Strain identifier
BacDive ID: 75
Type strain: 
Species: Roseomonas stagni
Strain Designation: HS-69
Strain history: <- K Furuhata, Azabu Univ., Japan
NCBI tax ID(s): 1123062 (strain), 484882 (species)
version 8.1 (current version)
General
@ref: 8353
BacDive-ID: 75
DSM-Number: 19981
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Roseomonas stagni HS-69 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pond water of Nomori no Ike.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123062 | strain |
| 484882 | species |
strain history
| @ref | history |
|---|---|
| 8353 | <- K. Furuhata, Azabu Univ., Sagamihara, Japan; HS-69 |
| 67770 | K. Furuhata HS-69. |
| 67771 | <- K Furuhata, Azabu Univ., Japan |
doi: 10.13145/bacdive75.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Acetobacteraceae
- genus: Roseomonas
- species: Roseomonas stagni
- full scientific name: Roseomonas stagni Furuhata et al. 2008
synonyms
- @ref: 20215
- synonym: Falsiroseomonas stagni
@ref: 8353
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Acetobacteraceae
genus: Roseomonas
species: Roseomonas stagni
full scientific name: Roseomonas stagni Furuhata et al. 2008
strain designation: HS-69
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 69480 | negative | 99.999 |
Culture and growth conditions
culture medium
- @ref: 8353
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8353 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 97 |
| 69480 | no | 99.992 |
observation
| @ref | observation |
|---|---|
| 67770 | quinones: Q-10 |
| 67771 | quinones: Q-10 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 8353 | pond water of Nomori no Ike | Shizuoka | Japan | JPN | Asia |
| 67770 | Pond water of Nomori no Ike in Shizuoka | Japan | JPN | Asia | |
| 67771 | From pond water of "Nomori No Ike" | Shizuoka | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Pond (small)
taxonmaps
- @ref: 69479
- File name: preview.99_49089.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_266;96_17919;97_27719;98_35318;99_49089&stattab=map
- Last taxonomy: Roseomonas stagni subclade
- 16S sequence: AB369258
- Sequence Identity:
- Total samples: 199
- soil counts: 7
- aquatic counts: 178
- animal counts: 12
- plant counts: 2
Safety information
risk assessment
- @ref: 8353
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8353
- description: Roseomonas stagni gene for 16S rRNA, partial sequence
- accession: AB369258
- length: 1439
- database: ena
- NCBI tax ID: 1123062
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Roseomonas stagni DSM 19981 | 1123062.3 | wgs | patric | 1123062 |
| 66792 | Roseomonas stagni DSM 19981 | 2602042029 | draft | img | 1123062 |
| 67770 | Falsiroseomonas stagni DSM 19981 | GCA_900114315 | scaffold | ncbi | 1123062 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8353 | 72.0 | high performance liquid chromatography (HPLC) |
| 67770 | 72 | high performance liquid chromatography (HPLC) |
| 67771 | 72.0 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 97 | no |
| motile | yes | 56.033 | no |
| flagellated | no | 85.375 | no |
| gram-positive | no | 98.621 | no |
| anaerobic | no | 98.88 | yes |
| aerobic | yes | 93.61 | yes |
| halophile | no | 92.51 | no |
| spore-forming | no | 94.578 | no |
| glucose-util | yes | 82.523 | no |
| thermophile | no | 93.274 | yes |
| glucose-ferment | no | 90.123 | no |
External links
@ref: 8353
culture collection no.: DSM 19981, JCM 15034, KCTC 22213
straininfo link
- @ref: 69759
- straininfo: 402956
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22307503 | Roseomonas riguiloci sp. nov., isolated from wetland freshwater. | Baik KS, Park SC, Choe HN, Kim SN, Moon JH, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.036186-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Methylobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Wetlands | Genetics |
| Phylogeny | 24366626 | Roseomonas tokyonensis sp. nov. isolated from a biofilm sample obtained from a cooling tower in Tokyo, Japan. | Furuhata K, Ishizaki N, Edagawa A, Fukuyama M | Biocontrol Sci | 10.4265/bio.18.205 | 2013 | Aerobiosis, Bacterial Typing Techniques, Biofilms/*growth & development, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Methylobacteriaceae/*classification/*isolation & purification/physiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tokyo | Genetics |
| Phylogeny | 26289445 | Roseomonas wooponensis sp. nov., isolated from wetland freshwater. | Lee JH, Kim MS, Baik KS, Kim HM, Lee KH, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000536 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Methylobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/chemistry, Ubiquinone/chemistry, *Wetlands | Transcriptome |
| Phylogeny | 32886590 | Roseomonas bella sp. nov., isolated from lake sediment. | Zhang JY, Jiang XB, Zhu D, Wang XM, Du ZJ, Mu DS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004436 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Methylobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
| Phylogeny | 32924923 | Roseomonas algicola sp. nov., isolated from a green alga, Pediastrum duplex. | Kim HM, Khan SA, Han DM, Chun BH, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004454 | 2020 | Acetobacteraceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Chlorophyceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 33034554 | Roseomonas selenitidurans sp. nov., isolated from urban soil, and emended description of Roseomonas frigidaquae. | Hou X, Liu H, Wei S, Ding Z, Sang F, Zhao Y, Dong Y, Li H, Wang Q, Zhao J, Deng H, Zhang C, Kong L, Gao Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004496 | 2020 | Bacterial Typing Techniques, Base Composition, China, Cities, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome Size, Methylobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 34623235 | Roseomonas ponticola sp. nov., a novel bacterium isolated from Pearl River estuary. | Yin LZ, Li JL, Fang BZ, Liu ZT, Wang P, Dong L, Duan L, Luo XQ, Li SH, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004994 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/chemistry, *Methylobacteriaceae/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rivers/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 34710024 | Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae. | Wu D, Liu H, Zhou Y, Wu X, Nie Y, Cai M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005064 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Methylobacteriaceae/classification/isolation & purification, Nucleic Acid Hybridization, *Oil and Gas Fields/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8353 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19981) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19981 | |||
| 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 | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 69759 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402956.1 | StrainInfo: A central database for resolving microbial strain identifiers |