Strain identifier
BacDive ID: 13170
Type strain: 
Species: Pseudomonas flexibilis
Strain Designation: 78-123
Strain history: Y.-H. Xin; CGMCC, China; 78-123.
NCBI tax ID(s): 1295129 (strain), 706570 (species)
version 9.1 (current version)
General
@ref: 18007
BacDive-ID: 13170
DSM-Number: 25351
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Pseudomonas flexibilis 78-123 is an aerobe, Gram-negative, motile bacterium that was isolated from sample of a bird's nest.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1295129 | strain |
| 706570 | species |
strain history
| @ref | history |
|---|---|
| 18007 | <- JCM <- Y.-G. Zhou, CGMCC; 78-123 |
| 67770 | Y.-H. Xin; CGMCC, China; 78-123. |
doi: 10.13145/bacdive13170.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas flexibilis
- full scientific name: Pseudomonas flexibilis (Hespell 1977) Shin et al. 2016
synonyms
@ref synonym 20215 Serpens flexibilis 20215 Pseudomonas tuomuerensis
@ref: 18007
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas flexibilis
full scientific name: Pseudomonas flexibilis (Hespell 1977) Shin et al. 2016
strain designation: 78-123
type strain: no
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 28888 | negative | rod-shaped | yes | |
| 69480 | negative | 97.833 |
Culture and growth conditions
culture medium
- @ref: 18007
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 18007 | positive | growth | 28 |
| 28888 | positive | growth | 15-42 |
| 62162 | positive | growth | 30 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 28888 | aerobe |
| 62162 | aerobe |
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
halophily
- @ref: 28888
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-6.5 %
observation
- @ref: 67770
- observation: quinones: Q-9
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28888 | 30089 | acetate | + | carbon source |
| 28888 | 22599 | arabinose | + | carbon source |
| 28888 | 51850 | methyl pyruvate | + | carbon source |
| 28888 | 30031 | succinate | + | carbon source |
| 28888 | 53423 | tween 40 | + | carbon source |
| 28888 | 53426 | tween 80 | + | carbon source |
| 28888 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28888 | catalase | + | 1.11.1.6 |
| 28888 | cytochrome oxidase | + | 1.9.3.1 |
| 28888 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 18007 | sample of a bird's nest | region of Tuomuer Peak of Tianshan Mountain, bank of Qiongtailan River | China | CHN | Asia |
| 62162 | Bird's nest,riverside Qiongtailan River | Tianshan Mountain,Tuomuer Peak | China | CHN | Asia |
| 67770 | Bird's nest on the bank of the Qiongtailan River in the region of Tuomuer Peak of Tianshan Mountain | Xin-jiang Uygur Autobomous Region, north-western China | China | CHN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Birds
taxonmaps
- @ref: 69479
- File name: preview.99_5121.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_2491;97_3042;98_3820;99_5121&stattab=map
- Last taxonomy: Pseudomonas flexibilis subclade
- 16S sequence: DQ868767
- Sequence Identity:
- Total samples: 1259
- soil counts: 688
- aquatic counts: 223
- animal counts: 229
- plant counts: 119
Safety information
risk assessment
- @ref: 18007
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 18007 | Pseudomonas tuomuerensis strain 78-123 16S ribosomal RNA gene, partial sequence | DQ868767 | 1411 | nuccore | 706570 |
| 124043 | Pseudomonas tuomuerensis strain JCM 14085 16S ribosomal RNA gene, partial sequence. | KP973997 | 1530 | nuccore | 706570 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas flexibilis strain CGMCC 1.1365 | 706570.4 | wgs | patric | 706570 |
| 66792 | Pseudomonas tuomuerensis JCM 14085 | 400095.4 | wgs | patric | 706570 |
| 66792 | Pseudomonas tuomuerensis JCM 14085 | 1295129.3 | wgs | patric | 1295129 |
| 66792 | Pseudomonas flexibilis JCM 14085 | 2728369709 | draft | img | 1295129 |
| 66792 | Pseudomonas flexibilis JCM 14085 | 2645728058 | draft | img | 1295129 |
| 66792 | Pseudomonas tuomuerensis CGMCC 1.1365 | 2596583557 | draft | img | 706570 |
| 67770 | Pseudomonas flexibilis JCM 14085 | GCA_001312105 | contig | ncbi | 1295129 |
| 67770 | Pseudomonas flexibilis CGMCC 1.1365 | GCA_900101515 | scaffold | ncbi | 706570 |
| 67770 | Pseudomonas flexibilis JCM 14085 | GCA_000806415 | contig | ncbi | 706570 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 18007 | 60.4 | thermal denaturation, midpoint method (Tm) |
| 28888 | 60.4 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.833 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.454 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.853 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 83.472 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.5 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 82.397 | no |
External links
@ref: 18007
culture collection no.: DSM 25351, CGMCC 1.1365, JCM 14085, CCUG 59930, CECT 7766
straininfo link
- @ref: 82378
- straininfo: 318381
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19126738 | Pseudomonas tuomuerensis sp. nov., isolated from a bird's nest. | Xin YH, Zhang DC, Liu HC, Zhou HL, Zhou YG | Int J Syst Evol Microbiol | 10.1099/ijs.0.000547-0 | 2009 | Animals, Bacterial Typing Techniques, Base Composition, *Birds, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, *Housing, Animal, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Phenotype |
| Phylogeny | 22878554 | Pseudomonas linyingensis sp. nov.: a novel bacterium isolated from wheat soil subjected to long-term herbicides application. | He WH, Wang YN, Du X, Zhou Y, Jia B, Bian J, Liu SJ, Chen GC | Curr Microbiol | 10.1007/s00284-012-0187-3 | 2012 | China, Herbicides/*analysis, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, *Soil Microbiology, Soil Pollutants/*analysis, Triticum/*growth & development | Genetics |
| Phylogeny | 23178721 | Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil. | Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Chen WM, Shen FT, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.045567-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/analysis, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Taiwan, Ubiquinone/analysis | Genetics |
| Phylogeny | 26516088 | Reclassification of Serpens flexibilis Hespell 1977 as Pseudomonas flexibilis comb. nov., with Pseudomonas tuomuerensis Xin et al. 2009 as a later heterotypic synonym. | Shin SK, Hwang CY, Cho YJ, Yi H | Syst Appl Microbiol | 10.1016/j.syapm.2015.09.007 | 2015 | Animals, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/analysis, Fatty Acids/analysis, Genome, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/*genetics/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 18007 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25351) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25351 | ||||
| 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 | ||||
| 28888 | 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 | 25328 | 28776041 | ||
| 62162 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 59930) | https://www.ccug.se/strain?id=59930 | ||||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 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 | ||||
| 82378 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID318381.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
| 124043 | Dr. Isabel Schober, Dr. Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy |