Strain identifier
BacDive ID: 6949
Type strain: 
Species: Methanobacterium veterum
Strain Designation: MK4
Strain history: <- V. Shcherbakova, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; MK4 <- K. Krivushin {2006}
NCBI tax ID(s): 408577 (species)
version 8.1 (current version)
General
@ref: 8288
BacDive-ID: 6949
DSM-Number: 19849
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Methanobacterium veterum MK4 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from ancient permafrost sediments.
NCBI tax id
- NCBI tax id: 408577
- Matching level: species
strain history
- @ref: 8288
- history: <- V. Shcherbakova, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; MK4 <- K. Krivushin {2006}
doi: 10.13145/bacdive6949.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanobacteria
- order: Methanobacteriales
- family: Methanobacteriaceae
- genus: Methanobacterium
- species: Methanobacterium veterum
- full scientific name: Methanobacterium veterum Krivushin et al. 2010
@ref: 8288
domain: Archaea
phylum: Euryarchaeota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanobacterium
species: Methanobacterium veterum
full scientific name: Methanobacterium veterum Krivushin et al. 2010
strain designation: MK4
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29342 | negative | 5 µm | 0.425 µm | rod-shaped | no | |
| 69480 | negative | 99.988 |
Culture and growth conditions
culture medium
- @ref: 8288
- name: METHANOBACTERIUM ESPANOLAE MEDIUM (DSMZ Medium 506)
- growth: yes
- link: https://mediadive.dsmz.de/medium/506
- composition: Name: METHANOBACTERIUM ESPANOLAE MEDIUM (DSMZ Medium 506) Composition: Na-acetate x 3 H2O 2.4728 g/l Na2CO3 0.49456 g/l (NH4)2SO4 0.445104 g/l K2HPO4 0.286845 g/l Na2S x 9 H2O 0.24728 g/l L-Cysteine HCl x H2O 0.24728 g/l KH2PO4 0.178042 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Nicotinic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8288 | positive | growth | 28 | mesophilic |
| 29342 | positive | growth | 10-46 | |
| 29342 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29342 | positive | growth | 5.2-9.4 | alkaliphile |
| 29342 | positive | optimum | 7.3 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 8288 | anaerobe | |
| 29342 | anaerobe | |
| 69480 | anaerobe | 99.679 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29342 | no | |
| 69481 | no | 100 |
| 69480 | no | 98.881 |
halophily
- @ref: 29342
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.3 %
metabolite utilization
- @ref: 29342
- Chebi-ID: 30089
- metabolite: acetate
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
- @ref: 8288
- sample type: ancient (3 million years old) permafrost sediments
- geographic location: Kolyma Lowland (70° 06' N 154° 04' E)
- country: Russia
- origin.country: RUS
- continent: Asia
- latitude: 70.1
- longitude: 154.067
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Sediment |
Safety information
risk assessment
- @ref: 8288
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8288
- description: Methanobacterium veterum strain MK4 16S ribosomal RNA gene, partial sequence
- accession: EF016285
- length: 1347
- database: ena
- NCBI tax ID: 408577
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanobacterium veterum MK4 | GCA_000745485 | scaffold | ncbi | 408577 |
| 66792 | Methanobacterium veterum MK4, DSM 19849 | 2582580744 | draft | img | 408577 |
| 66792 | Methanobacterium veterum MK4 | GCA_027110455 | scaffold | ncbi | 408577 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8288 | 33.8±0.3 | thermal denaturation, midpoint method (Tm) |
| 29342 | 33.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 89.282 | no |
| flagellated | no | 97.048 | yes |
| gram-positive | no | 96.769 | yes |
| anaerobic | yes | 96.928 | yes |
| aerobic | no | 93.769 | no |
| halophile | no | 88.84 | yes |
| spore-forming | no | 94.461 | yes |
| thermophile | no | 96.223 | no |
| glucose-util | yes | 65.314 | no |
| glucose-ferment | no | 67.219 | no |
External links
@ref: 8288
culture collection no.: DSM 19849, VKM B-2440
straininfo link
- @ref: 76411
- straininfo: 368575
literature
- topic: Phylogeny
- Pubmed-ID: 19654368
- title: Methanobacterium veterum sp. nov., from ancient Siberian permafrost.
- authors: Krivushin KV, Shcherbakova VA, Petrovskaya LE, Rivkina EM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.011205-0
- year: 2009
- mesh: Base Sequence, Freezing, Methane/metabolism, Methanobacteriaceae/*classification/genetics/metabolism, Molecular Sequence Data, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Siberia, *Soil Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8288 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19849) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19849 | |||
| 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 | |||
| 29342 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25754 | 28776041 | |
| 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) | |||
| 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 | |||
| 76411 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID368575.1 | StrainInfo: A central database for resolving microbial strain identifiers |