Strain identifier
BacDive ID: 17960
Type strain: 
Species: Acidaminobacter hydrogenoformans
Strain history: CIP <- 1999, T.A. Hansen, Univ. Groningen, The Netherlands <- A.J.M. Stams: strain glu 65
NCBI tax ID(s): 1120920 (strain), 65403 (species)
version 9.3 (current version)
General
@ref: 1225
BacDive-ID: 17960
DSM-Number: 2784
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Acidaminobacter hydrogenoformans DSM 2784 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1120920 | strain |
| 65403 | species |
strain history
| @ref | history |
|---|---|
| 1225 | <- A. J. M. Stams, Univ. Groningen, The Netherlands; Glu 65 <- A. J. M. Stams and T. A. Hansen {1982} |
| 120003 | CIP <- 1999, T.A. Hansen, Univ. Groningen, The Netherlands <- A.J.M. Stams: strain glu 65 |
doi: 10.13145/bacdive17960.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Acidaminobacter
- species: Acidaminobacter hydrogenoformans
- full scientific name: Acidaminobacter hydrogenoformans Stams and Hansen 1985
@ref: 1225
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridia, not assigned to family
genus: Acidaminobacter
species: Acidaminobacter hydrogenoformans
full scientific name: Acidaminobacter hydrogenoformans Stams and Hansen 1985
type strain: yes
Morphology
cell morphology
- @ref: 120003
- gram stain: negative
- cell shape: rod-shaped
Culture and growth conditions
culture medium
| @ref | name | growth | composition | link |
|---|---|---|---|---|
| 39471 | MEDIUM 224 - for anaerobic bacteria TGV | yes | Distilled water make up to (1000.000 ml);Glucose (10.000 g);Yeast extract (20.000 g);Resazurin (2.000 mg);Trypto casein soy broth (30.000 g);L-Cysteine (0.500 g);Hemin solution - M00149 (25.000 ml);Vitamins solution - M00850 (10.000 ml) | |
| 1225 | ACIDAMINOBACTER MEDIUM (DSMZ Medium 292) | yes | Name: ACIDAMINOBACTER MEDIUM (DSMZ Medium 292) Composition: Na2SO4 2.99103 g/l NaHCO3 1.99402 g/l Glycine 1.49551 g/l NaCl 1.19641 g/l KCl 0.398804 g/l MgCl2 x 6 H2O 0.398804 g/l Na2S x 9 H2O 0.299103 g/l KH2PO4 0.199402 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water | https://mediadive.dsmz.de/medium/292 |
| 120003 | CIP Medium 402 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=402 | |
| 120003 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 39471 | positive | growth | 30 |
| 1225 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1225 | anaerobe | |
| 125439 | anaerobe | 92.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | isolation date |
|---|---|---|---|---|---|---|
| 1225 | mud | Ems-Dollard estuary | Netherlands | NLD | Europe | |
| 120003 | Environment, Estuarine mud | Ems Dollart | Netherlands | NLD | Europe | 1984 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
taxonmaps
- @ref: 69479
- File name: preview.99_38081.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2669;96_11953;97_14489;98_27951;99_38081&stattab=map
- Last taxonomy: Acidaminobacter hydrogenoformans subclade
- 16S sequence: AF016691
- Sequence Identity:
- Total samples: 3583
- soil counts: 361
- aquatic counts: 2114
- animal counts: 1056
- plant counts: 52
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 1225 | 1 | Risk group (German classification) |
| 120003 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 1225
- description: Acidaminobacter hydrogenoformans 16S ribosomal RNA gene, complete sequence
- accession: AF016691
- length: 1468
- database: nuccore
- NCBI tax ID: 65403
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acidaminobacter hydrogenoformans DSM 2784 | GCA_900103005 | scaffold | ncbi | 1120920 |
| 66792 | Acidaminobacter hydrogenoformans DSM 2784 | 1120920.3 | wgs | patric | 1120920 |
| 66792 | Acidaminobacter hydrogenoformans DSM 2784 | 2599185234 | draft | img | 1120920 |
GC content
- @ref: 1225
- GC-content: 48.1
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 55.056 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 73.942 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 88.839 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 56.69 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 85.058 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 75.149 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 73.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 57.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 72.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 92.6 |
External links
@ref: 1225
culture collection no.: DSM 2784, Glu 65, CIP 106102
straininfo link
- @ref: 86947
- straininfo: 265430
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1225 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2784) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2784 | |||
| 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 | |||
| 39471 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18194 | ||||
| 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 | |||
| 86947 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265430.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 120003 | Curators of the CIP | Collection of Institut Pasteur (CIP 106102) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106102 | |||
| 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 |