Strain identifier
BacDive ID: 133754
Type strain: 
Species: Methylomonas koyamae
Strain Designation: Fw12E-Y
Strain history: S. Asakawa Fw12E-Y.
NCBI tax ID(s): 1294261 (strain), 702114 (species)
version 9.3 (current version)
General
@ref: 30405
BacDive-ID: 133754
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, motile, rod-shaped
description: Methylomonas koyamae Fw12E-Y is a Gram-negative, motile, rod-shaped bacterium that was isolated from freshwater .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1294261 | strain |
| 702114 | species |
strain history
- @ref: 67770
- history: S. Asakawa Fw12E-Y.
doi: 10.13145/bacdive133754.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Methylococcales
- family: Methylococcaceae
- genus: Methylomonas
- species: Methylomonas koyamae
- full scientific name: Methylomonas koyamae Ogiso et al. 2012
@ref: 30405
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Methylococcales
family: Methylococcaceae
genus: Methylomonas
species: Methylomonas koyamae
strain designation: Fw12E-Y
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 30405 | negative | rod-shaped | yes | |
| 125438 | negative | 98.5 | ||
| 125439 | negative | 99.6 |
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 30405 | positive | growth | 10-40 |
| 30405 | positive | optimum | 30 |
| 67770 | positive | growth | 30 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30405 | positive | growth | 5.5-7 |
| 30405 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 92.3
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.6
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30405 | NaCl | positive | growth | 0-0.5 % |
| 30405 | NaCl | positive | optimum | 0.10 % |
observation
- @ref: 67770
- observation: quinones: MQ-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 30405 | freshwater (river, lake, pond) | |||
| 67770 | Floodwater of a rice paddy field | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #River (Creek) |
taxonmaps
- @ref: 69479
- File name: preview.99_2403.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_194;96_668;97_774;98_1874;99_2403&stattab=map
- Last taxonomy: Methylomonas koyamae subclade
- 16S sequence: AB538964
- Sequence Identity:
- Total samples: 1358
- soil counts: 294
- aquatic counts: 915
- animal counts: 74
- plant counts: 75
Sequence information
16S sequences
- @ref: 30405
- description: Methylomonas koyamae gene for 16S rRNA, partial sequence
- accession: AB538964
- length: 1458
- database: nuccore
- NCBI tax ID: 1294261
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylomonas koyamae Fw12E-Y | GCA_019669905 | complete | ncbi | 702114 |
| 66792 | Methylomonas koyamae JCM 16701 | 1294261.13 | wgs | patric | 1294261 |
| 66792 | Methylomonas koyamae strain Fw12E-Y | 702114.23 | wgs | patric | 702114 |
| 66792 | Methylomonas koyamae JCM 16701 | 2728369704 | draft | img | 1294261 |
| 67770 | Methylomonas koyamae JCM 16701 | GCA_001312005 | contig | ncbi | 1294261 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 30405 | 57.1 | |
| 67770 | 57.1 | 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 | aerobe | 92.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 82.2 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.6 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.5 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 85.045 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 67.481 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.764 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.082 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 67.038 | no |
External links
@ref: 30405
culture collection no.: JCM 16701, NBRC 105905, NCIMB 14606
straininfo link
- @ref: 91585
- straininfo: 380525
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21984674 | Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field. | Ogiso T, Ueno C, Dianou D, Huy TV, Katayama A, Kimura M, Asakawa S | Int J Syst Evol Microbiol | 10.1099/ijs.0.035261-0 | 2011 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Methane/metabolism, Methylomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology | Genetics |
| Phylogeny | 33145620 | Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice. | Zhu P, Cheng M, Pei D, Liu Y, Yan X | Antonie Van Leeuwenhoek | 10.1007/s10482-020-01487-2 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Methylococcaceae/genetics, *Methylomonas/genetics, *Oryza, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil | Transcriptome |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
| 30405 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26742 | 28776041 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
| 91585 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID380525.1 | ||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | ||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |