Strain identifier
BacDive ID: 7150
Type strain: 
Species: Methylobacterium organophilum
Strain Designation: XX
Strain history: T. Urakami TK 0047 <-- ATCC 27886 <-- R. Hanson XX.
NCBI tax ID(s): 410 (species)
version 8.1 (current version)
General
@ref: 432
BacDive-ID: 7150
DSM-Number: 760
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Methylobacterium organophilum XX is a mesophilic bacterium that was isolated from sediment.
NCBI tax id
- NCBI tax id: 410
- Matching level: species
strain history
| @ref | history |
|---|---|
| 432 | <- R.S. Hanson, strain XX. Strain obtained directly from the laboratory where the strain was isolated. Not identical to DSM 18172, obtained via the NCIMB |
| 67770 | T. Urakami TK 0047 <-- ATCC 27886 <-- R. Hanson XX. |
doi: 10.13145/bacdive7150.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Methylobacterium
- species: Methylobacterium organophilum
- full scientific name: Methylobacterium organophilum Patt et al. 1976 (Approved Lists 1980)
@ref: 432
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium organophilum
full scientific name: Methylobacterium organophilum Patt et al. 1976
strain designation: XX
type strain: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 432 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Methanol Distilled water |
| 38089 | MEDIUM 54 - for Methylobacterium organophilum and M. rhodinum | yes | Distilled water make up to (995.000 ml);Iron (II) sulphate heptahydrate (4.000 mg);Zinc sulphate heptahydrate (0.100 mg);ManganeseII chloride tetrahydrate (0.030 mg);Boric acid (0.300 mg);Magnesium sulphate heptahydrate (1.000 g);Calcium chloride dihydrat | |
| 121432 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
| 121432 | CIP Medium 54 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=54 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 432 | positive | growth | 30 | mesophilic |
| 38089 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 432 | sediment | Madison, Lake Mendota | USA | USA | North America |
| 67770 | Lake Mendota | Madison, WI | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Sediment |
Safety information
risk assessment
- @ref: 432
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 432 | Methylobacterium organophilum gene for 16S ribosomal RNA, partial sequence, strain:ATCC 27886 | AB175638 | 1433 | ena | 410 |
| 432 | Methylobacterium radiotolerans gene for 16S ribosomal RNA, partial sequence, strain:DSM 760 | AB175637 | 1433 | ena | 31998 |
| 67770 | Methylobacterium organophilum gene for 16S ribosomal RNA, partial sequence, strain:JCM 2833 | AB175639 | 1433 | ena | 410 |
| 67770 | Methylobacterium organophilum gene for 16S rRNA, strain: JCM 2833 | D32226 | 1405 | ena | 410 |
| 67770 | M.organophilum 16S rRNA | M29028 | 1316 | ena | 410 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylobacterium organophilum strain DSM 760 | 410.10 | wgs | patric | 410 |
| 66792 | Methylobacterium organophilum DSM 760 | 2756170276 | draft | img | 410 |
| 66792 | Methylobacterium organophilum NBRC 15689 | GCA_022179465 | contig | ncbi | 410 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 432 | 66.0 | |
| 67770 | 66 | thermal denaturation, midpoint method (Tm) |
| 67770 | 66.8 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 97.546 | no |
| anaerobic | no | 98.258 | no |
| halophile | no | 89.231 | no |
| spore-forming | no | 92.41 | no |
| glucose-util | yes | 87.96 | no |
| aerobic | yes | 91.52 | no |
| flagellated | no | 75.899 | no |
| motile | yes | 91.121 | no |
| thermophile | no | 99.461 | yes |
| glucose-ferment | no | 87.792 | no |
External links
@ref: 432
culture collection no.: DSM 760, ATCC 27886, NCIB 11278, JCM 2833, BCRC 10934, CCM 4460, CIP 101049, HAMBI 2263, IFO 15689, LMG 6083, NBRC 15689, NCCB 78041, NCIMB 11278, VKM B-2066
straininfo link
- @ref: 76604
- straininfo: 3561
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 2855527 | Localization of a pyrroloquinoline quinone biosynthesis gene near the methanol dehydrogenase structural gene in Methylobacterium organophilum DSM 760. | Mazodier P, Biville F, Turlin E, Gasser F | J Gen Microbiol | 10.1099/00221287-134-9-2513 | 1988 | Alcohol Oxidoreductases/*genetics, Cloning, Molecular, DNA Transposable Elements, *Genes, *Genes, Bacterial, Methanol, Methylococcaceae/*genetics, Mutation, PQQ Cofactor, Quinolones/*biosynthesis, R Factors, Restriction Mapping | |
| Phylogeny | 8132470 | Isolation, phenotypic characterization, and complementation analysis of mutants of Methylobacterium extorquens AM1 unable to synthesize pyrroloquinoline quinone and sequences of pqqD, pqqG, and pqqC. | Morris CJ, Biville F, Turlin E, Lee E, Ellermann K, Fan WH, Ramamoorthi R, Springer AL, Lidstrom ME | J Bacteriol | 10.1128/jb.176.6.1746-1755.1994 | 1994 | Amino Acid Sequence, Base Sequence, Genes, Bacterial/*genetics/physiology, *Genetic Complementation Test, Gram-Negative Aerobic Bacteria/*genetics/isolation & purification/metabolism, Molecular Sequence Data, Mutation/*genetics/physiology, PQQ Cofactor, Phenotype, Quinolones/*metabolism, Sequence Homology, Amino Acid | Metabolism |
| Metabolism | 9043136 | Sequence analysis of pqq genes required for biosynthesis of pyrroloquinoline quinone in Methylobacterium extorquens AM1 and the purification of a biosynthetic intermediate. | Toyama H, Chistoserdova L, Lidstrom ME | Microbiology (Reading) | 10.1099/00221287-143-2-595 | 1997 | Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Endopeptidases/genetics/metabolism, Escherichia coli/metabolism, *Genes, Bacterial, Genetic Complementation Test, Gram-Negative Aerobic Bacteria/*genetics, Molecular Sequence Data, Mutation, NAD/metabolism, Oxygen/metabolism, PQQ Cofactor, Quinolones/*metabolism, Restriction Mapping, Sequence Analysis, DNA, Sequence Homology, Amino Acid | Transcriptome |
| Phylogeny | 13130002 | Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester. | Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie H | Int J Syst Evol Microbiol | 10.1099/ijs.0.02540-0 | 2003 | Aerobiosis, Bradyrhizobiaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species Specificity | Genetics |
| Phylogeny | 17329786 | Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood. | Aslam Z, Lee CS, Kim KH, Im WT, Ten LN, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64625-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fermentation, Korea, Methylobacterium/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology | Genetics |
| Phylogeny | 22199216 | Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum. | Tani A, Sahin N, Kimbara K | Int J Syst Evol Microbiol | 10.1099/ijs.0.037713-0 | 2011 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Gnaphalium/*microbiology, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ubiquinone/analysis | Genetics |
| Phylogeny | 23291886 | Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces. | Wellner S, Lodders N, Glaeser SP, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.047787-0 | 2013 | Bacterial Typing Techniques, Caryophyllaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Methanol/*metabolism, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, *Pigmentation, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Trifolium/*microbiology | Genetics |
| Phylogeny | 23475343 | Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes. | Tani A, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.048215-0 | 2013 | Bacterial Typing Techniques, Base Composition, Bryophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ubiquinone/analogs & derivatives/analysis | Genetics |
| Phylogeny | 24556636 | Psychroglaciecola arctica gen. nov., sp. nov., isolated from Arctic glacial foreland soil. | Qu Z, Jiang F, Chang X, Qiu X, Ren L, Fang C, Peng F | Int J Syst Evol Microbiol | 10.1099/ijs.0.060913-0 | 2014 | Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Methylobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Svalbard, Ubiquinone/chemistry | Genetics |
| Phylogeny | 31463788 | Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T | J Microbiol | 10.1007/s12275-019-9007-9 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Genotype, Lipids/chemistry, Methylobacterium/*classification/genetics/*isolation & purification/radiation effects, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry, Whole Genome Sequencing | Genetics |
| Metabolism | 31541329 | Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Kim MK, Seo T | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01331-2 | 2019 | Base Composition/genetics, Cardiolipins/metabolism, Fatty Acids/*metabolism, *Gamma Rays, Genotype, Methylobacterium/genetics/*metabolism/*radiation effects, Phosphatidylethanolamines/metabolism, Phosphatidylglycerols/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Phylogeny |
| Phylogeny | 32100693 | Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Lee B, Jang W, Kim MK, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004054 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Methylobacterium/*classification/isolation & purification/radiation effects, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 33841347 | Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains. | Volpiano CG, Sant'Anna FH, Ambrosini A, de Sao Jose JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP | Front Microbiol | 10.3389/fmicb.2021.614957 | 2021 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 432 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 760) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-760 | |
| 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 | |
| 38089 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/12581 | ||
| 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/ | ||
| 76604 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3561.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 121432 | Curators of the CIP | Collection of Institut Pasteur (CIP 101049) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101049 |