Strain identifier
BacDive ID: 17857
Type strain: 
Species: Methanoregula formicica
Strain Designation: SMSP
Strain history: <- H. Imachi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; SMSP <- Y. Yashiro {2008}
NCBI tax ID(s): 882104 (species)
version 8.1 (current version)
General
@ref: 16134
BacDive-ID: 17857
DSM-Number: 22288
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, rod-shaped
description: Methanoregula formicica SMSP is an anaerobe, mesophilic, rod-shaped archaeon that was isolated from methanogenic granular sludge.
NCBI tax id
- NCBI tax id: 882104
- Matching level: species
strain history
- @ref: 16134
- history: <- H. Imachi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; SMSP <- Y. Yashiro {2008}
doi: 10.13145/bacdive17857.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanoregulaceae
- genus: Methanoregula
- species: Methanoregula formicica
- full scientific name: Methanoregula formicica Yashiro et al. 2011
@ref: 16134
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanoregulaceae
genus: Methanoregula
species: Methanoregula formicica
full scientific name: Methanoregula formicica Yashiro et al. 2011
strain designation: SMSP
type strain: yes
Morphology
cell morphology
- @ref: 29522
- cell length: 4 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
- @ref: 16134
- name: PELOTOMACULUM MEDIUM (DSMZ Medium 960)
- growth: yes
- link: https://mediadive.dsmz.de/medium/960
- composition: Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na-formate 2.71457 g/l Na2CO3 1.49701 g/l NH4Cl 0.538922 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Yeast extract 0.0998004 g/l Na acetate 0.0998004 g/l 2-Mercaptoethanesulfonic acid 0.0798403 g/l Nitrilotriacetic acid 0.0127745 g/l FeCl2 x 4 H2O 0.000998004 g/l NaCl 0.000998004 g/l Sodium resazurin 0.000499002 g/l ZnCl2 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16134 | positive | growth | 30 | mesophilic |
| 29522 | positive | growth | 10-40 | |
| 29522 | positive | optimum | 31.5 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29522 | positive | growth | 7.0-7.6 |
| 29522 | positive | optimum | 7.4 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 16134 | anaerobe |
| 29522 | anaerobe |
halophily
- @ref: 29522
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
Isolation, sampling and environmental information
isolation
- @ref: 16134
- sample type: methanogenic granular sludge
- geographic location: Ehime, Saijo
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Activated sludge |
| #Condition | #Anoxic (anaerobic) |
Safety information
risk assessment
- @ref: 16134
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16134
- description: Methanoregula formicicum SMSP gene for 16S rRNA, partial sequence
- accession: AB479390
- length: 1397
- database: ena
- NCBI tax ID: 593750
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanoregula formicica SMSP | GCA_000327485 | complete | ncbi | 593750 |
| 66792 | Methanoregula formicica SMSP, DSM 22288 | 2508501105 | complete | img | 593750 |
| 66792 | Methanoregula formicica SMSP | 593750.7 | complete | patric | 593750 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16134 | 56.2 | high performance liquid chromatography (HPLC) |
| 29522 | 56.2 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 91.424 | yes |
| flagellated | no | 96.593 | yes |
| gram-positive | no | 95.521 | no |
| anaerobic | yes | 98.519 | yes |
| aerobic | no | 95.783 | yes |
| halophile | no | 93.175 | yes |
| spore-forming | no | 93.021 | no |
| thermophile | no | 91.45 | no |
| glucose-util | yes | 56.428 | no |
| glucose-ferment | no | 63.555 | no |
External links
@ref: 16134
culture collection no.: DSM 22288, NBRC 105244
straininfo link
- @ref: 86848
- straininfo: 405601
literature
- topic: Phylogeny
- Pubmed-ID: 19667393
- title: Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge.
- authors: Yashiro Y, Sakai S, Ehara M, Miyazaki M, Yamaguchi T, Imachi H
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.014811-0
- year: 2009
- mesh: Anaerobiosis, Archaeal Proteins/genetics, Base Composition, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Formates/metabolism, Hydrogen-Ion Concentration, Methane/*metabolism, Methanomicrobiales/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Oxidoreductases/genetics, Phylogeny, Propionates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Temperature
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16134 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22288) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22288 | |||
| 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 | |||
| 29522 | 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 | 25919 | 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) | |||
| 86848 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405601.1 | StrainInfo: A central database for resolving microbial strain identifiers |