Strain identifier
BacDive ID: 131340
Type strain: 
Species: Bradymonas sediminis
Strain Designation: FA350
Strain history: <- Z.-J. Du, Shandong University at Weihai; FA350 <- Q.-Q. Liu, College of Marine Science, Shandong University at Weihai, PR China
NCBI tax ID(s): 1548548 (species)
version 8.1 (current version)
General
@ref: 22567
BacDive-ID: 131340
DSM-Number: 28820
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Bradymonas sediminis FA350 is a mesophilic, Gram-negative bacterium that was isolated from coastal marine sediment.
NCBI tax id
- NCBI tax id: 1548548
- Matching level: species
strain history
- @ref: 22567
- history: <- Z.-J. Du, Shandong University at Weihai; FA350 <- Q.-Q. Liu, College of Marine Science, Shandong University at Weihai, PR China
doi: 10.13145/bacdive131340.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Bradymonadales
- family: Bradymonadaceae
- genus: Bradymonas
- species: Bradymonas sediminis
- full scientific name: Bradymonas sediminis Wang et al. 2015
@ref: 22567
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Bradymonadaceae, not assigned to order
family: Bradymonadaceae
genus: Bradymonas
species: Bradymonas sediminis
full scientific name: Bradymonas sediminis Wang et al. 2015
strain designation: FA350
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.997
multimedia
- @ref: 22567
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28820.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 22567
- name: BRADYMONAS SEDIMINIS MEDIUM (DSMZ Medium 1588)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1588
- composition: Name: BRADYMONAS SEDIMINIS MEDIUM (DSMZ Medium 1588) Composition: Agar 19.0 g/l Peptone 10.0 g/l NaCl 5.0 g/l Meat extract 3.0 g/l D(+)-Trehalose 1.0 g/l Tap water Natural sea water
culture temp
- @ref: 22567
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.98 |
Isolation, sampling and environmental information
isolation
- @ref: 22567
- sample type: coastal marine sediment
- geographic location: Weihai, Xiaoshi Island (37° 31' 36'' N 122° 00' 58'' E)
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 37.5267
- longitude: 122.016
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_164657.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_970;96_61725;97_79963;98_108170;99_164657&stattab=map
- Last taxonomy: Bradymonas sediminis subclade
- 16S sequence: KM034744
- Sequence Identity:
- Total samples: 1244
- soil counts: 143
- aquatic counts: 565
- animal counts: 506
- plant counts: 30
Safety information
risk assessment
- @ref: 22567
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22567
- description: Bradymonas sediminis strain FA350 16S ribosomal RNA gene, partial sequence
- accession: KM034744
- length: 1461
- database: ena
- NCBI tax ID: 1548548
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bradymonas sediminis FA350 | GCA_003258315 | complete | ncbi | 1548548 |
| 66792 | Bradymonas sediminis DSM 28820 | GCA_004362595 | scaffold | ncbi | 1548548 |
| 66792 | Bradymonas sediminis strain DSM 28820 | 1548548.14 | wgs | patric | 1548548 |
| 66792 | Bradymonas sediminis DSM 28820 | 2770939511 | draft | img | 1548548 |
| 66792 | Bradymonas sediminis FA350 | 2839912435 | complete | img | 1548548 |
GC content
- @ref: 22567
- GC-content: 44.6
- method: fluorimetric
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 93.342 | no |
| gram-positive | no | 96.463 | no |
| anaerobic | no | 98.726 | no |
| aerobic | yes | 62.496 | no |
| halophile | no | 57.68 | no |
| spore-forming | no | 86.439 | no |
| glucose-util | yes | 71.915 | no |
| thermophile | no | 93.861 | no |
| motile | no | 62.446 | no |
| glucose-ferment | no | 92.165 | no |
External links
@ref: 22567
culture collection no.: DSM 28820, CICC 10904
straininfo link
- @ref: 89781
- straininfo: 397639
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25713043 | Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov. | Wang ZJ, Liu QQ, Zhao LH, Du ZJ, Chen GJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.000135 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Islands, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 31237538 | Lujinxingia litoralis gen. nov., sp. nov. and Lujinxingia sediminis sp. nov., two new representatives in the order Bradymonadales. | Guo LY, Li CM, Wang S, Mu DS, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003556 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/isolation & purification, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 32390976 | Persicimonas caeni gen. nov., sp. nov., the Representative of a Novel Wide-Ranging Predatory Taxon in Bradymonadales. | Wang S, Mu D, Du ZJ | Front Microbiol | 10.3389/fmicb.2020.00698 | 2020 | ||
| Phylogeny | 35580024 | Microvenator marinus gen. nov., sp. nov., isolated from marine sediment, and description of Microvenatoraceae fam. nov. and Lujinxingiaceae fam. nov. | Wang S, Chen GJ, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005380 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria, *Fatty Acids/chemistry, Geologic Sediments/microbiology, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA | Transcriptome |
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 | |||
| 22567 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28820 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28820) | |||
| 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 | |
| 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 | |||
| 89781 | 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-ID397639.1 |