Strain identifier
BacDive ID: 11062
Type strain:
Species: Aeromicrobium ginsengisoli
Strain history: <- MK Kim, Kyunghee Uni.
NCBI tax ID(s): 363867 (species)
General
@ref: 16219
BacDive-ID: 11062
DSM-Number: 22238
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Aeromicrobium ginsengisoli DSM 22238 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of a ginseng field.
NCBI tax id
- NCBI tax id: 363867
- Matching level: species
strain history
@ref | history |
---|---|
16219 | <- JCM/RIKEN <- D.-C. Yang; Gsoil 098 |
67770 | D.-C. Yang Gsoil 098. |
67771 | <- MK Kim, Kyunghee Uni. |
doi: 10.13145/bacdive11062.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Aeromicrobium
- species: Aeromicrobium ginsengisoli
- full scientific name: Aeromicrobium ginsengisoli Kim et al. 2008
@ref: 16219
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Aeromicrobium
species: Aeromicrobium ginsengisoli
full scientific name: Aeromicrobium ginsengisoli Kim et al. 2008
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32044 | positive | 0.5-1.2 µm | 0.3-0.4 µm | coccus-shaped | no | |
67771 | positive | |||||
69480 | no | 94.215 | ||||
69480 | positive | 100 |
pigmentation
- @ref: 32044
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16219 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
16219 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
16219 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16219 | positive | growth | 28 | mesophilic |
32044 | positive | growth | 04-30 | |
32044 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32044 | positive | growth | 5-8.5 | alkaliphile |
32044 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32044 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.983 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32044 | NaCl | positive | growth | 03-04 % |
32044 | NaCl | positive | optimum | 3 % |
observation
@ref | observation |
---|---|
32044 | aggregates in chains |
67770 | quinones: MK-9(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32044 | 37054 | 3-hydroxybutyrate | + | carbon source |
32044 | 30089 | acetate | + | carbon source |
32044 | 16449 | alanine | + | carbon source |
32044 | 22599 | arabinose | + | carbon source |
32044 | 22653 | asparagine | + | carbon source |
32044 | 17057 | cellobiose | + | carbon source |
32044 | 16236 | ethanol | + | carbon source |
32044 | 28757 | fructose | + | carbon source |
32044 | 33984 | fucose | + | carbon source |
32044 | 28260 | galactose | + | carbon source |
32044 | 24265 | gluconate | + | carbon source |
32044 | 17234 | glucose | + | carbon source |
32044 | 29987 | glutamate | + | carbon source |
32044 | 17754 | glycerol | + | carbon source |
32044 | 17716 | lactose | + | carbon source |
32044 | 25017 | leucine | + | carbon source |
32044 | 25115 | malate | + | carbon source |
32044 | 17306 | maltose | + | carbon source |
32044 | 37684 | mannose | + | carbon source |
32044 | 506227 | N-acetylglucosamine | + | carbon source |
32044 | 28044 | phenylalanine | + | carbon source |
32044 | 26271 | proline | + | carbon source |
32044 | 17272 | propionate | + | carbon source |
32044 | 15361 | pyruvate | + | carbon source |
32044 | 26546 | rhamnose | + | carbon source |
32044 | 17822 | serine | + | carbon source |
32044 | 30031 | succinate | + | carbon source |
32044 | 17992 | sucrose | + | carbon source |
32044 | 27082 | trehalose | + | carbon source |
32044 | 16296 | D-tryptophan | + | carbon source |
32044 | 31011 | valerate | + | carbon source |
32044 | 18222 | xylose | + | carbon source |
32044 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 32044
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16219 | soil of a ginseng field | Daejeon | Republic of Korea | KOR | Asia |
67770 | Soil of a ginseng field | Daejeon | Republic of Korea | KOR | Asia |
67771 | From soil of ginseng field | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_5495.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1793;97_2145;98_4103;99_5495&stattab=map
- Last taxonomy: Aeromicrobium
- 16S sequence: AB245394
- Sequence Identity:
- Total samples: 2046
- soil counts: 1209
- aquatic counts: 148
- animal counts: 459
- plant counts: 230
Safety information
risk assessment
- @ref: 16219
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16219
- description: Aeromicrobium ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 098
- accession: AB245394
- length: 1483
- database: ena
- NCBI tax ID: 363867
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Aeromicrobium ginsengisoli strain JCM 14732 | 363867.3 | wgs | patric | 363867 |
66792 | Aeromicrobium ginsengisoli JCM 14732 | 2866597551 | draft | img | 363867 |
67770 | Aeromicrobium ginsengisoli JCM 14732 | GCA_004134905 | contig | ncbi | 363867 |
GC content
@ref | GC-content | method |
---|---|---|
16219 | 66.8 | high performance liquid chromatography (HPLC) |
32044 | 66.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 91.09 | no |
anaerobic | no | 99.179 | no |
halophile | no | 92.126 | no |
spore-forming | no | 90.72 | no |
glucose-util | yes | 88.061 | yes |
aerobic | yes | 95.543 | yes |
motile | no | 94.105 | yes |
flagellated | no | 98.362 | yes |
thermophile | no | 98.791 | yes |
glucose-ferment | no | 88.659 | no |
External links
@ref: 16219
culture collection no.: DSM 22238, JCM 14732, KCTC 19207, GBS 39, Gsoil 098
straininfo link
- @ref: 80311
- straininfo: 291516
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18768598 | Aeromicrobium ginsengisoli sp. nov., isolated from a ginseng field. | Kim MK, Park MJ, Im WT, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.64871-0 | 2008 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/analysis | Genetics |
Phylogeny | 20081024 | Aeromicrobium halocynthiae sp. nov., a taurocholic acid-producing bacterium isolated from the marine ascidian Halocynthia roretzi. | Kim SH, Yang HO, Sohn YC, Kwon HC | Int J Syst Evol Microbiol | 10.1099/ijs.0.016618-0 | 2010 | Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Taurocholic Acid/*biosynthesis, Urochordata/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 26354190 | Aeromicrobium camelliae sp. nov., isolated from Pu'er tea. | Niu L, Xiong M, Tang T, Song L, Hu X, Zhao M, Zhang K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000583 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tea/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 29289978 | Aeromicrobium panacisoli sp. nov. Isolated from Soil of Ginseng Cultivating Field. | Siddiqi MZ, Lee SY, Choi KD, Im WT | Curr Microbiol | 10.1007/s00284-017-1426-4 | 2017 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Panax/*growth & development, Phylogeny, Republic of Korea, *Soil Microbiology | Metabolism |
Phylogeny | 32692642 | Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii) and plateau pika (Ochotona curzoniae), respectively. | Li J, Lei W, Yang J, Lu S, Jin D, Lai XH, Zhang S, Cheng Y, Mi F, Huang Y, Pu J, Dong K, Tian Z, Wu X, Huang Y, Wang S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004331 | 2020 | Actinobacteria/*classification/isolation & purification, Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/microbiology, Lagomorpha/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16219 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22238) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22238 | |||
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 | |||
32044 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28294 | 28776041 | |
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) | |||
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 | |||
80311 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID291516.1 | StrainInfo: A central database for resolving microbial strain identifiers |