Strain identifier
BacDive ID: 24162
Type strain: 
Species: Methanococcoides vulcani
Strain history: S. L'Haridon SLH33.
NCBI tax ID(s): 1353158 (species)
version 8.1 (current version)
General
@ref: 21015
BacDive-ID: 24162
DSM-Number: 26966
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative
description: Methanococcoides vulcani DSM 26966 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from deep-sea sediment covered by an orange microbial mat, 1938 m depth.
NCBI tax id
- NCBI tax id: 1353158
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21015 | <- S. L'Haridon, IUEM, Univ. Brest, Plouzané, France; SLH33 |
| 67770 | S. L'Haridon SLH33. |
doi: 10.13145/bacdive24162.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanosarcinales
- family: Methanosarcinaceae
- genus: Methanococcoides
- species: Methanococcoides vulcani
- full scientific name: Methanococcoides vulcani L'Haridon et al. 2014
@ref: 21015
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanococcoides
species: Methanococcoides vulcani
full scientific name: Methanococcoides vulcani L'Haridon et al. 2014
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.974
colony morphology
- @ref: 21015
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 21015
- name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141c
- composition: Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c) Composition: NaHCO3 4.89237 g/l Trimethylammonium chloride 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 CaCl2 x 2 H2O 0.000978474 g/l FeSO4 x 7 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 H3BO3 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l Nicotinic acid 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Biotin 1.95695e-05 g/l Folic acid 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 | range |
|---|---|---|---|---|
| 21015 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 21015 | anaerobe | |
| 69480 | anaerobe | 99.25 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.949 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 21015 | deep-sea sediment covered by an orange microbial mat, 1938 m depth | Eastern Mediterranean Sea, Napoli Mud Volcano | Greece | GRC | Europe | 33.724 | 24.684 |
| 67770 | Deep marine sediment, covered by a dense orange microbial mat, in Napoli Mud Volcano | eastern Mediterranean Sea |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Microbial community | #Microbial mat |
Safety information
risk assessment
- @ref: 21015
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21015
- description: Methanococcoides vulcani strain SLH33 from Mediterranean Sea 16S ribosomal RNA gene, partial sequence
- accession: KC631821
- length: 1443
- database: ena
- NCBI tax ID: 1353158
Genome sequences
- @ref: 67770
- description: Methanococcoides vulcani SLH 33
- accession: GCA_900111645
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 1353158
GC content
- @ref: 21015
- GC-content: 43.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 92.82 | no |
| flagellated | no | 97.171 | no |
| gram-positive | no | 97.216 | no |
| anaerobic | yes | 98.674 | yes |
| aerobic | no | 96.441 | no |
| halophile | no | 80.706 | no |
| spore-forming | no | 95.751 | no |
| glucose-ferment | no | 69.154 | no |
| thermophile | no | 93.29 | no |
| glucose-util | yes | 66.913 | no |
External links
@ref: 21015
culture collection no.: DSM 26966, JCM 19278, SLH 33
straininfo link
- @ref: 88118
- straininfo: 399129
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24614846 | Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides. | L'Haridon S, Chalopin M, Colombo D, Toffin L | Int J Syst Evol Microbiol | 10.1099/ijs.0.058289-0 | 2014 | Base Composition, Betaine/metabolism, Choline/metabolism, DNA, Bacterial/genetics, Deanol/metabolism, Hydrothermal Vents/*microbiology, Mediterranean Sea, Methanosarcinaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| Phylogeny | 35583432 | Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea. | Liang L, Sun Y, Dong Y, Ahmad T, Chen Y, Wang J, Wang F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005384 | 2022 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Methanosarcinaceae, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 21015 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26966 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26966) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 88118 | 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-ID399129.1 |