Strain identifier
BacDive ID: 18091
Type strain: 
Species: Caldithrix palaeochoryensis
Strain Designation: MC
Strain history: <- M. Miroshnichenko, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; strain MC <- M. Miroshnichenko {2008}
NCBI tax ID(s): 650508 (species)
version 9 (current version)
General
@ref: 16046
BacDive-ID: 18091
DSM-Number: 21940
keywords: 16S sequence, Bacteria, anaerobe, motile, rod-shaped
description: Caldithrix palaeochoryensis MC is an anaerobe, motile, rod-shaped bacterium that was isolated from hydrothermal vent.
NCBI tax id
- NCBI tax id: 650508
- Matching level: species
strain history
- @ref: 16046
- history: <- M. Miroshnichenko, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; strain MC <- M. Miroshnichenko {2008}
doi: 10.13145/bacdive18091.20240510.9
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/calditrichota
- domain: Bacteria
- phylum: Calditrichota
- class: Calditrichia
- order: Calditrichales
- family: Calditrichaceae
- genus: Caldithrix
- species: Caldithrix palaeochoryensis
- full scientific name: Caldithrix palaeochoryensis Miroshnichenko et al. 2010
@ref: 16046
domain: Bacteria
phylum: Calditrichaeota
class: Calditrichae
order: Deferribacterales
family: Calditrichaceae
genus: Caldithrix
species: Caldithrix palaeochoryensis
full scientific name: Caldithrix palaeochoryensis Miroshnichenko et al. 2010
strain designation: MC
type strain: yes
Morphology
cell morphology
- @ref: 29595
- cell length: 04-12 µm
- cell width: 0.2-0.3 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29595
- production: yes
Culture and growth conditions
culture medium
- @ref: 16046
- name: CALDITHRIX MEDIUM (DSMZ Medium 946a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/946a
- composition: Name: CALDITHRIX MEDIUM (DSMZ Medium 946a; with strain-specific modifications) Composition: MgCl2 x 6 H2O 5.44016 g/l Yeast extract 2.96736 g/l NaNO3 1.48368 g/l Na2CO3 0.98912 g/l KCl 0.642928 g/l Na2S x 9 H2O 0.593472 g/l KH2PO4 0.326409 g/l NH4Cl 0.326409 g/l NaBr 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l SrCl2 x 6 H2O 0.0148368 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l Na3-citrate 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l H3BO3 9.8912e-05 g/l KI 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 16046 | positive | growth | 55 |
| 29595 | positive | growth | 40-65 |
| 29595 | positive | optimum | 60 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29595 | positive | growth | 6.2-7.5 |
| 29595 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 16046 | anaerobe |
| 29595 | anaerobe |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29595 | NaCl | positive | growth | 0.5-6.5 % |
| 29595 | NaCl | positive | optimum | 3 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29595 | 22599 | arabinose | + | carbon source |
| 29595 | 28757 | fructose | + | carbon source |
| 29595 | 28260 | galactose | + | carbon source |
| 29595 | 17234 | glucose | + | carbon source |
| 29595 | 15361 | pyruvate | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 16046
- sample type: hydrothermal vent
- geographic location: Milos Island, Palaeochori Bay
- country: Greece
- origin.country: GRC
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 16046
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16046
- description: Caldithrix palaeochoryensis strain MC 16S ribosomal RNA gene, partial sequence
- accession: FJ999729
- length: 1482
- database: nuccore
- NCBI tax ID: 650508
GC content
| @ref | GC-content | method |
|---|---|---|
| 16046 | 43.3 | high performance liquid chromatography (HPLC) |
| 29595 | 43.3 |
External links
@ref: 16046
culture collection no.: DSM 21940, VKM B-2536
straininfo link
- @ref: 87079
- straininfo: 403151
literature
- topic: Phylogeny
- Pubmed-ID: 19854873
- title: Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix.
- authors: Miroshnichenko ML, Kolganova TV, Spring S, Chernyh N, Bonch-Osmolovskaya EA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.016667-0
- year: 2009
- mesh: Anaerobiosis, Bacteria/*classification/genetics/*isolation & purification/metabolism, Base Composition, Chemoautotrophic Growth, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16046 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21940) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21940 | |||
| 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 | |||
| 29595 | 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 | 25987 | 28776041 | |
| 87079 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403151.1 | StrainInfo: A central database for resolving microbial strain identifiers |