Strain identifier
BacDive ID: 7029
Type strain: 
Species: Methanoculleus chikugoensis
Strain Designation: MG62
Strain history: S. Asakawa MG62.
NCBI tax ID(s): 1293042 (strain), 118126 (species)
version 9.3 (current version)
General
@ref: 5051
BacDive-ID: 7029
DSM-Number: 13459
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic
description: Methanoculleus chikugoensis MG62 is an anaerobe, mesophilic archaeon that was isolated from paddy field soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1293042 | strain |
| 118126 | species |
strain history
| @ref | history |
|---|---|
| 5051 | <- S. Asakawa, Kyushu National Agricultural Experiment Station, Nishigoshi, Kumamoto, Japan; MG62 <- S. Asakawa; {1995} |
| 67770 | S. Asakawa MG62. |
doi: 10.13145/bacdive7029.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanomicrobiaceae
- genus: Methanoculleus
- species: Methanoculleus chikugoensis
- full scientific name: Methanoculleus chikugoensis Dianou et al. 2001
@ref: 5051
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanomicrobiaceae
genus: Methanoculleus
species: Methanoculleus chikugoensis
full scientific name: Methanoculleus chikugoensis Dianou et al. 2001
strain designation: MG62
type strain: yes
Morphology
cell morphology
- @ref: 125439
- gram stain: negative
- confidence: 98.3
colony morphology
- @ref: 5051
- incubation period: 8-14 days
Culture and growth conditions
culture medium
- @ref: 5051
- name: METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141b
- composition: Name: METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 5051 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5051 | anaerobe | |
| 125438 | anaerobe | 90.129 |
| 125439 | obligate anaerobe | 99 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 96
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5051 | paddy field soil | Fukuoka prefecture, Chikugo city | Japan | JPN | Asia |
| 67770 | Paddy field soil | Chikugo, Fukuoka | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Condition | #Anoxic (anaerobic) | |
| #Condition | #Humid |
taxonmaps
- @ref: 69479
- File name: preview.99_187663.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17869;96_68879;97_89527;98_122141;99_187663&stattab=map
- Last taxonomy: Methanoculleus chikugoensis subclade
- 16S sequence: AB038795
- Sequence Identity:
- Total samples: 48
- soil counts: 1
- aquatic counts: 46
- plant counts: 1
Safety information
risk assessment
- @ref: 5051
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5051
- description: Methanoculleus chikugoensis gene for 16S rRNA, partial sequence, strain:MG62
- accession: AB038795
- length: 1430
- database: nuccore
- NCBI tax ID: 118126
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanoculleus chikugoensis MG62 | GCA_019669965 | complete | ncbi | 118126 |
| 66792 | Methanoculleus chikugoensis JCM 10825 | GCA_001315965 | contig | ncbi | 1293042 |
| 66792 | Methanoculleus chikugoensis strain MG62 | 118126.5 | complete | patric | 118126 |
| 66792 | Methanoculleus chikugoensis JCM 10825 | 1293042.3 | wgs | patric | 1293042 |
GC content
- @ref: 5051
- GC-content: 62.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate anaerobe | 99 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 55.2 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 70.372 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 90.129 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 91.159 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.149 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 75.907 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 87 | no |
External links
@ref: 5051
culture collection no.: DSM 13459, JCM 10825, NBRC 101202
straininfo link
- @ref: 76489
- straininfo: 311043
literature
- topic: Phylogeny
- Pubmed-ID: 11594593
- title: Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA-DNA hybridization among Methanoculleus species.
- authors: Dianou D, Miyaki T, Asakawa S, Morii H, Nagaoka K, Oyaizu H, Matsumoto S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-51-5-1663
- year: 2001
- mesh: Base Composition, DNA, Archaeal/analysis/*genetics, DNA, Ribosomal/analysis, Japan, Lipids/analysis, Methane/*metabolism, Methanomicrobiaceae/*classification/genetics/isolation & purification/physiology/ultrastructure, Molecular Sequence Data, Nucleic Acid Hybridization, *Oryza/growth & development, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5051 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13459) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13459 | |
| 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 | |
| 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 | |
| 76489 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID311043.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |