Strain identifier
BacDive ID: 24159
Type strain:
Species: Methanoculleus horonobensis
Strain Designation: T10
Strain history: S. Shimizu T10.
NCBI tax ID(s): 528314 (species)
General
@ref: 21017
BacDive-ID: 24159
DSM-Number: 21626
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative, ovoid-shaped
description: Methanoculleus horonobensis T10 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from deep aquifer water from a Miocene diatomaceous hard shale .
NCBI tax id
- NCBI tax id: 528314
- Matching level: species
strain history
@ref | history |
---|---|
21017 | <- S. Shimizu, Horonobe RISE; T10 |
67770 | S. Shimizu T10. |
doi: 10.13145/bacdive24159.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanomicrobiaceae
- genus: Methanoculleus
- species: Methanoculleus horonobensis
- full scientific name: Methanoculleus horonobensis Shimizu et al. 2013
@ref: 21017
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanomicrobiaceae
genus: Methanoculleus
species: Methanoculleus horonobensis
full scientific name: Methanoculleus horonobensis Shimizu et al. 2013
strain designation: T10
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31146 | negative | 1.15 µm | 1.15 µm | ovoid-shaped | no | |
69480 | negative | 99.922 |
Culture and growth conditions
culture medium
- @ref: 21017
- name: METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141b
- composition: Name: METHANOCULLEUS SP. MEDIUM (DSMZ Medium 141b) Composition: NaHCO3 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 FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 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 Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 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 |
---|---|---|---|---|
21017 | positive | growth | 37 | mesophilic |
31146 | positive | growth | 25-45 | |
31146 | positive | optimum | 39.5 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31146 | positive | growth | 5.8-8.2 |
31146 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
21017 | anaerobe | |
31146 | anaerobe | |
69480 | anaerobe | 99.632 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.967 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31146 | NaCl | positive | growth | 0-7.54 % |
31146 | NaCl | positive | optimum | 0.87 % |
metabolite utilization
- @ref: 31146
- Chebi-ID: 15740
- metabolite: formate
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
21017 | deep aquifer water from a Miocene diatomaceous hard shale (Wakkanai formation) | Hokkaido, Horonobe | Japan | JPN | Asia |
67770 | Groundwater from a deep diatomaceous shale formation located in Horonobe | Hokkaido | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Groundwater |
#Environmental | #Terrestrial | #Geologic |
taxonmaps
- @ref: 69479
- File name: preview.99_190335.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17869;96_69167;97_90152;98_124004;99_190335&stattab=map
- Last taxonomy: Methanoculleus horonobensis subclade
- 16S sequence: AB436897
- Sequence Identity:
- Total samples: 4
- aquatic counts: 3
- animal counts: 1
Safety information
risk assessment
- @ref: 21017
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21017
- description: Methanoculleus horonobensis gene for 16S rRNA, partial sequence
- accession: AB436897
- length: 1432
- database: ena
- NCBI tax ID: 528314
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
67770 | Methanoculleus horonobensis JCM 15517 | GCA_001602375 | contig | ncbi | 528314 |
66792 | Methanoculleus horonobensis strain T10 | 528314.3 | wgs | patric | 528314 |
GC content
@ref | GC-content | method |
---|---|---|
21017 | 62.9 | high performance liquid chromatography (HPLC) |
31146 | 62.9 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 96.528 | yes |
anaerobic | yes | 98.625 | yes |
halophile | no | 86.691 | yes |
spore-forming | no | 95.171 | no |
glucose-util | yes | 73.08 | no |
motile | no | 89.024 | yes |
thermophile | no | 95.174 | yes |
aerobic | no | 96.11 | no |
flagellated | no | 96.728 | yes |
glucose-ferment | no | 60.744 | no |
External links
@ref: 21017
culture collection no.: DSM 21626, JCM 15517
straininfo link
- @ref: 88115
- straininfo: 406551
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23832970 | Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation. | Shimizu S, Ueno A, Tamamura S, Naganuma T, Kaneko K | Int J Syst Evol Microbiol | 10.1099/ijs.0.053520-0 | 2013 | Base Composition, DNA, Archaeal/genetics, Groundwater/*microbiology, Japan, Methanomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Genetics | 27034500 | Draft Genome Sequences of Methanoculleus horonobensis Strain JCM 15517, Methanoculleus thermophilus Strain DSM 2373, and Methanofollis ethanolicus Strain JCM 15103, Hydrogenotrophic Methanogens Belonging to the Family Methanomicrobiaceae. | Narihiro T, Kusada H, Yoneda Y, Tamaki H | Genome Announc | 10.1128/genomeA.00199-16 | 2016 |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
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 | |||
21017 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21626 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21626) | |||
31146 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27474 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
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 | |||
88115 | 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-ID406551.1 |