Strain identifier
BacDive ID: 13834
Type strain: 
Species: Roseibium aggregatum
Strain Designation: B1
Strain history: IAM 12614 <-- ATCC 25650 <-- R. Ahrens B1.
NCBI tax ID(s): 384765 (strain), 187304 (species)
version 8.1 (current version)
General
@ref: 5033
BacDive-ID: 13834
DSM-Number: 13394
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Roseibium aggregatum B1 is a mesophilic bacterium that was isolated from sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 187304 | species |
| 384765 | strain |
strain history
| @ref | history |
|---|---|
| 5033 | <- LMG <- R. Ahrens; B1 (Agrobacterium aggregatum) |
| 67770 | IAM 12614 <-- ATCC 25650 <-- R. Ahrens B1. |
doi: 10.13145/bacdive13834.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Stappiaceae
- genus: Roseibium
- species: Roseibium aggregatum
- full scientific name: Roseibium aggregatum (Uchino et al. 1999 ex Ahrens 1968) Hördt et al. 2020
synonyms
@ref synonym 20215 Labrenzia aggregata 20215 Stappia aggregata
@ref: 5033
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Stappiaceae
genus: Roseibium
species: Roseibium aggregatum
full scientific name: Roseibium aggregatum (Uchino et al. 1999) Hördt et al. 2020
strain designation: B1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5033
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5033 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location |
|---|---|---|
| 5033 | sediment | Baltic Sea |
| 67770 | Sediment | Baltic Sea |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_1518.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_685;97_793;98_918;99_1518&stattab=map
- Last taxonomy: Labrenzia aggregata
- 16S sequence: AB681109
- Sequence Identity:
- Total samples: 1300
- soil counts: 148
- aquatic counts: 979
- animal counts: 146
- plant counts: 27
Safety information
risk assessment
- @ref: 5033
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Proteobacterium CFW-10 16S ribosomal RNA, partial sequence | AF123060 | 135 | ena | 93655 |
| 20218 | Stappia aggregata gene for 16S rRNA, partial sequence | D88520 | 1405 | ena | 384765 |
| 20218 | Labrenzia aggregata gene for 16S rRNA, partial sequence, strain: NBRC 16684 | AB681109 | 1408 | ena | 187304 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Labrenzia aggregata IAM 12614 | 384765.3 | wgs | patric | 384765 |
| 66792 | Labrenzia aggregata IAM 12614 | 639857019 | draft | img | 384765 |
| 67770 | Roseibium aggregatum IAM 12614 | GCA_000168975 | contig | ncbi | 384765 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 98.467 | no |
| anaerobic | no | 98.572 | no |
| halophile | no | 62.943 | no |
| spore-forming | no | 95.263 | no |
| glucose-util | yes | 91.831 | no |
| aerobic | yes | 89.342 | no |
| flagellated | no | 53.982 | no |
| thermophile | no | 99.033 | yes |
| motile | yes | 88.258 | no |
| glucose-ferment | no | 87.432 | no |
External links
@ref: 5033
culture collection no.: DSM 13394, ATCC 25650, IAM 12614, LMG 8171, NCMB 2208, JCM 20685, IFO 16684, LMG 122, NBRC 16684, NCIMB 2208
straininfo link
- @ref: 83010
- straininfo: 482
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 12501429 | Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. | Uchino Y, Hirata A, Yokota A, Sugiyama J | J Gen Appl Microbiol | 10.2323/jgam.44.201 | 1998 | ||
| Phylogeny | 16403869 | Stappia marina sp. nov., a marine bacterium isolated from the Yellow Sea. | Kim BC, Park JR, Bae JW, Rhee SK, Kim KH, Oh JW, Park YH | Int J Syst Evol Microbiol | 10.1099/ijs.0.63735-0 | 2006 | Aldehyde Oxidoreductases/genetics, Alphaproteobacteria/chemistry/*classification/isolation & purification/physiology, Bacterial Proteins/metabolism, Bacteriochlorophylls/biosynthesis, Base Composition, Base Sequence, Catalase/metabolism, Fatty Acids, Korea, Molecular Sequence Data, Multienzyme Complexes/genetics, Nitrates/metabolism, Oxidoreductases/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, Species Specificity, *Water Microbiology | Metabolism |
| Phylogeny | 16514028 | Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake. | Donachie SP, Bowman JP, Alam M | Int J Syst Evol Microbiol | 10.1099/ijs.0.63440-0 | 2006 | Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/chemistry, Fresh Water/*microbiology, Hawaii, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride | Phenotype |
| Metabolism | 16542399 | Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria. | King GM | FEMS Microbiol Ecol | 10.1111/j.1574-6941.2006.00065.x | 2006 | Aerobiosis/physiology, Alphaproteobacteria/*metabolism, Anaerobiosis/physiology, Bradyrhizobium/metabolism, Burkholderia/metabolism, Carbon Monoxide/*metabolism, Gram-Negative Aerobic Rods and Cocci/*metabolism, Nitrates/*metabolism, Oxidation-Reduction, *Soil Microbiology, Trees, Xanthobacter/metabolism | |
| Metabolism | 24831290 | Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1. | Ghasempur S, Eswaramoorthy S, Hillerich BS, Seidel RD, Swaminathan S, Almo SC, Gerlt JA | Biochemistry | 10.1021/bi5004298 | 2014 | Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/physiology, Molecular Sequence Data, Protein Structure, Secondary, Pseudomonas aeruginosa/*chemistry/genetics/physiology, Signal Transduction/genetics/*physiology, Sugar Acids/*chemistry/metabolism, Transcriptome | Genetics |
| Phylogeny | 25086475 | Influence of plaque-forming bacterium, Rhodobacteraceae sp. on the growth of Chlorella vulgaris. | Chen Z, Zhang J, Lei X, Zhang B, Cai G, Zhang H, Li Y, Zheng W, Tian Y, Xu H, Zheng T | Bioresour Technol | 10.1016/j.biortech.2014.07.021 | 2014 | Biofilms/*growth & development, Biomass, Chlorella vulgaris/*growth & development, Colony Count, Microbial, Lipids/biosynthesis, Phylogeny, Rhodobacteraceae/*physiology/ultrastructure | |
| Metabolism | 25608448 | A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. | Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA | J Am Chem Soc | 10.1021/ja5103986 | 2015 | Amino Acid Isomerases/genetics/metabolism, Genome, Bacterial, Hydro-Lyases/genetics/*metabolism, Hydroxyproline/chemistry/*metabolism, Models, Molecular, Rhodobacteraceae/*enzymology/genetics/metabolism, Substrate Specificity | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5033 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13394) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13394 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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/ | ||||
| 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 | |||
| 83010 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID482.1 | StrainInfo: A central database for resolving microbial strain identifiers |