Strain identifier
BacDive ID: 6924
Type strain: 
Species: Methanobacterium formicicum
Strain Designation: MF
Strain history: DSM 1535 <-- R. S. Wolfe and W. E. Balch <-- M. P. Bryant MF.
NCBI tax ID(s): 1300163 (strain), 2162 (species)
version 8.1 (current version)
General
@ref: 812
BacDive-ID: 6924
DSM-Number: 1535
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic
description: Methanobacterium formicicum MF is an anaerobe, mesophilic archaeon that was isolated from anaerobic sewage sludge digester.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1300163 | strain |
| 2162 | species |
strain history
| @ref | history |
|---|---|
| 812 | <- R. S. Wolfe and W. E. Balch, University of Illinois, Urbana, USA; MF <- M. P. Bryant {1966} |
| 67770 | DSM 1535 <-- R. S. Wolfe and W. E. Balch <-- M. P. Bryant MF. |
doi: 10.13145/bacdive6924.20230509.8.1
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: 812
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: MF
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 812 | 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 |
| 812 | 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 812 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 812
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 812 | anaerobic sewage sludge digester | Illinois, Urbana | USA | USA | North America |
| 67770 | Sewage sludge digestor | Urbana, IL | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | #Anaerobic digestor |
| #Engineered | #Waste | #Sewage sludge |
| #Condition | #Anoxic (anaerobic) |
Safety information
risk assessment
- @ref: 812
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Enterococcus faecalis clone OCM055 16S ribosomal RNA gene, partial sequence | GU417238 | 447 | ena | 1351 |
| 812 | Methanobacterium formicicum DSMZ1535 16S ribosomal RNA, partial sequence | AF169245 | 1376 | ena | 2162 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanobacterium formicicum JCM 10132 | GCA_001316325 | contig | ncbi | 1300163 |
| 66792 | Methanobacterium formicicum JCM 10132 | 2681813006 | draft | img | 1300163 |
| 66792 | Methanobacterium formicicum DSM 1535 | 2645727909 | complete | img | 2162 |
| 66792 | Methanobacterium formicicum strain DSM 1535 | 2162.9 | complete | patric | 2162 |
| 66792 | Methanobacterium formicicum JCM 10132 | 1300163.3 | wgs | patric | 1300163 |
| 66792 | Methanobacterium formicicum MF | GCA_029848115 | contig | ncbi | 2162 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 812 | 40.7 | |
| 67770 | 40.7 | Buoyant density centrifugation (BD) |
External links
@ref: 812
culture collection no.: DSM 1535, ATCC 33274, JCM 10132, OCM 55, NBIMCC 876, NBRC 100475, VKM B-1957
straininfo link
- @ref: 76388
- straininfo: 44946
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17012556 | Syntrophomonas cellicola sp. nov., a spore-forming syntrophic bacterium isolated from a distilled-spirit-fermenting cellar, and assignment of Syntrophospora bryantii to Syntrophomonas bryantii comb. nov. | Wu C, Liu X, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.64377-0 | 2006 | Alcoholic Beverages, Bacteria, Anaerobic/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition, China, Crotonates/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/*metabolism, Fermentation, Methanobacterium/*growth & development/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/physiology | Metabolism |
| Phylogeny | 17223300 | Syntrophomonas wolfei subsp. methylbutyratica subsp. nov., and assignment of Syntrophomonas wolfei subsp. saponavida to Syntrophomonas saponavida sp. nov. comb. nov. | Wu C, Dong X, Liu X | Syst Appl Microbiol | 10.1016/j.syapm.2006.12.001 | 2007 | Bacteria, Anaerobic/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/*analysis, DNA, Ribosomal/*analysis, Molecular Sequence Data, Phylogeny, Spores, Bacterial | Genetics |
| Phylogeny | 17329794 | Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum. | Sousa DZ, Smidt H, Alves MM, Stams AJM | Int J Syst Evol Microbiol | 10.1099/ijs.0.64734-0 | 2007 | Anaerobiosis, Bacteria, Anaerobic/*classification/*metabolism, Bioreactors, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/*metabolism, Methanobacterium/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
| Phylogeny | 20639228 | Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil. | Kitamura K, Fujita T, Akada S, Tonouchi A | Int J Syst Evol Microbiol | 10.1099/ijs.0.026013-0 | 2010 | Anaerobiosis, Autotrophic Processes, Base Composition, Carbon Dioxide, Cell Wall/ultrastructure, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Japan, Methane/metabolism, Methanobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Oryza/growth & development, Phylogeny, Propionates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature | Metabolism |
| Phylogeny | 23625260 | Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field. | Honda T, Fujita T, Tonouchi A | Int J Syst Evol Microbiol | 10.1099/ijs.0.052225-0 | 2013 | Amino Acids/metabolism, Bacteria, Anaerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Coculture Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
| Genetics | 25270020 | Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.). | Maus I, Stantscheff R, Wibberg D, Stolze Y, Winkler A, Puhler A, Konig H, Schluter A | J Biotechnol | 10.1016/j.jbiotec.2014.09.018 | 2014 | Base Sequence, *Genome, Bacterial, Methane/metabolism, Methanobacterium/*genetics/metabolism, Molecular Sequence Data, Sequence Analysis, DNA, Waste Disposal, Fluid | Metabolism |
| Phylogeny | 32504807 | Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus DeltaH. | Prathiviraj R, Chellapandi P | Anaerobe | 10.1016/j.anaerobe.2020.102216 | 2020 | Comparative Genomic Hybridization, DNA, Archaeal/genetics, Genome, Archaeal, Metabolic Networks and Pathways/*genetics, Methanobacteriaceae/*genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Stress, Physiological/*genetics | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 812 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1535) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1535 | |||
| 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/ | ||||
| 76388 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44946.1 | StrainInfo: A central database for resolving microbial strain identifiers |