Strain identifier
BacDive ID: 6980
Type strain: 
Species: Methanosphaera stadtmanae
Strain Designation: MCB-3
Strain history: DSM 3091 <-- T. L. Miller MCB-3.
NCBI tax ID(s): 339860 (strain), 2317 (species)
version 8.1 (current version)
General
@ref: 1297
BacDive-ID: 6980
DSM-Number: 3091
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative
description: Methanosphaera stadtmanae MCB-3 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from human faeces.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 2317 | species |
| 339860 | strain |
strain history
| @ref | history |
|---|---|
| 1297 | <- T. L. Miller, New York State Department of Health, Albany, New York, USA; MCB-3 (Methanosphaera stadtmaniae) |
| 67770 | DSM 3091 <-- T. L. Miller MCB-3. |
doi: 10.13145/bacdive6980.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanobacteria
- order: Methanobacteriales
- family: Methanobacteriaceae
- genus: Methanosphaera
- species: Methanosphaera stadtmanae
- full scientific name: Methanosphaera stadtmanae corrig. Miller and Wolin 1985
synonyms
- @ref: 20215
- synonym: Methanosphaera stadtmaniae
@ref: 1297
domain: Archaea
phylum: Euryarchaeota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanosphaera
species: Methanosphaera stadtmanae
full scientific name: Methanosphaera stadtmanae Miller and Wolin 1985
strain designation: MCB-3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.951
Culture and growth conditions
culture medium
- @ref: 1297
- name: METHANOSPHAERA (MCB-3) MEDIUM (DSMZ Medium 322)
- growth: yes
- link: https://mediadive.dsmz.de/medium/322
- composition: Name: METHANOSPHAERA (MCB-3) MEDIUM (DSMZ Medium 322) Composition: Methanol 7.70428 g/l NaHCO3 3.89105 g/l KH2PO4 2.72374 g/l Trypticase peptone 1.94553 g/l Yeast extract 1.94553 g/l NH4Cl 0.972763 g/l K2HPO4 0.583658 g/l NaCl 0.583658 g/l Na2S x 9 H2O 0.486381 g/l L-Cysteine HCl x H2O 0.486381 g/l Na-acetate 0.486381 g/l Na-formate 0.486381 g/l (NH4)2SO4 0.291829 g/l MgSO4 x 7 H2O 0.145914 g/l CaCl2 x 2 H2O 0.077821 g/l Nitrilotriacetic acid 0.0145914 g/l MnSO4 x H2O 0.00486381 g/l FeSO4 x 7 H2O 0.00291829 g/l Na2SeO4 0.00184825 g/l ZnSO4 x 7 H2O 0.00175097 g/l CoSO4 x 7 H2O 0.00175097 g/l NiCl2 x 6 H2O 0.000680934 g/l Sodium resazurin 0.000486381 g/l Pyridoxine hydrochloride 0.000194553 g/l AlK(SO4)2 x 12 H2O 0.000194553 g/l Calcium D-(+)-pantothenate 9.72763e-05 g/l CuSO4 x 5 H2O 9.72763e-05 g/l Thiamine HCl 9.72763e-05 g/l Nicotinic acid 9.72763e-05 g/l Riboflavin 9.72763e-05 g/l (DL)-alpha-Lipoic acid 9.72763e-05 g/l p-Aminobenzoic acid 9.72763e-05 g/l H3BO3 9.72763e-05 g/l Na2MoO4 x 2 H2O 9.72763e-05 g/l Biotin 3.89105e-05 g/l Folic acid 3.89105e-05 g/l Na2WO4 x 2 H2O 3.89105e-06 g/l Na2SeO3 x 5 H2O 2.91829e-06 g/l Vitamin B12 1.94553e-06 g/l H2SO4 Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1297 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1297 | anaerobe | |
| 69480 | anaerobe | 99.531 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.91 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 1297 | human faeces | USA | USA | North America |
| 67770 | Human feces |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_187271.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17658;96_68840;97_89485;98_121835;99_187271&stattab=map
- Last taxonomy: Methanosphaera
- 16S sequence: JQ346752
- Sequence Identity:
- Total samples: 3993
- soil counts: 76
- aquatic counts: 194
- animal counts: 3685
- plant counts: 38
Safety information
risk assessment
- @ref: 1297
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methanosphaera stadtmanae DSM 3091 strain MCB-3 16S ribosomal RNA gene, partial sequence | JQ346752 | 1267 | ena | 339860 |
| 20218 | Methanosphaera stadtmanii 16S ribosomal RNA | M59139 | 1425 | ena | 2317 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanosphaera stadtmanae DSM 3091 | GCA_000012545 | complete | ncbi | 339860 |
| 66792 | Methanosphaera stadtmanae DSM 3091 | 637000163 | complete | img | 339860 |
| 66792 | Methanosphaera stadtmanae DSM 3091 | 339860.19 | complete | patric | 339860 |
GC content
- @ref: 1297
- GC-content: 26.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 93.405 | no |
| flagellated | no | 97.253 | no |
| gram-positive | no | 94.426 | no |
| anaerobic | yes | 98.349 | no |
| halophile | no | 88.487 | no |
| spore-forming | no | 94.383 | no |
| thermophile | no | 92.191 | yes |
| glucose-util | yes | 66.513 | no |
| aerobic | no | 95.231 | yes |
| glucose-ferment | no | 54.366 | no |
External links
@ref: 1297
culture collection no.: DSM 3091, ATCC 43021, JCM 11832, OCM 149
straininfo link
- @ref: 76441
- straininfo: 47692
literature
| topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 11109487 | Purification of the NADP+:F420 oxidoreductase of Methanosphaera stadtmanae. | Elias DA, Juck DF, Berry KA, Sparling R | Can J Microbiol | 2000 | Kinetics, Methanobacteriaceae/*enzymology, Molecular Weight, NADH, NADPH Oxidoreductases/*isolation & purification/metabolism, NADP/metabolism, Protein Subunits | Metabolism | |
| Phylogeny | 18338569 | [Molecular diversity of rumen Archaea from Jinnan cattle]. | Pei C, Mao S, Zhu W | Wei Sheng Wu Xue Bao | 2008 | Animals, Archaea/classification/*genetics/*isolation & purification, Cattle, China, DNA Primers/genetics, DNA, Archaeal/genetics, DNA, Ribosomal/genetics, *Genetic Variation, Molecular Sequence Data, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology | Genetics | |
| Metabolism | 19759898 | High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. | Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M | PLoS One | 2009 | Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, DNA, Archaeal/*analysis, Feces, Female, *Gene Expression Regulation, Bacterial, Humans, Infant, Infant, Newborn, Infections/*epidemiology/*microbiology, Intestines/*microbiology, Male, Methanobacteriaceae/*metabolism, Methanobrevibacter/*metabolism, *Microbiological Techniques, Middle Aged, RNA, Ribosomal, 16S/metabolism, Reverse Transcriptase Polymerase Chain Reaction/*methods | Pathogenicity | 10.1371/journal.pone.0007063 |
| Phylogeny | 22859731 | Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. | Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M | Int J Syst Evol Microbiol | 2012 | Aged, 80 and over, Archaea/*classification/genetics/isolation & purification, Base Composition, DNA, Archaeal/genetics, Feces/*microbiology, Genome, Archaeal, Humans, Male, Methane/*metabolism, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics | 10.1099/ijs.0.033712-0 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1297 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3091) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3091 | |||
| 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 | |
| 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) | |||
| 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 | |
| 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. | 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 | |||
| 76441 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47692.1 | StrainInfo: A central database for resolving microbial strain identifiers |