Strain identifier
BacDive ID: 133743
Type strain: 
Species: Gluconacetobacter tumulicola
Strain Designation: K5929-2-1b
Strain history: J. Sugiyama K5929-2-1b.
NCBI tax ID(s): 1017177 (species)
version 8.1 (current version)
General
@ref: 30374
BacDive-ID: 133743
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Gluconacetobacter tumulicola K5929-2-1b is an aerobe, Gram-negative, motile bacterium that was isolated from Plaster wall.
NCBI tax id
- NCBI tax id: 1017177
- Matching level: species
strain history
- @ref: 67770
- history: J. Sugiyama K5929-2-1b.
doi: 10.13145/bacdive133743.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Acetobacteraceae
- genus: Gluconacetobacter
- species: Gluconacetobacter tumulicola
- full scientific name: Gluconacetobacter tumulicola Tazato et al. 2012
@ref: 30374
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Acetobacteraceae
genus: Gluconacetobacter
species: Gluconacetobacter tumulicola
strain designation: K5929-2-1b
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30374 | negative | 1.6 µm | 0.75 µm | rod-shaped | yes | |
| 69480 | yes | 96.735 | ||||
| 69480 | negative | 99.998 |
pigmentation
- @ref: 30374
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30374 | positive | growth | 15-30 | |
| 30374 | positive | optimum | 25 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 30374
- ability: positive
- type: growth
- pH: 3-6.8
- PH range: acidophile
Physiology and metabolism
oxygen tolerance
- @ref: 30374
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.992 |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30374 | 16236 | ethanol | + | carbon source |
| 30374 | 28757 | fructose | + | carbon source |
| 30374 | 17234 | glucose | + | carbon source |
| 30374 | 29864 | mannitol | + | carbon source |
| 30374 | 17268 | myo-inositol | + | carbon source |
| 30374 | 33942 | ribose | + | carbon source |
| 30374 | 30911 | sorbitol | + | carbon source |
| 30374 | 17992 | sucrose | + | carbon source |
enzymes
- @ref: 30374
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 30374 | Plaster wall | ||||
| 67770 | Black viscous substance in a plaster hole on central area of the ceiling in the stone chamber of the Kitora Tumulus in Asuka Village | Nara Pref. | Japan | JPN | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Built environment
taxonmaps
- @ref: 69479
- File name: preview.99_57177.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_64;97_2865;98_3566;99_57177&stattab=map
- Last taxonomy: Gluconacetobacter
- 16S sequence: AB627116
- Sequence Identity:
- Total samples: 1490
- soil counts: 360
- aquatic counts: 144
- animal counts: 740
- plant counts: 246
Sequence information
16S sequences
- @ref: 30374
- description: Gluconacetobacter tumulicola gene for 16S rRNA, partial sequence, strain: K5929-2-1b
- accession: AB627116
- length: 1418
- database: nuccore
- NCBI tax ID: 1017177
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gluconacetobacter tumulicola strain LMG 27725 | 1017177.4 | wgs | patric | 1017177 |
| 67770 | Gluconacetobacter tumulicola LMG 27725 | GCA_014174215 | contig | ncbi | 1017177 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 30374 | 64.7 | |
| 67770 | 64.7 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 88.684 | yes |
| flagellated | no | 79.361 | no |
| gram-positive | no | 97.756 | yes |
| anaerobic | no | 98.248 | yes |
| aerobic | yes | 83.625 | yes |
| halophile | no | 95.023 | no |
| spore-forming | no | 95.181 | no |
| thermophile | no | 97.707 | no |
| glucose-util | yes | 91.372 | yes |
| glucose-ferment | no | 89.389 | no |
External links
@ref: 30374
culture collection no.: JCM 17774, NCIMB 14760, BCRC 80742, LMG 27725
straininfo link
- @ref: 91580
- straininfo: 380880
literature
- topic: Phylogeny
- Pubmed-ID: 22038998
- title: Gluconacetobacter tumulicola sp. nov. and Gluconacetobacter asukensis sp. nov., isolated from the stone chamber interior of the Kitora Tumulus.
- authors: Tazato N, Nishijima M, Handa Y, Kigawa R, Sano C, Sugiyama J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.034595-0
- year: 2011
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gluconacetobacter/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Paintings, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | ID_cross_reference | 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 | ||
| 30374 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26714 | 28776041 |
| 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 | ||
| 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. | 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 | ||
| 91580 | 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-ID380880.1 |