Strain identifier
BacDive ID: 5788
Type strain: 
Species: Gemmatimonas aurantiaca
Strain Designation: T-27
Strain history: S. Hanada T-27.
NCBI tax ID(s): 379066 (strain), 173480 (species)
version 8.1 (current version)
General
@ref: 5395
BacDive-ID: 5788
DSM-Number: 14586
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Gemmatimonas aurantiaca T-27 is a mesophilic bacterium that was isolated from sludge from laboratory reactor.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 379066 | strain |
| 173480 | species |
strain history
| @ref | history |
|---|---|
| 5395 | <- S. Hamada; T-27 <- K. Nakamura |
| 67770 | S. Hanada T-27. |
doi: 10.13145/bacdive5788.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/gemmatimonadota
- domain: Bacteria
- phylum: Gemmatimonadota
- class: Gemmatimonadia
- order: Gemmatimonadales
- family: Gemmatimonadaceae
- genus: Gemmatimonas
- species: Gemmatimonas aurantiaca
- full scientific name: Gemmatimonas aurantiaca Zhang et al. 2003
@ref: 5395
domain: Bacteria
phylum: Gemmatimonadetes
class: Gemmatimonadetes
order: Gemmatimonadales
family: Gemmatimonadaceae
genus: Gemmatimonas
species: Gemmatimonas aurantiaca
full scientific name: Gemmatimonas aurantiaca Zhang et al. 2003 emend. Zeng et al. 2015
strain designation: T-27
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5395
- 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 |
|---|---|---|---|---|
| 5395 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 5395 | sludge from laboratory reactor | Japan | JPN | Asia |
| 67770 | Laboratory-scale anaerobic-aerobic sequential batch reactor operated under EBPR conditions |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioreactor | |
| #Engineered | #Laboratory | |
| #Environmental | #Terrestrial | #Mud (Sludge) |
taxonmaps
- @ref: 69479
- File name: preview.99_7424.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_51;96_3473;97_4259;98_5442;99_7424&stattab=map
- Last taxonomy: Gemmatimonas aurantiaca subclade
- 16S sequence: AB072735
- Sequence Identity:
- Total samples: 2606
- soil counts: 654
- aquatic counts: 1743
- animal counts: 127
- plant counts: 82
Safety information
risk assessment
- @ref: 5395
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Gemmatimonas aurantiaca gene for 16S rRNA, partial sequence
- accession: AB072735
- length: 1446
- database: ena
- NCBI tax ID: 379066
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gemmatimonas aurantiaca T-27 | GCA_000010305 | complete | ncbi | 379066 |
| 66792 | Gemmatimonas aurantiaca T-27 | 379066.3 | complete | patric | 379066 |
GC content
- @ref: 67770
- GC-content: 66
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 73.66 | no |
| flagellated | no | 82.202 | no |
| gram-positive | no | 97.267 | no |
| anaerobic | no | 97.323 | no |
| halophile | no | 97.852 | no |
| spore-forming | no | 90.067 | no |
| thermophile | no | 90.508 | no |
| glucose-util | yes | 66.516 | no |
| aerobic | yes | 78.454 | no |
| glucose-ferment | no | 88.874 | no |
External links
@ref: 5395
culture collection no.: DSM 14586, JCM 11422, NBRC 100505
straininfo link
- @ref: 75267
- straininfo: 111713
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 12892144 | Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. | Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K | Int J Syst Evol Microbiol | 10.1099/ijs.0.02520-0 | 2003 | Base Composition, Base Sequence, Biodegradation, Environmental, Bioreactors, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gram-Negative Aerobic Rods and Cocci/*classification/genetics/isolation & purification/*metabolism, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, Polyphosphates/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Waste Disposal, Fluid, Water Pollutants, Chemical/metabolism | Metabolism |
| Metabolism | 19959572 | Carotenoids of Gemmatimonas aurantiaca (Gemmatimonadetes): identification of a novel carotenoid, deoxyoscillol 2-rhamnoside, and proposed biosynthetic pathway of oscillol 2,2'-dirhamnoside. | Takaichi S, Maoka T, Takasaki K, Hanada S | Microbiology (Reading) | 10.1099/mic.0.034249-0 | 2009 | Bacteria/*chemistry/enzymology, Bacterial Proteins/metabolism, Carotenoids/*biosynthesis/chemistry, Chromatography, High Pressure Liquid, Glycosides/*biosynthesis/chemistry, Hexosyltransferases/metabolism, Hydro-Lyases/metabolism, Lycopene, Molecular Structure | Enzymology |
| Cultivation | 25281372 | A hidden pitfall in the preparation of agar media undermines microorganism cultivability. | Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka M, Nakatsu CH, Kamagata Y | Appl Environ Microbiol | 10.1128/AEM.02741-14 | 2014 | Agar/adverse effects/*chemistry, Bacteria/genetics/*growth & development/isolation & purification/metabolism, Culture Media/*adverse effects/chemistry/metabolism, Environmental Microbiology, Hot Temperature | Metabolism |
| Phylogeny | 25899503 | Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca. | Zeng Y, Selyanin V, Lukes M, Dean J, Kaftan D, Feng F, Koblizek M | Int J Syst Evol Microbiol | 10.1099/ijs.0.000272 | 2015 | Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, Base Sequence, China, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/chemistry, Fresh Water/microbiology, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 26873585 | Longimicrobium terrae gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers. | Pascual J, Garcia-Lopez M, Bills GF, Genilloud O | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000974 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Electron Transport Complex IV/genetics, Fatty Acids/chemistry, Forests, Gram-Negative Aerobic Rods and Cocci/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Metabolism | 28389533 | Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27. | Park D, Kim H, Yoon S | Appl Environ Microbiol | 10.1128/AEM.00502-17 | 2017 | Bacteria, Aerobic/enzymology/genetics/*isolation & purification/*metabolism, Bacterial Proteins/genetics/metabolism, Nitrous Oxide/*metabolism, Oxidation-Reduction, Oxidoreductases/genetics/metabolism, Oxygen/metabolism | Enzymology |
| Phylogeny | 29458671 | Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes. | Pascual J, Foesel BU, Geppert A, Huber KJ, Boedeker C, Luckner M, Wanner G, Overmann J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002619 | 2018 | Agriculture, Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Electron Transport Complex IV/genetics, Fatty Acids/chemistry, Namibia, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Metabolism | 31580255 | Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27. | Chee-Sanford J, Tian D, Sanford R | Microbiology (Reading) | 10.1099/mic.0.000847 | 2019 | Ammonium Compounds/metabolism, Bacteria/growth & development/*metabolism, Carbon/metabolism, Culture Media, Greenhouse Gases/*metabolism, Nitrates/metabolism, Nitrites/metabolism, Nitrous Oxide/*metabolism, Oxidation-Reduction, Oxygen/analysis/metabolism | Cultivation |
| Phylogeny | 35418546 | N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils. | Oshiki M, Toyama Y, Suenaga T, Terada A, Kasahara Y, Yamaguchi T, Araki N | Microbes Environ | 10.1264/jsme2.ME21090 | 2022 | Bacteria/genetics, Denitrification, *Nitrous Oxide, RNA, Messenger, RNA, Ribosomal, 16S/genetics, *Soil, Soil Microbiology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5395 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14586) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14586 | |||
| 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 | |||
| 75267 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID111713.1 | StrainInfo: A central database for resolving microbial strain identifiers |