Strain identifier
BacDive ID: 24159
Type strain: 
Species: Methanoculleus horonobensis
Strain Designation: T10
Strain history: S. Shimizu T10.
NCBI tax ID(s): 528314 (species)
version 9.3 (current version)
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 Research Institute for the Subsurface Environment, Horonobe-cho, Hokkaido, Japan.; T10 |
| 67770 | S. Shimizu T10. |
doi: 10.13145/bacdive24159.20250331.9.3
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 | |
| 125439 | negative | 98.3 |
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 |
|---|---|---|---|
| 21017 | positive | growth | 37 |
| 31146 | positive | growth | 25-45 |
| 31146 | positive | optimum | 39.5 |
| 67770 | positive | growth | 37 |
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 | |
| 125438 | anaerobe | 90.433 |
| 125439 | obligate anaerobe | 99.2 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 96.8
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: nuccore
- 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
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 71.621 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 90.433 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.445 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 89.085 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 78.675 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 85.5 | yes |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 57.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate anaerobe | 99.2 |
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/ | |||
| 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 | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |