Strain identifier
BacDive ID: 130818
Type strain: 
Species: Anoxybacter fermentans
Strain Designation: DY22613
Strain history: X. Zeng DY22613.
NCBI tax ID(s): 1323375 (species)
version 9.1 (current version)
General
@ref: 22142
BacDive-ID: 130818
DSM-Number: 28033
keywords: genome sequence, 16S sequence, Bacteria, anaerobe
description: Anoxybacter fermentans DY22613 is an anaerobe bacterium that was isolated from deep sea hydrothermal sulfide deposit, depth of 2891 m.
NCBI tax id
- NCBI tax id: 1323375
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22142 | <- X. Zeng, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; DY22613 <- X. Zeng {2012} |
| 67770 | X. Zeng DY22613. |
doi: 10.13145/bacdive130818.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Halanaerobiales
- family: Halanaerobiales, not assigned to family
- genus: Anoxybacter
- species: Anoxybacter fermentans
- full scientific name: Anoxybacter fermentans Zeng et al. 2015
@ref: 22142
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridia, not assigned to order
family: Clostridia, not assigned to family
genus: Anoxybacter
species: Anoxybacter fermentans
full scientific name: Anoxybacter fermentans Zeng et al. 2015
strain designation: DY22613
type strain: yes
Culture and growth conditions
culture medium
- @ref: 22142
- name: MARINITOGA MEDIUM (DSMZ Medium 904)
- growth: yes
- link: https://mediadive.dsmz.de/medium/904
- composition: Name: MARINITOGA MEDIUM (DSMZ Medium 904) Composition: Sea Salt 30.0 g/l PIPES 6.0 g/l D-Glucose 2.5 g/l Tryptone 1.0 g/l Yeast extract 1.0 g/l Na2S x 9 H2O 0.5 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 22142 | positive | growth | 60 |
| 67770 | positive | growth | 60 |
Physiology and metabolism
oxygen tolerance
- @ref: 22142
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | latitude | longitude |
|---|---|---|---|---|---|
| 22142 | deep sea hydrothermal sulfide deposit, depth of 2891 m | East Pacific Rise | International waters | -3.1 | -102.6 |
| 67770 | Deep-sea hydrothermal vent |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Condition | #Sulfuric | |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_50847.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5054;96_22912;97_28651;98_36522;99_50847&stattab=map
- Last taxonomy: Anoxybacter fermentans subclade
- 16S sequence: KC794015
- Sequence Identity:
- Total samples: 129
- soil counts: 10
- aquatic counts: 89
- animal counts: 27
- plant counts: 3
Safety information
risk assessment
- @ref: 22142
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22142
- description: Anoxybacter fermentans strain DY22613 16S ribosomal RNA gene, partial sequence
- accession: KC794015
- length: 1500
- database: nuccore
- NCBI tax ID: 1323375
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Anoxybacter fermentans DY22613 | GCA_003991135 | complete | ncbi | 1323375 |
| 66792 | Anoxybacter fermentans DY22613 | 2837169743 | complete | img | 1323375 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 22142 | 36.7 | sequence analysis |
| 67770 | 36.7 | genome sequence analysis |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 52 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 73.013 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 82.848 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 91.511 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 62.947 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | yes | 57.685 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 78.379 | no |
External links
@ref: 22142
culture collection no.: DSM 28033, JCM 19466, MCCC 1A06456
straininfo link
- @ref: 89306
- straininfo: 404111
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25505345 | Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent. | Zeng X, Zhang Z, Li X, Zhang X, Cao J, Jebbar M, Alain K, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.068221-0 | 2014 | Bacteria, Anaerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ferric Compounds/metabolism, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
| 32208240 | Extracellular electron transfer in fermentative bacterium Anoxybacter fermentans DY22613(T) isolated from deep-sea hydrothermal sulfides. | Li X, Zeng X, Qiu D, Zhang Z, Zhang X, Shao Z | Sci Total Environ | 10.1016/j.scitotenv.2020.137723 | 2020 | Bacteria, Electron Transport, *Electrons, Ferric Compounds, Oxidation-Reduction, Sulfides | ||
| Genetics | 32883438 | Complete genome sequence of Anoxybacter fermentans DY22613(T), a piezophilic dissimilatory Fe(III)-reducing bacterium isolated from East Pacific Rise hydrothermal sulfides. | Li X, Qiu D, Zeng X, Shao Z | Mar Genomics | 10.1016/j.margen.2020.100755 | 2020 | Firmicutes/*genetics, *Genome, Bacterial, Hydrothermal Vents/*microbiology, Iron/metabolism, Oxidation-Reduction, Pacific Ocean, Sulfides, Whole Genome Sequencing | Metabolism |
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 22142 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28033 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28033) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89306 | 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-ID404111.1 |