Strain identifier
BacDive ID: 133827
Type strain: 
Species: Pontibacter lucknowensis
Strain Designation: DM9
NCBI tax ID(s): 1077936 (species)
version 8.1 (current version)
General
@ref: 30615
BacDive-ID: 133827
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Pontibacter lucknowensis DM9 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1077936
- Matching level: species
doi: 10.13145/bacdive133827.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Hymenobacteraceae
- genus: Pontibacter
- species: Pontibacter lucknowensis
- full scientific name: Pontibacter lucknowensis Dwivedi et al. 2013
@ref: 30615
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Pontibacter
species: Pontibacter lucknowensis
strain designation: DM9
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 30615 | negative | 2.2 µm | 0.65 µm | rod-shaped | yes | gliding | |
| 69480 | negative | 99.996 |
pigmentation
- @ref: 30615
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30615 | positive | growth | 06-45 | |
| 30615 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30615 | positive | growth | 06-09 | alkaliphile |
| 30615 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30615
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.984 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30615 | NaCl | positive | growth | 0-4 % |
| 30615 | NaCl | positive | optimum | 2 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30615 | 22599 | arabinose | + | carbon source |
| 30615 | 17057 | cellobiose | + | carbon source |
| 30615 | 17234 | glucose | + | carbon source |
| 30615 | 17716 | lactose | + | carbon source |
| 30615 | 17306 | maltose | + | carbon source |
| 30615 | 29864 | mannitol | + | carbon source |
| 30615 | 26546 | rhamnose | + | carbon source |
| 30615 | 33942 | ribose | + | carbon source |
| 30615 | 30911 | sorbitol | + | carbon source |
| 30615 | 53424 | tween 20 | + | carbon source |
| 30615 | 53426 | tween 80 | + | carbon source |
| 30615 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30615 | catalase | + | 1.11.1.6 |
| 30615 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 30615
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_3596.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_1869;97_2246;98_2756;99_3596&stattab=map
- Last taxonomy: Pontibacter lucknowensis
- 16S sequence: JN561788
- Sequence Identity:
- Total samples: 35
- soil counts: 13
- aquatic counts: 11
- animal counts: 11
Sequence information
16S sequences
- @ref: 30615
- description: Pontibacter lucknowensis strain DM9 16S ribosomal RNA gene, partial sequence
- accession: JN561788
- length: 1400
- database: nuccore
- NCBI tax ID: 1077936
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pontibacter lucknowensis DM9 | GCA_900156415 | scaffold | ncbi | 1077936 |
| 66792 | Pontibacter lucknowensis DM9 | 2681812905 | draft | img | 1077936 |
GC content
- @ref: 30615
- GC-content: 49.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.445 | no |
| flagellated | no | 96.116 | no |
| gram-positive | no | 98.51 | yes |
| anaerobic | no | 99.251 | no |
| aerobic | yes | 90.613 | yes |
| halophile | no | 79.019 | no |
| spore-forming | no | 94.26 | no |
| thermophile | no | 95.925 | yes |
| glucose-util | yes | 86.811 | yes |
| glucose-ferment | no | 86.687 | no |
External links
@ref: 30615
culture collection no.: CCM 7955, MTCC 11079
literature
- topic: Phylogeny
- Pubmed-ID: 22427446
- title: Pontibacter lucknowensis sp. nov., isolated from a hexachlorocyclohexane dump site.
- authors: Dwivedi V, Niharika N, Lal R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.040147-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analogs & derivatives/analysis, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|
| 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 | |||
| 30615 | 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 | 26946 | 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | |
| 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 |