Strain identifier
BacDive ID: 7239
Type strain: 
Species: Methylophilus methylotrophus
Strain history: <- NCIMB <- T. R. Owen, ICI <- D. Byrom, ICI; AS1
NCBI tax ID(s): 1122236 (strain), 17 (species)
version 8.1 (current version)
General
@ref: 2288
BacDive-ID: 7239
DSM-Number: 5691
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Methylophilus methylotrophus DSM 5691 is an aerobe, mesophilic, motile bacterium that was isolated from activated sludge.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122236 | strain |
| 17 | species |
strain history
- @ref: 2288
- history: <- NCIMB <- T. R. Owen, ICI <- D. Byrom, ICI; AS1
doi: 10.13145/bacdive7239.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Nitrosomonadales
- family: Methylophilaceae
- genus: Methylophilus
- species: Methylophilus methylotrophus
- full scientific name: Methylophilus methylotrophus Jenkins et al. 1987
@ref: 2288
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Methylophilales
family: Methylophilaceae
genus: Methylophilus
species: Methylophilus methylotrophus
full scientific name: Methylophilus methylotrophus Jenkins et al. 1987
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.21 | |
| 69480 | 99.999 | negative |
colony morphology
- @ref: 61745
- incubation period: 4 days
Culture and growth conditions
culture medium
- @ref: 2288
- name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606)
- growth: yes
- link: https://mediadive.dsmz.de/medium/606
- composition: Name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606) Composition: Agar 15.0 g/l Methanol 1.584 g/l K2HPO4 1.2 g/l KH2PO4 0.62 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l NaCl 0.1 g/l CaCl2 x 6 H2O 0.05 g/l FeCl3 x 6 H2O 0.001 g/l ZnSO4 x 7 H2O 7e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l MnSO4 x 5 H2O 1e-05 g/l CuSO4 x 5 H2O 5e-06 g/l CoCl2 x 6 H2O 5e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 2288 | positive | growth | 30 | mesophilic |
| 61745 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 61745
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | continent | country | origin.country |
|---|---|---|---|---|
| 2288 | activated sludge | Europe | ||
| 61745 | Activated sludge | Europe | United Kingdom | GBR |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_1013.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_174;96_581;97_680;98_790;99_1013&stattab=map
- Last taxonomy: Methylophilus
- 16S sequence: AB193724
- Sequence Identity:
- Total samples: 4460
- soil counts: 376
- aquatic counts: 1592
- animal counts: 2109
- plant counts: 383
Safety information
risk assessment
- @ref: 2288
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methylophilus methylotrophus (ATCC 53528) 16S ribosomal RNA | L15475 | 1486 | ena | 17 |
| 20218 | Methylophilus methylotrophus gene for 16S rRNA | AB193724 | 1498 | ena | 17 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylophilus methylotrophus DSM 46235 = ATCC 53528 | GCA_000378225 | scaffold | ncbi | 1122236 |
| 66792 | Methylophilus methylotrophus DSM 46235 = ATCC 53528 | 1122236.3 | wgs | patric | 1122236 |
| 66792 | Methylophilus methylotrophus ATCC 53528 | 2518645588 | draft | img | 1122236 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 89.41 | no |
| flagellated | yes | 62.574 | no |
| gram-positive | no | 99.019 | no |
| anaerobic | no | 98.72 | yes |
| aerobic | yes | 84.03 | yes |
| halophile | no | 94.128 | no |
| spore-forming | no | 95.252 | no |
| thermophile | no | 97.281 | yes |
| glucose-util | yes | 60.025 | no |
| glucose-ferment | no | 91.393 | no |
External links
@ref: 2288
culture collection no.: DSM 5691, ATCC 53528, CCUG 58724, DSM 46235, NCIMB 10515, LMG 6787, BCRC 15784, KCTC 1759, AS 1
straininfo link
- @ref: 76691
- straininfo: 3574
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 1693657 | 16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs. | Tsuji K, Tsien HC, Hanson RS, DePalma SR, Scholtz R, LaRoche S | J Gen Microbiol | 10.1099/00221287-136-1-1 | 1990 | Base Sequence, Methylococcaceae/*classification/genetics, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/*analysis, RNA, Ribosomal/*analysis, RNA, Ribosomal, 16S/*analysis | Genetics |
| Phylogeny | 6308129 | Genetic mapping in Methylophilus methylotrophus AS1. | Moore AT, Nayudu M, Holloway BW | J Gen Microbiol | 10.1099/00221287-129-3-785 | 1983 | *Chromosome Mapping, Chromosomes, Bacterial, DNA Restriction Enzymes, DNA, Bacterial, Genetic Complementation Test, Genetic Linkage, Genetic Markers, Methylococcaceae/*genetics, Mutation, Nucleic Acid Hybridization, Plasmids, Pseudomonas aeruginosa/genetics | Enzymology |
| Enzymology | 8515233 | Identification of methanol-regulated promoter sequences from the facultative methylotrophic bacterium Methylobacterium organophilum XX. | Xu HH, Viebahn M, Hanson RS | J Gen Microbiol | 10.1099/00221287-139-4-743 | 1993 | Base Sequence, Cloning, Molecular, DNA Probes, DNA, Bacterial/genetics, Genes, Bacterial, Genetic Vectors, Gram-Negative Aerobic Bacteria/*genetics/metabolism, Methanol/*metabolism/pharmacology, Molecular Sequence Data, Mutation, *Promoter Regions, Genetic/drug effects, Transcription, Genetic | Metabolism |
| 9274053 | Creating auxotrophic mutants in Methylophilus methylotrophus AS1 by combining electroporation and chemical mutagenesis. | Kim CS, Wood TK | Appl Microbiol Biotechnol | 10.1007/s002530051023 | 1997 | Amino Acids/genetics, Electroporation, Gram-Negative Aerobic Bacteria/*genetics, Growth Substances/genetics, Methylnitronitrosoguanidine/pharmacology, *Mutagenesis, Mutagens/pharmacology | ||
| Metabolism | 15277749 | Characterization of the L-lysine biosynthetic pathway in the obligate methylotroph Methylophilus methylotrophus. | Gunji Y, Tsujimoto N, Shimaoka M, Ogawa-Miyata Y, Sugimoto S, Yasueda H | Biosci Biotechnol Biochem | 10.1271/bbb.68.1449 | 2004 | Amino Acid Sequence, Amino Acids/metabolism, Aspartate Kinase/genetics/metabolism, Aspartate-Semialdehyde Dehydrogenase/genetics/metabolism, Base Sequence, Carboxy-Lyases/genetics/metabolism, Cloning, Molecular, DNA, Bacterial/chemistry/genetics, Dihydrodipicolinate Reductase, Feedback, Hydro-Lyases/genetics/metabolism, Lysine/*biosynthesis, Methylophilus methylotrophus/*enzymology/genetics/*metabolism, Molecular Sequence Data, Mutagenesis, Site-Directed, Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism, Recombinant Proteins/genetics/metabolism, Sequence Alignment | Enzymology |
| Enzymology | 16483680 | L-Lysine biosynthetic pathway of Methylophilus methylotrophus and construction of an L-lysine producer. | Tsujimoto N, Gunji Y, Ogawa-Miyata Y, Shimaoka M, Yasueda H | J Biotechnol | 10.1016/j.jbiotec.2005.12.026 | 2006 | Aspartate-Semialdehyde Dehydrogenase/*genetics, Carboxy-Lyases/*genetics, Dihydrodipicolinate Reductase/*genetics, Gene Expression Regulation, Enzymologic/genetics, Genetic Vectors/genetics, Lysine/*biosynthesis, Methanol/metabolism, Methylophilus methylotrophus/*enzymology, Plasmids/biosynthesis, Protein Engineering/methods | Metabolism |
| Metabolism | 16870294 | Enhancement of L-lysine production in methylotroph Methylophilus methylotrophus by introducing a mutant LysE exporter. | Gunji Y, Yasueda H | J Biotechnol | 10.1016/j.jbiotec.2006.06.003 | 2006 | Amino Acid Transport Systems, Basic/genetics, Bacterial Proteins/genetics, Bioreactors, Lysine/genetics/*metabolism, Methanol/metabolism, Methylophilus methylotrophus/genetics/*metabolism, Molecular Sequence Data, Mutation, Transformation, Bacterial/*genetics/physiology | Genetics |
| Metabolism | 18460806 | Disruption of metF increased L-lysine production by Methylophilus methylotrophus from methanol. | Ishikawa K, Asahara T, Gunji Y, Yasueda H, Asano K | Biosci Biotechnol Biochem | 10.1271/bbb.70818 | 2008 | 5,10-Methylenetetrahydrofolate Reductase (FADH2)/deficiency/*genetics/*metabolism, Lysine/*biosynthesis, Methanol/*metabolism, Methionine/metabolism, Methylophilus methylotrophus/enzymology/*metabolism, Mutation, Phosphotransferases (Alcohol Group Acceptor)/metabolism | Enzymology |
| Genetics | 19880640 | Aromatic amino acid auxotrophs constructed by recombinant marker exchange in Methylophilus methylotrophus AS1 cells expressing the aroP-encoded transporter of Escherichia coli. | Yomantas YA, Tokmakova IL, Gorshkova NV, Abalakina EG, Kazakova SM, Gak ER, Mashko SV | Appl Environ Microbiol | 10.1128/AEM.02217-09 | 2009 | Amino Acid Transport Systems/*genetics, Amino Acids, Aromatic/*deficiency, Bacteriophage mu/genetics, Base Sequence, DNA, Bacterial/chemistry/genetics, Escherichia coli Proteins/*genetics, Methylophilus methylotrophus/*genetics, Molecular Sequence Data, Mutagenesis, Insertional, *Recombination, Genetic, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2288 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5691) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5691 | |||
| 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 | |
| 61745 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58724) | https://www.ccug.se/strain?id=58724 | |||
| 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) | |||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 76691 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3574.1 | StrainInfo: A central database for resolving microbial strain identifiers |