Strain identifier
BacDive ID: 7053
Type strain: 
Species: Methanomethylovorans hollandica
Strain history: <- B. P. Lomans, University of Nijmegen, Department of Microbiology and Evolutionary Biology, Nijmegen, Netherlands; DMS1 <- B. P. Lomans {1994}
NCBI tax ID(s): 867904 (strain), 101192 (species)
version 8.1 (current version)
General
@ref: 6214
BacDive-ID: 7053
DSM-Number: 15978
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative
description: Methanomethylovorans hollandica DSM 15978 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from anaerobic sediment of eutrophic freshwater pond.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 101192 | species |
| 867904 | strain |
strain history
- @ref: 6214
- history: <- B. P. Lomans, University of Nijmegen, Department of Microbiology and Evolutionary Biology, Nijmegen, Netherlands; DMS1 <- B. P. Lomans {1994}
doi: 10.13145/bacdive7053.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanosarcinales
- family: Methanosarcinaceae
- genus: Methanomethylovorans
- species: Methanomethylovorans hollandica
- full scientific name: Methanomethylovorans hollandica Lomans et al. 2004
@ref: 6214
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanomethylovorans
species: Methanomethylovorans hollandica
full scientific name: Methanomethylovorans hollandica Lomans et al. 2004
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.995
colony morphology
- @ref: 6214
- incubation period: 3-7 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_15978_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 6214
- name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)
- growth: yes
- link: https://mediadive.dsmz.de/medium/503
- composition: Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Trimethylamine-HCl 1.99402 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l Methanol 0.631705 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l Nicotinic acid 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Calcium pantothenate 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
- @ref: 6214
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6214 | anaerobe | |
| 69480 | anaerobe | 98.648 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.375 |
Isolation, sampling and environmental information
isolation
- @ref: 6214
- sample type: anaerobic sediment of eutrophic freshwater pond
- geographic location: Nijmegen, Dekkerswald
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_187202.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17802;96_68856;97_89503;98_121784;99_187202&stattab=map
- Last taxonomy: Methanomethylovorans hollandica subclade
- 16S sequence: AF120163
- Sequence Identity:
- Total samples: 432
- soil counts: 45
- aquatic counts: 368
- animal counts: 1
- plant counts: 18
Safety information
risk assessment
- @ref: 6214
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6214
- description: Methanomethylovorans hollandica 16S ribosomal RNA gene, partial sequence
- accession: AF120163
- length: 1449
- database: ena
- NCBI tax ID: 867904
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanomethylovorans hollandica DSM 15978 | GCA_000328665 | complete | ncbi | 867904 |
| 66792 | Methanomethylovorans hollandica DSM 15978 | 2509601008 | complete | img | 867904 |
| 66792 | Methanomethylovorans hollandica DSM 15978 | 867904.9 | complete | patric | 867904 |
| 66792 | Methanomethylovorans hollandica DSM 15978 | 867904.13 | plasmid | patric | 867904 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 88.311 | no |
| flagellated | no | 96.27 | no |
| gram-positive | no | 96.353 | no |
| anaerobic | yes | 98.604 | no |
| aerobic | no | 93.75 | yes |
| halophile | no | 85.315 | no |
| spore-forming | no | 95.734 | no |
| thermophile | no | 94.646 | yes |
| glucose-util | yes | 72.475 | no |
| glucose-ferment | no | 68.885 | no |
External links
@ref: 6214
culture collection no.: DSM 15978, NBRC 107637, DMS 1
straininfo link
- @ref: 76510
- straininfo: 131425
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10427061 | Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. | Lomans BP, Maas R, Luderer R, Op den Camp HJ, Pol A, van der Drift C, Vogels GD | Appl Environ Microbiol | 10.1128/AEM.65.8.3641-3650.1999 | 1999 | Base Sequence, DNA Primers/genetics, DNA, Bacterial/genetics/isolation & purification, Ecosystem, Fresh Water/microbiology, Geologic Sediments/*microbiology, Methanosarcinaceae/genetics/growth & development/*isolation & purification, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, Sulfhydryl Compounds/metabolism, Sulfides/metabolism | Enzymology |
| Phylogeny | 16280511 | Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. | Jiang B, Parshina SN, van Doesburg W, Lomans BP, Stams AJM | Int J Syst Evol Microbiol | 10.1099/ijs.0.63818-0 | 2005 | Anaerobiosis, Base Sequence, Bioreactors/microbiology, Methanol/*metabolism, Methanosarcinaceae/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sulfides/*metabolism, Temperature | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6214 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15978) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15978 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 76510 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131425.1 | StrainInfo: A central database for resolving microbial strain identifiers |