Strain identifier
BacDive ID: 5412
Type strain: 
Species: Alkalibacter saccharofermentans
Strain Designation: Z-79820
Strain history: <- T. N. Zhilina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Z-79820 <- T. N. Zhilina {1998}
NCBI tax ID(s): 1120975 (strain), 235931 (species)
version 9.3 (current version)
General
@ref: 5565
BacDive-ID: 5412
DSM-Number: 14828
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic
description: Alkalibacter saccharofermentans Z-79820 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from mixture of mud and surface cyanobacterial mat from a lagoon.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 235931 | species |
| 1120975 | strain |
strain history
- @ref: 5565
- history: <- T. N. Zhilina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Z-79820 <- T. N. Zhilina {1998}
doi: 10.13145/bacdive5412.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Eubacteriaceae
- genus: Alkalibacter
- species: Alkalibacter saccharofermentans
- full scientific name: Alkalibacter saccharofermentans Garnova et al. 2005
@ref: 5565
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Eubacteriaceae
genus: Alkalibacter
species: Alkalibacter saccharofermentans
full scientific name: Alkalibacter saccharofermentans Garnova et al. 2005
strain designation: Z-79820
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5565
- name: ANAEROBRANCA GOTTSCHALKII MEDIUM (DSMZ Medium 895)
- growth: yes
- link: https://mediadive.dsmz.de/medium/895
- composition: Name: ANAEROBRANCA GOTTSCHALKII MEDIUM (DSMZ Medium 895; with strain-specific modifications) Composition: D-Glucose 4.93583 g/l Na2CO3 2.9615 g/l Tryptone 1.97433 g/l (NH4)2SO4 0.987167 g/l L-Cysteine HCl x H2O 0.493583 g/l K2HPO4 0.493583 g/l NH4Cl 0.394867 g/l Yeast extract 0.246792 g/l Na2S2O3 x 5 H2O 0.0987167 g/l MgSO4 x 7 H2O 0.029615 g/l Nitrilotriacetic acid 0.0148075 g/l NaCl 0.00987167 g/l MnSO4 x H2O 0.00493583 g/l ZnSO4 x 7 H2O 0.0017769 g/l CoSO4 x 7 H2O 0.0017769 g/l FeSO4 x 7 H2O 0.000987167 g/l CaCl2 x 2 H2O 0.000987167 g/l Sodium resazurin 0.000493583 g/l NiCl2 x 6 H2O 0.00029615 g/l AlK(SO4)2 x 12 H2O 0.000197433 g/l CuSO4 x 5 H2O 9.87167e-05 g/l H3BO3 9.87167e-05 g/l Pyridoxine hydrochloride 9.87167e-05 g/l Na2MoO4 x 2 H2O 9.87167e-05 g/l p-Aminobenzoic acid 4.93583e-05 g/l (DL)-alpha-Lipoic acid 4.93583e-05 g/l Calcium D-(+)-pantothenate 4.93583e-05 g/l Nicotinic acid 4.93583e-05 g/l Riboflavin 4.93583e-05 g/l Thiamine HCl 4.93583e-05 g/l Folic acid 1.97433e-05 g/l Biotin 1.97433e-05 g/l Na2WO4 x 2 H2O 3.94867e-06 g/l Na2SeO3 x 5 H2O 2.9615e-06 g/l Vitamin B12 9.87167e-07 g/l Distilled water
culture temp
- @ref: 5565
- growth: positive
- type: growth
- temperature: 35
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5565 | anaerobe | |
| 125439 | anaerobe | 99.5 |
Isolation, sampling and environmental information
isolation
- @ref: 5565
- sample type: mixture of mud and surface cyanobacterial mat from a lagoon
- geographic location: southeastern Transbaikal region, Lake Nizhnee Beloe
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Microbial community | #Microbial mat |
| #Host | #Microbial | #Bacteria |
taxonmaps
- @ref: 69479
- File name: preview.99_65306.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2123;96_9228;97_11096;98_13634;99_65306&stattab=map
- Last taxonomy: Alkalibacter saccharofermentans subclade
- 16S sequence: AY312403
- Sequence Identity:
- Total samples: 91
- soil counts: 5
- aquatic counts: 26
- animal counts: 60
Safety information
risk assessment
- @ref: 5565
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5565
- description: Alkalibacter saccharofermentans strain Z-79820 16S ribosomal RNA gene, partial sequence
- accession: AY312403
- length: 1465
- database: nuccore
- NCBI tax ID: 235931
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alkalibacter saccharofermentans DSM 14828 | GCA_900128885 | scaffold | ncbi | 1120975 |
| 66792 | Alkalibacter saccharofermentans DSM 14828 | 1120975.4 | wgs | patric | 1120975 |
| 66792 | Alkalibacter saccharofermentans DSM 14828 | 2582581275 | draft | img | 1120975 |
GC content
- @ref: 5565
- GC-content: 42.1
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 72.41 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 89.419 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 97.461 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 60.51 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 88.512 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 77.045 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 62.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 61.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 88.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.5 |
External links
@ref: 5565
culture collection no.: DSM 14828, Uniqem U-218, VKM B-2308
straininfo link
- @ref: 74901
- straininfo: 138967
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15127306 | Anaerobic, alkaliphilic, saccharolytic bacterium Alkalibacter saccharofermentans gen. nov., sp. nov. from a soda lake in the Transbaikal region of Russia. | Garnova ES, Zhilina TN, Tourova TP, Kostrikina NA, Zavarzin GA | Extremophiles | 10.1007/s00792-004-0390-7 | 2004 | Bacteria, Anaerobic/*classification/isolation & purification, Enterobacteriaceae/*classification/genetics/isolation & purification/ultrastructure, Fresh Water/*microbiology, Geography, Hydrogen-Ion Concentration, Phylogeny, Russia | Enzymology |
| Phylogeny | 36001361 | Alkalibacter rhizosphaerae sp. nov., a CO-utilizing bacterium isolated from tidal flat sediment, and emended description of the genus Alkalibacter. | Namirimu T, Yu J, Yang JA, Yang SH, Kim YJ, Kwon KK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005495 | 2022 | Bacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Geologic Sediments/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5565 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14828) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14828 | |||
| 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 | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 74901 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID138967.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |