Strain identifier
BacDive ID: 10422
Type strain:
Species: Lebetimonas acidiphila
Strain history: K. Takai Pd55.
NCBI tax ID(s): 267990 (species)
General
@ref: 6399
BacDive-ID: 10422
DSM-Number: 16356
keywords: 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped
description: Lebetimonas acidiphila DSM 16356 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from in situ colonization system deployed in a hydrothermal diffusing flow .
NCBI tax id
- NCBI tax id: 267990
- Matching level: species
strain history
@ref | history |
---|---|
6399 | <- K. Takai, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Pd55 <- K. Takai {2003} |
67770 | K. Takai Pd55. |
doi: 10.13145/bacdive10422.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Nautiliales
- family: Nautiliaceae
- genus: Lebetimonas
- species: Lebetimonas acidiphila
- full scientific name: Lebetimonas acidiphila Takai et al. 2005
@ref: 6399
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Nautiliales
family: Nautiliaceae
genus: Lebetimonas
species: Lebetimonas acidiphila
full scientific name: Lebetimonas acidiphila Takai et al. 2005
type strain: yes
Morphology
cell morphology
- @ref: 31331
- gram stain: negative
- cell length: 2 µm
- cell width: 0.7 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 6399
- name: LEBETIMONAS MEDIUM (DSMZ Medium 795a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/795a
- composition: Name: LEBETIMONAS MEDIUM (DSMZ Medium 795a) Composition: Sulfur 9.86193 g/l MgCl2 x 6 H2O 5.42406 g/l NaHCO3 1.97239 g/l NH4Cl 1.23274 g/l Tryptone 0.986193 g/l Yeast extract 0.986193 g/l KCl 0.641026 g/l KH2PO4 0.493097 g/l Na2S x 9 H2O 0.493097 g/l Na-formate 0.197239 g/l NaBr 0.0986193 g/l MgSO4 x 7 H2O 0.0295858 g/l Nitrilotriacetic acid 0.0147929 g/l SrCl2 x 6 H2O 0.0147929 g/l NaCl 0.00986193 g/l Na3-citrate 0.00986193 g/l MnSO4 x H2O 0.00493097 g/l ZnSO4 x 7 H2O 0.00177515 g/l CoSO4 x 7 H2O 0.00177515 g/l CaCl2 x 2 H2O 0.000986193 g/l FeSO4 x 7 H2O 0.000986193 g/l Sodium resazurin 0.000493097 g/l NiCl2 x 6 H2O 0.000295858 g/l AlK(SO4)2 x 12 H2O 0.000197239 g/l H3BO3 9.86193e-05 g/l Pyridoxine hydrochloride 9.86193e-05 g/l Na2MoO4 x 2 H2O 9.86193e-05 g/l CuSO4 x 5 H2O 9.86193e-05 g/l p-Aminobenzoic acid 4.93097e-05 g/l Nicotinic acid 4.93097e-05 g/l Riboflavin 4.93097e-05 g/l Thiamine HCl 4.93097e-05 g/l Calcium D-(+)-pantothenate 4.93097e-05 g/l KI 4.93097e-05 g/l (DL)-alpha-Lipoic acid 4.93097e-05 g/l Folic acid 1.97239e-05 g/l Biotin 1.97239e-05 g/l Na2WO4 x 2 H2O 3.94477e-06 g/l Na2SeO3 x 5 H2O 2.95858e-06 g/l Vitamin B12 9.86193e-07 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6399 | positive | growth | 55 | thermophilic |
31331 | positive | growth | 30-68 | |
31331 | positive | optimum | 50 | thermophilic |
67770 | positive | growth | 50 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31331 | positive | growth | 4.2-7.0 |
31331 | positive | optimum | 5.2 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6399 | anaerobe |
31331 | anaerobe |
spore formation
- @ref: 31331
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31331 | NaCl | positive | growth | 0.6-5 % |
31331 | NaCl | positive | optimum | 2 % |
metabolite production
- @ref: 31331
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | latitude | longitude |
---|---|---|---|---|
6399 | in situ colonization system deployed in a hydrothermal diffusing flow (maximum temperature of 78°C) | TOTO caldera in the Mariana Arc | 12.7134 | -143.539 |
67770 | in situ colonization system deployed in a hydrothermal diffusing flow at the TOTO caldera in the Marina Arc |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Bioremediation | #In situ |
#Engineered | #Laboratory | #Lab enrichment |
#Environmental | #Aquatic | #Thermal spring |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_1724.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_250;96_981;97_1141;98_1363;99_1724&stattab=map
- Last taxonomy: Lebetimonas acidiphila subclade
- 16S sequence: AB167820
- Sequence Identity:
- Total samples: 136
- soil counts: 9
- aquatic counts: 105
- animal counts: 16
- plant counts: 6
Safety information
risk assessment
- @ref: 6399
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6399
- description: Lebetimonas acidiphila gene for small subunit rRNA, partial sequence
- accession: AB167820
- length: 1431
- database: ena
- NCBI tax ID: 267990
GC content
@ref | GC-content | method |
---|---|---|
6399 | 34.0 | high performance liquid chromatography (HPLC) |
31331 | 24 | |
67770 | 34 | high performance liquid chromatography (HPLC) |
External links
@ref: 6399
culture collection no.: DSM 16356, JCM 12420, PD Pd55, PD 55
straininfo link
- @ref: 79704
- straininfo: 135117
literature
- topic: Phylogeny
- Pubmed-ID: 15653874
- title: Lebetimonas acidiphila gen. nov., sp. nov., a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal fumarole in the Mariana Arc.
- authors: Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH, Horikoshi K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63330-0
- year: 2005
- mesh: Anaerobiosis, Bacterial Typing Techniques, DNA, Ribosomal, Epsilonproteobacteria/*classification/genetics/growth & development/physiology, Genes, rRNA, *Hot Temperature, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology
- topic2: Stress
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6399 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16356) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16356 | |||
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 | |||
31331 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27645 | 28776041 | |
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 | |||
79704 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID135117.1 | StrainInfo: A central database for resolving microbial strain identifiers |