Strain identifier
BacDive ID: 6928
Type strain: 
Species: Methanobacterium formicicum
Strain Designation: PP1
Strain history: <- G.D. Vogels, PP1
NCBI tax ID(s): 1204725 (strain), 2162 (species)
version 8.1 (current version)
General
@ref: 1427
BacDive-ID: 6928
DSM-Number: 3637
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic
description: Methanobacterium formicicum PP1 is an anaerobe, mesophilic archaeon that was isolated from from giant amoeba Pelomyxa palustris.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1204725 | strain |
| 2162 | species |
strain history
- @ref: 1427
- history: <- G.D. Vogels, PP1
doi: 10.13145/bacdive6928.20230509.8.1
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 formicicum
- full scientific name: Methanobacterium formicicum Schnellen 1947 (Approved Lists 1980)
@ref: 1427
domain: Archaea
phylum: Euryarchaeota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanobacterium
species: Methanobacterium formicicum
full scientific name: Methanobacterium formicicum Schnellen 1947 emend. Judicial Commission 1992
strain designation: PP1
type strain: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 1427 | MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523) | yes | https://mediadive.dsmz.de/medium/1523 | Name: MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523) Composition: Brain heart infusion 5.98802 g/l Proteose peptone 5.98802 g/l NaHCO3 3.99202 g/l Yeast extract 1.99601 g/l Na-formate 1.99601 g/l Na-acetate 0.998004 g/l Na2S x 9 H2O 0.499002 g/l KH2PO4 0.499002 g/l L-Cysteine HCl x H2O 0.499002 g/l MgSO4 x 7 H2O 0.399202 g/l NH4Cl 0.399202 g/l NaCl 0.399202 g/l CaCl2 x 2 H2O 0.0499002 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l Pyridoxine hydrochloride 0.000299401 g/l Thiamine-HCl x 2 H2O 0.000199601 g/l Nicotinic acid 0.000199601 g/l CoCl2 x 6 H2O 0.000189621 g/l Calcium pantothenate 9.98004e-05 g/l Vitamin B12 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l p-Aminobenzoic acid 7.98403e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l D-(+)-biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water |
| 1427 | METHANOBACTERIUM MEDIUM (DSMZ Medium 119) | yes | https://mediadive.dsmz.de/medium/119 | Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water |
culture temp
- @ref: 1427
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 1427
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 1427
- sample type: from giant amoeba Pelomyxa palustris
- host species: Pelomyxa palustris
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
- Cat1: #Host
- Cat2: #Protozoa
- Cat3: #Protist
Safety information
risk assessment
- @ref: 1427
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Sporomusa paucivorans 16S ribosomal RNA
- accession: M59117
- length: 1502
- database: ena
- NCBI tax ID: 2376
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanobacterium formicicum DSM 3637 | GCA_000302455 | contig | ncbi | 1204725 |
| 66792 | Methanobacterium formicicum DSM 3637 | 2519899733 | draft | img | 1204725 |
| 66792 | Methanobacterium formicicum DSM 3637 | 1204725.3 | wgs | patric | 1204725 |
GC content
- @ref: 1427
- GC-content: 37.7
External links
@ref: 1427
culture collection no.: DSM 3637
straininfo link
- @ref: 76392
- straininfo: 47736
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 1550443 | Effect of coculture of anaerobic fungi isolated from ruminants and non-ruminants with methanogenic bacteria on cellulolytic and xylanolytic enzyme activities. | Teunissen MJ, Kets EP, Op den Camp HJ, Huis in't Veld JH, Vogels GD | Arch Microbiol | 10.1007/BF00245287 | 1992 | Anaerobiosis, Animals, Cellulase/metabolism, Cellulose/*metabolism, Chytridiomycota/enzymology/growth & development/*metabolism, Euryarchaeota/enzymology/growth & development/*metabolism, Fermentation, Formates/metabolism, Glycoside Hydrolases/metabolism, Hydrogen/metabolism, Methane/metabolism, Ruminants/*microbiology, Xylan Endo-1,3-beta-Xylosidase, Xylans/*metabolism, beta-Glucosidase/metabolism | Enzymology |
| Genetics | 23209223 | Draft genome sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium isolated from the methane producer amoeba Pelomyxa palustris. | Gutierrez G | J Bacteriol | 10.1128/JB.01829-12 | 2012 | Archamoebae/*microbiology, Base Composition, Base Sequence, DNA, Archaeal/genetics, *Genome, Archaeal, Methane/biosynthesis, Methanobacterium/*genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Archaeal/genetics, Sequence Analysis, DNA, Symbiosis | Phylogeny |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1427 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3637) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3637 | |||
| 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) | |||
| 76392 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47736.1 | StrainInfo: A central database for resolving microbial strain identifiers |