Strain identifier
BacDive ID: 24716
Type strain: 
Species: Natranaerobaculum magadiense
Strain Designation: Z-1001
Strain history: <- D. G. Zavarzina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Z-1001 <- D. G. Zavarzina {2010}
NCBI tax ID(s): 929101 (species)
version 9 (current version)
General
@ref: 21297
BacDive-ID: 24716
DSM-Number: 24923
keywords: 16S sequence, Bacteria, anaerobe, spore-forming, Gram-positive, motile, rod-shaped
description: Natranaerobaculum magadiense Z-1001 is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from bottom sediments of soda lake.
NCBI tax id
- NCBI tax id: 929101
- Matching level: species
strain history
- @ref: 21297
- history: <- D. G. Zavarzina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Z-1001 <- D. G. Zavarzina {2010}
doi: 10.13145/bacdive24716.20240510.9
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Natranaerobiales
- family: Natranaerobiaceae
- genus: Natranaerobaculum
- species: Natranaerobaculum magadiense
- full scientific name: Natranaerobaculum magadiense Zavarzina et al. 2013
@ref: 21297
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Natranaerobiales
family: Natranaerobiaceae
genus: Natranaerobaculum
species: Natranaerobaculum magadiense
full scientific name: Natranaerobaculum magadiense Zavarzina et al. 2013
strain designation: Z-1001
type strain: yes
Morphology
cell morphology
- @ref: 31164
- gram stain: positive
- cell length: 5 µm
- cell width: 0.35 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 21297
- name: NATRONIELLA MEDIUM (DSMZ Medium 784)
- growth: yes
- link: https://mediadive.dsmz.de/medium/784
- composition: Name: NATRONIELLA MEDIUM (DSMZ Medium 784; with strain-specific modifications) Composition: Na2CO3 67.5273 g/l NaHCO3 37.7358 g/l NaCl 15.8888 g/l Na2S2O3 x 5 H2O 2.48262 g/l Yeast extract 1.9861 g/l NH4Cl 0.993049 g/l Na2S x 9 H2O 0.993049 g/l KH2PO4 0.19861 g/l KCl 0.19861 g/l MgCl2 x 6 H2O 0.0993049 g/l Na2-EDTA x 2 H2O 0.00516385 g/l FeCl2 x 4 H2O 0.00148957 g/l Sodium resazurin 0.000496524 g/l CoCl2 x 6 H2O 0.000188679 g/l Pyridoxine hydrochloride 9.93049e-05 g/l MnCl2 x 4 H2O 9.93049e-05 g/l ZnCl2 6.95134e-05 g/l Calcium D-(+)-pantothenate 4.96524e-05 g/l Nicotinic acid 4.96524e-05 g/l Riboflavin 4.96524e-05 g/l Thiamine HCl 4.96524e-05 g/l (DL)-alpha-Lipoic acid 4.96524e-05 g/l p-Aminobenzoic acid 4.96524e-05 g/l Na2MoO4 x 2 H2O 3.57498e-05 g/l NiCl2 x 6 H2O 2.38332e-05 g/l Biotin 1.9861e-05 g/l Folic acid 1.9861e-05 g/l H3BO3 5.95829e-06 g/l CuCl2 x 2 H2O 1.9861e-06 g/l Vitamin B12 9.93049e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 21297 | positive | growth | 45 |
| 31164 | positive | growth | 20-57 |
| 31164 | positive | optimum | 47.5 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31164 | positive | growth | 7.5-10.7 | alkaliphile |
| 31164 | positive | optimum | 9.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 21297 | anaerobe |
| 31164 | anaerobe |
spore formation
- @ref: 31164
- spore formation: yes
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31164 | NaCl | positive | growth | 0.0-8.99 % |
| 31164 | NaCl | positive | optimum | 7.54 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31164 | 30089 | acetate | + | carbon source |
| 31164 | 15740 | formate | + | carbon source |
| 31164 | 24996 | lactate | + | carbon source |
| 31164 | 17272 | propionate | + | carbon source |
| 31164 | 30031 | succinate | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 21297
- sample type: bottom sediments of soda lake
- geographic location: Lake Magadi
- country: Kenya
- origin.country: KEN
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_181902.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_569;96_14943;97_18250;98_22719;99_181902&stattab=map
- Last taxonomy: Natranaerobaculum magadiense subclade
- 16S sequence: HQ322120
- Sequence Identity:
- Total samples: 72
- soil counts: 8
- aquatic counts: 41
- animal counts: 21
- plant counts: 2
Safety information
risk assessment
- @ref: 21297
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 21297 | Natranaerobaculum magadiense strain Z-1001 16S ribosomal RNA gene, partial sequence | HQ322118 | 1499 | nuccore | 929101 |
| 21297 | Natranaerobaculum magadiense strain Z-1001 16S ribosomal RNA gene, partial sequence | HQ322119 | 1498 | nuccore | 929101 |
| 21297 | Natranaerobaculum magadiense strain Z-1001 16S ribosomal RNA gene, partial sequence | HQ322120 | 1498 | nuccore | 929101 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 21297 | 35.6 | thermal denaturation, midpoint method (Tm) |
| 31164 | 35.6 |
External links
@ref: 21297
culture collection no.: DSM 24923, VKM B-2666
straininfo link
- @ref: 88546
- straininfo: 399270
literature
- topic: Phylogeny
- Pubmed-ID: 23859946
- title: Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment.
- authors: Zavarzina DG, Zhilina TN, Kuznetsov BB, Kolganova TV, Osipov GA, Kotelev MS, Zavarzin GA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.054536-0
- year: 2013
- mesh: Bacteria, Anaerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Kenya, Lakes/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water Microbiology
- topic2: Enzymology
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 | |||
| 21297 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24923 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24923) | |||
| 31164 | 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 | 27492 | 28776041 | |
| 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/ | |||
| 88546 | 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-ID399270.1 |