Strain identifier
BacDive ID: 2908
Type strain: 
Species: Brachymonas denitrificans
Strain Designation: AS-P1
Strain history: A. Hiraishi AS-P1.
NCBI tax ID(s): 1121117 (strain), 28220 (species)
version 9.3 (current version)
General
@ref: 5622
BacDive-ID: 2908
DSM-Number: 15123
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Brachymonas denitrificans AS-P1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soybean curd waste sludge.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 28220 | species |
| 1121117 | strain |
strain history
| @ref | history |
|---|---|
| 5622 | <- JCM <- A. Hiraishi; AS-P1 |
| 67770 | A. Hiraishi AS-P1. |
doi: 10.13145/bacdive2908.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Brachymonas
- species: Brachymonas denitrificans
- full scientific name: Brachymonas denitrificans Hiraishi et al. 1995
@ref: 5622
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Brachymonas
species: Brachymonas denitrificans
full scientific name: Brachymonas denitrificans Hiraishi et al. 1995
strain designation: AS-P1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 98.5 |
| 125439 | negative | 99.2 |
colony morphology
- @ref: 56744
- incubation period: 3 days
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_15123_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_15123_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_15123_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_15123_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 5622
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 5622 | positive | growth | 30 |
| 56744 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 56744 | aerobe | |
| 125439 | obligate aerobe | 98.3 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 93.101 |
| 125439 | no | 98 |
observation
- @ref: 67770
- observation: quinones: Q-8, RQ-8
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 56744 C12:0 9 12 56744 C14:0 0.4 14 56744 C16:0 24 16 56744 C17:0 0.3 17 56744 C18:0 0.7 18 56744 C10:0 3OH 1.4 11.423 56744 C12:0 3OH 1.9 13.455 56744 C16:0 2OH 0.7 17.233 56744 C16:1 ω7c 41.7 15.819 56744 C18:1 ω7c /12t/9t 15.8 17.824 56744 C18:1 ω9c 0.4 17.769 56744 C18:2 ω6,9c/C18:0 ANTE 1.8 17.724 56744 C19:0 CYCLO ω9c 0.4 18.87 56744 Unidentified 0.6 9.979 56744 Unidentified 0.4 10.459 56744 Unidentified 0.5 18.073 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 5622 | soybean curd waste sludge | Japan | JPN | Asia |
| 56744 | Sludge,soybean curd waste | |||
| 67770 | Soybean curd waste sludge |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Food |
| #Engineered | #Waste | #Solid plant waste |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Fruit (Seed) |
taxonmaps
- @ref: 69479
- File name: preview.99_11728.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_5918;97_7122;98_8796;99_11728&stattab=map
- Last taxonomy: Brachymonas denitrificans subclade
- 16S sequence: D14320
- Sequence Identity:
- Total samples: 2225
- soil counts: 132
- aquatic counts: 1459
- animal counts: 598
- plant counts: 36
Safety information
risk assessment
- @ref: 5622
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5622
- description: Brachymonas denitrificans gene for 16S rRNA
- accession: D14320
- length: 1452
- database: nuccore
- NCBI tax ID: 28220
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Brachymonas denitrificans DSM 15123 | 1121117.3 | wgs | patric | 1121117 |
| 66792 | Brachymonas denitrificans DSM 15123 | 2599185145 | draft | img | 1121117 |
| 67770 | Brachymonas denitrificans DSM 15123 | GCA_900110225 | scaffold | ncbi | 1121117 |
GC content
- @ref: 5622
- GC-content: 64.9
- 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 | 98.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.09 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.101 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 78.053 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.471 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 77.031 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 87 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 98.3 |
External links
@ref: 5622
culture collection no.: DSM 15123, JCM 9216, CCUG 45365, CGMCC 1.7100
straininfo link
- @ref: 72431
- straininfo: 65713
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 17391334 | Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii. | Halet D, Defoirdt T, Van Damme P, Vervaeren H, Forrez I, Van de Wiele T, Boon N, Sorgeloos P, Bossier P, Verstraete W | FEMS Microbiol Ecol | 10.1111/j.1574-6941.2007.00305.x | 2007 | Animals, Aquaculture/methods, Artemia/*microbiology, Bacteria/growth & development/isolation & purification/*metabolism, Bioreactors, *Germ-Free Life, Hydroxybutyrates/*metabolism, Polyesters/*metabolism, Survival Analysis, Vibrio/*pathogenicity, Vibrio Infections/microbiology/*prevention & control | Enzymology |
| Phylogeny | 19643891 | Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas. | Halpern M, Shaked T, Schumann P | Int J Syst Evol Microbiol | 10.1099/ijs.0.007211-0 | 2009 | Animals, Chironomidae/*microbiology, Comamonadaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Ovum/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5622 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15123) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15123 | |||
| 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 | |||
| 56744 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 45365) | https://www.ccug.se/strain?id=45365 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 72431 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID65713.1 | 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 |