Strain identifier
BacDive ID: 131580
Type strain: 
Species: Acetobacteroides hydrogenigenes
Strain Designation: RL-C
Strain history: Y.-L. Qiu and Y. Sekiguchi strain RL-C.
NCBI tax ID(s): 979970 (species)
version 9.3 (current version)
General
@ref: 23376
BacDive-ID: 131580
DSM-Number: 24657
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Acetobacteroides hydrogenigenes RL-C is a mesophilic bacterium that was isolated from reed swamp.
NCBI tax id
- NCBI tax id: 979970
- Matching level: species
strain history
| @ref | history |
|---|---|
| 23376 | <- Y.-L. Qiu, Qingdao Institute of Bioenergy & Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao; RL-C |
| 67770 | Y.-L. Qiu and Y. Sekiguchi strain RL-C. |
doi: 10.13145/bacdive131580.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Williamwhitmaniaceae
- genus: Acetobacteroides
- species: Acetobacteroides hydrogenigenes
- full scientific name: Acetobacteroides hydrogenigenes Su et al. 2014
@ref: 23376
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Williamwhitmaniaceae
genus: Acetobacteroides
species: Acetobacteroides hydrogenigenes
full scientific name: Acetobacteroides hydrogenigenes Su et al. 2014
strain designation: RL-C
type strain: yes
Morphology
cell morphology
- @ref: 125439
- gram stain: negative
- confidence: 99.7
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 23376 | ACETOBACTEROIDES MEDIUM (DSMZ Medium 1647) | yes | https://mediadive.dsmz.de/medium/1647 | Name: ACETOBACTEROIDES MEDIUM (DSMZ Medium 1647) Composition: NaHCO3 2.5 g/l NH4Cl 0.824796 g/l Na2S x 9 H2O 0.3 g/l L-Cysteine HCl x H2O 0.3 g/l MgCl2 x 6 H2O 0.2 g/l Yeast extract 0.2 g/l Glucose 0.18 g/l KH2PO4 0.14 g/l Nitrilotriacetic acid 0.0128 g/l Resazurin 0.001 g/l NaCl 0.001 g/l FeCl2 x 4 H2O 0.001 g/l NiCl2 x 6 H2O 0.0001 g/l ZnCl2 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l CaCl2 x 2 H2O 0.0001 g/l Na2WO4 x 2 H2O 4e-05 g/l CoCl2 x 6 H2O 3e-05 g/l Na2SeO3 x 5 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l CuCl2 2e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 1e-05 g/l p-Aminobenzoic acid 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Riboflavin 5e-06 g/l Lipoic acid 5e-06 g/l Nicotinic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Na2SeO3 4e-06 g/l Na2WO4 4e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water |
| 23376 | TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323) | yes | https://mediadive.dsmz.de/medium/323 | Name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323) Composition: Agar 12.0 g/l Na2CO3 2.5 g/l D-Glucose 2.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l L-Cysteine HCl x H2O 1.0 g/l (NH4)2SO4 0.9 g/l NaCl 0.9 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l MgSO4 x 7 H2O 0.19 g/l CaCl2 x 2 H2O 0.12 g/l Sodium resazurin 0.0005 g/l n-Butyric acid iso-Butyric acid DL-2-Methylbutyric acid n-Valeric acid iso-Valeric acid Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 23376 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.9
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 23376 | reed swamp | Shandong Province, Qingdao (36° 00' 00'' N 120° 00' 00'' E) | China | CHN | Asia | 36 | 120 |
| 67770 | Reed swamp in Qingdao | Shandong Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Wetland (Swamp) |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_101102.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1713;96_7255;97_8701;98_10668;99_101102&stattab=map
- Last taxonomy: Acetobacteroides hydrogenigenes subclade
- 16S sequence: AB611036
- Sequence Identity:
- Total samples: 469
- soil counts: 16
- aquatic counts: 431
- animal counts: 9
- plant counts: 13
Safety information
risk assessment
- @ref: 23376
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23376
- description: Acetobacteroides hydrogenigenes gene for 16S rRNA, partial sequence
- accession: AB611036
- length: 1440
- database: nuccore
- NCBI tax ID: 979970
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acetobacteroides hydrogenigenes RL-C | GCA_004340205 | scaffold | ncbi | 979970 |
| 66792 | Acetobacteroides hydrogenigenes strain RL-C | 979970.3 | wgs | patric | 979970 |
| 66792 | Acetobacteroides hydrogenigenes DSM 24657 | 2731639222 | draft | img | 979970 |
GC content
- @ref: 23376
- GC-content: 51.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 89.727 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 69.934 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 84.611 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.768 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 92.053 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 81 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 60 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.7 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 89.8 |
External links
@ref: 23376
culture collection no.: DSM 24657, CGMCC 1.5173, JCM 17603
straininfo link
- @ref: 89986
- straininfo: 405703
literature
- topic: Phylogeny
- Pubmed-ID: 24899658
- title: Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp.
- authors: Su XL, Tian Q, Zhang J, Yuan XZ, Shi XS, Guo RB, Qiu YL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.063917-0
- year: 2014
- mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogen/metabolism, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *Wetlands
- topic2: Genetics
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 | |||
| 23376 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24657 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24657) | |||
| 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/ | |||
| 89986 | 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-ID405703.1 | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |