
Strain history: DSM 4136 <-- H. Schlesner IFAM 1439.
NCBI tax ID(s): 240016 (strain), 2736 (species)
version 8.1 (current version)
General
@ref: 1598
BacDive-ID: 17210
DSM-Number: 4136
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Verrucomicrobium spinosum DSM 4136 is a mesophilic, Gram-negative bacterium that was isolated from fresh water from lake.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 240016 | strain |
| 2736 | species |
strain history
| @ref | history |
|---|---|
| 1598 | <- H. Schlesner, IFAM |
| 67770 | DSM 4136 <-- H. Schlesner IFAM 1439. |
doi: 10.13145/bacdive17210.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/verrucomicrobiota
- domain: Bacteria
- phylum: Verrucomicrobiota
- class: Verrucomicrobiia
- order: Verrucomicrobiales
- family: Verrucomicrobiaceae
- genus: Verrucomicrobium
- species: Verrucomicrobium spinosum
- full scientific name: Verrucomicrobium spinosum Schlesner 1988
@ref: 1598
domain: Bacteria
phylum: Verrucomicrobia
class: Verrucomicrobiae
order: Verrucomicrobiales
family: Verrucomicrobiaceae
genus: Verrucomicrobium
species: Verrucomicrobium spinosum
full scientific name: Verrucomicrobium spinosum Schlesner 1988
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.981
Culture and growth conditions
culture medium
- @ref: 1598
- name: M13 VERRUCOMICROBIUM MEDIUM (DSMZ Medium 607)
- growth: yes
- link: https://mediadive.dsmz.de/medium/607
- composition: Name: M13 VERRUCOMICROBIUM MEDIUM (DSMZ Medium 607) Composition: NaCl 5.86925 g/l MgCl2 x 6 H2O 1.24525 g/l Na2SO4 0.97925 g/l MgSO4 x 7 H2O 0.594 g/l CaCl2 0.2755 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.2 g/l KCl 0.166 g/l CaCl2 x 2 H2O 0.0667 g/l NaHCO3 0.048 g/l H3BO3 0.0065 g/l SrCl2 0.006 g/l KBr 0.0015 g/l ZnSO4 x 7 H2O 0.001095 g/l NaF 0.00075 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Nicotinamide 5e-05 g/l Riboflavin 5e-05 g/l Calcium pantothenate 5e-05 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Vitamin B12 1e-06 g/l Tris-HCl buffer Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1598 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 95 |
| 69480 | no | 99.971 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1598 | fresh water from lake | Holstein, Vollstedter See | Germany | DEU | Europe |
| 67770 | Surface water of an eutrophic lake (Vollstedter See | Holstein | Germany | DEU | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
taxonmaps
- @ref: 69479
- File name: preview.99_3492.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15914;96_1817;97_2180;98_2675;99_3492&stattab=map
- Last taxonomy: Verrucomicrobium spinosum subclade
- 16S sequence: X90515
- Sequence Identity:
- Total samples: 22110
- soil counts: 10809
- aquatic counts: 4307
- animal counts: 3476
- plant counts: 3518
Safety information
risk assessment
- @ref: 1598
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | V.spinosum partial 16S rRNA (part 1) | X59721 | 285 | ena | 240016 |
| 20218 | V.spinosum 16S partial rRNA (part 2) | X59722 | 229 | ena | 240016 |
| 20218 | V.spinosum DNA for 16S ribosomal RNA gene | X90515 | 1492 | ena | 240016 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Verrucomicrobium spinosum DSM 4136 | 240016.6 | wgs | patric | 240016 |
| 66792 | Verrucomicrobium spinosum DSM 4136 = JCM 18804 | 240016.10 | wgs | patric | 240016 |
| 66792 | Verrucomicrobium spinosum DSM 4136 | 641736179 | complete | img | 240016 |
| 66792 | Verrucomicrobium spinosum JCM 18804 | 2734481932 | draft | img | 240016 |
| 67770 | Verrucomicrobium spinosum DSM 4136 = JCM 18804 | GCA_000172155 | complete | ncbi | 240016 |
| 67770 | Verrucomicrobium spinosum DSM 4136 = JCM 18804 | GCA_001313125 | contig | ncbi | 240016 |
GC content
- @ref: 67770
- GC-content: 58.4-58.8
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
- trait: spore-forming
- prediction: no
- confidence: 95
- training_data: no
External links
@ref: 1598
culture collection no.: DSM 4136, ATCC 43997, IFAM 1439, JCM 18804
straininfo link
- @ref: 86209
- straininfo: 42166
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21184215 | Random transposon mutagenesis of Verrucomicrobium spinosum DSM 4136(T). | Domman DB, Steven BT, Ward NL | Arch Microbiol | 10.1007/s00203-010-0666-5 | 2010 | Bacteria/*genetics, DNA, Bacterial/genetics, Electroporation, Gene Library, Mutagenesis, Insertional/*methods, Phylogeny, *Retroelements, Sequence Analysis, DNA, Transformation, Genetic | Transcriptome |
| Phylogeny | 23041636 | 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 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Verrucomicrobia/*classification/genetics, Vitamin K 2/analysis | Genetics |
| Enzymology | 23785498 | 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 | Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/isolation & purification/*metabolism, Gene Expression, Genome, Bacterial, Glutamic Acid/*metabolism, Kinetics, Models, Molecular, Molecular Sequence Data, Open Reading Frames, Peptide Synthases/chemistry/genetics/isolation & purification/*metabolism, Peptidoglycan/chemistry/metabolism, Protein Conformation, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Alignment, Verrucomicrobia/*enzymology/genetics/ultrastructure | Metabolism |
| Enzymology | 27047475 | 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 | ||
| Phylogeny | 32038004 | 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 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hungary, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Verrucomicrobia/*classification/isolation & purification, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1598 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4136) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4136 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 86209 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42166.1 | StrainInfo: A central database for resolving microbial strain identifiers |