Strain identifier
BacDive ID: 134036
Type strain: 
Species: Gemmobacter lanyuensis
Strain Designation: Orc-4
NCBI tax ID(s): 1054497 (species)
version 8.1 (current version)
General
@ref: 31111
BacDive-ID: 134036
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, rod-shaped
description: Gemmobacter lanyuensis Orc-4 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater .
NCBI tax id
- NCBI tax id: 1054497
- Matching level: species
doi: 10.13145/bacdive134036.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Gemmobacter
- species: Gemmobacter lanyuensis
- full scientific name: Gemmobacter lanyuensis Sheu et al. 2013
@ref: 31111
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Gemmobacter
species: Gemmobacter lanyuensis
strain designation: Orc-4
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31111 | negative | 2 µm | 0.45 µm | rod-shaped | no | |
| 69480 | negative | 99.993 |
pigmentation
- @ref: 31111
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 31111 | positive | growth | 15-40 | |
| 31111 | positive | optimum | 27.5 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31111 | positive | growth | 6.0-9.0 | alkaliphile |
| 31111 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31111
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31111 | no | |
| 69481 | no | 99 |
| 69480 | no | 99.995 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31111 | NaCl | positive | growth | 0-1 % |
| 31111 | NaCl | positive | optimum | 0.25 % |
observation
- @ref: 31111
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31111 | 17754 | glycerol | + | carbon source |
| 31111 | 24996 | lactate | + | carbon source |
| 31111 | 29864 | mannitol | + | carbon source |
| 31111 | 37684 | mannose | + | carbon source |
| 31111 | 51850 | methyl pyruvate | + | carbon source |
| 31111 | 4853 | esculin | + | hydrolysis |
| 31111 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31111 | acid phosphatase | + | 3.1.3.2 |
| 31111 | alkaline phosphatase | + | 3.1.3.1 |
| 31111 | catalase | + | 1.11.1.6 |
| 31111 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 31111
- sample type: freshwater (river, lake, pond)
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #River (Creek) |
taxonmaps
- @ref: 69479
- File name: preview.99_117552.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_3623;98_15523;99_117552&stattab=map
- Last taxonomy: Gemmobacter lanyuensis
- 16S sequence: JN104393
- Sequence Identity:
- Total samples: 181
- soil counts: 1
- aquatic counts: 159
- animal counts: 21
Sequence information
16S sequences
- @ref: 31111
- description: Gemmobacter lanyuensis strain Orc-4 16S ribosomal RNA gene, partial sequence
- accession: JN104393
- length: 1404
- database: nuccore
- NCBI tax ID: 1054497
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gemmobacter lanyuensis KCTC 23714 | GCA_014652355 | scaffold | ncbi | 1054497 |
| 66792 | Gemmobacter lanyuensis strain KCTC 23714 | 1054497.3 | wgs | patric | 1054497 |
GC content
- @ref: 31111
- GC-content: 63.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 60.831 | yes |
| flagellated | no | 85.802 | yes |
| gram-positive | no | 98.793 | yes |
| anaerobic | no | 95.933 | no |
| aerobic | yes | 64.199 | yes |
| halophile | no | 90.324 | yes |
| spore-forming | no | 96.154 | yes |
| thermophile | no | 93.79 | yes |
| glucose-util | yes | 87.931 | no |
| glucose-ferment | no | 88.917 | no |
External links
@ref: 31111
culture collection no.: BCRC 80378, LMG 26667, KCTC 23714
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23728371 | Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring. | Sheu SY, Shiau YW, Wei YT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.052399-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Hydroxybutyrates, Molecular Sequence Data, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 32553048 | Gemmobacter serpentinus sp. nov., isolated from conserved forages. | Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J, Im J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004276 | 2020 | Animal Feed/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kansas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
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 | ||
| 31111 | 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 | 27440 | 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 | ||
| 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 |