Strain identifier
BacDive ID: 1905
Type strain:
Species: Trinickia caryophylli
Strain Designation: 720, ICBPC 113
Strain history: LMG 2155 <-- NCPPB 2151 <-- ICPB PC113 <-- N. A. MacLean.
NCBI tax ID(s): 28094 (species)
General
@ref: 12714
BacDive-ID: 1905
DSM-Number: 50341
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, plant pathogen
description: Trinickia caryophylli 720 is a mesophilic, motile plant pathogen that was isolated from carnation .
NCBI tax id
- NCBI tax id: 28094
- Matching level: species
strain history
@ref | history |
---|---|
12714 | <- ATCC <- R.W. Ballard; 720 <- M.P. Starr, ICPB; PC 113 <- N.A. MacLean |
67770 | LMG 2155 <-- NCPPB 2151 <-- ICPB PC113 <-- N. A. MacLean. |
doi: 10.13145/bacdive1905.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Trinickia
- species: Trinickia caryophylli
- full scientific name: Trinickia caryophylli (Burkholder 1942) Estrada-de Los Santos et al. 2018
synonyms
@ref synonym 20215 Pseudomonas caryophylli 20215 Burkholderia caryophylli 20215 Phytomonas caryophylli 20215 Paraburkholderia caryophylli
@ref: 12714
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Trinickia
species: Trinickia caryophylli
full scientific name: Trinickia caryophylli (Burkholder 1942) Estrada-de Los Santos et al. 2018
strain designation: 720, ICBPC 113
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 92.779 | |
69480 | 99.94 | negative |
Culture and growth conditions
culture medium
- @ref: 12714
- 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 | range |
---|---|---|---|---|
12714 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.991 |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | + | builds acid from | |
68371 | gluconate | + | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | + | builds acid from | 18333 |
68371 | L-fucose | + | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | + | builds acid from | 17924 |
68371 | D-mannitol | + | builds acid from | 16899 |
68371 | myo-inositol | + | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | + | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | + | builds acid from | 65327 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | D-arabinose | + | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68369 | malate | + | assimilation | 25115 |
68369 | adipate | - | assimilation | 17128 |
68369 | gluconate | + | assimilation | 24265 |
68369 | maltose | - | assimilation | 17306 |
68369 | N-acetylglucosamine | + | assimilation | 59640 |
68369 | D-mannitol | + | assimilation | 16899 |
68369 | D-mannose | + | assimilation | 16024 |
68369 | L-arabinose | + | assimilation | 30849 |
68369 | D-glucose | + | assimilation | 17634 |
68369 | gelatin | - | hydrolysis | 5291 |
68369 | esculin | - | hydrolysis | 4853 |
68369 | urea | - | hydrolysis | 16199 |
68369 | arginine | - | hydrolysis | 29016 |
68369 | D-glucose | - | fermentation | 17634 |
68369 | tryptophan | - | energy source | 27897 |
68369 | nitrate | + | reduction | 17632 |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12714 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | + | - | + | - | +/- | + |
12714 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | - | - | + | - | - | + |
12714 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | - | - | + | - | - | + |
12714 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | + | - | + | - | - | + |
12714 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | - | - | + | - | - | + |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12714 | - | +/- | - | + | + | +/- | + | - | +/- | - | + | + | + | + | - | + | - | + | + | + | - | - | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | +/- | - | - | - | - | - | + | + | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
12714 | carnation (Dianthus caryophyllus) | Dianthus caryophyllus | USA | USA | North America | |
47209 | Dianthus caryophyllus | USA | USA | North America | 1951 | |
67770 | Dianthus caryophyllus (carnation) | Dianthus caryophyllus |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
taxonmaps
- @ref: 69479
- File name: preview.99_3683.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_2288;98_2816;99_3683&stattab=map
- Last taxonomy: Burkholderia
- 16S sequence: AB021423
- Sequence Identity:
- Total samples: 166
- soil counts: 81
- aquatic counts: 10
- animal counts: 16
- plant counts: 59
Safety information
risk assessment
- @ref: 12714
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | P.caryophylli 16S ribosomal RNA | X67039 | 1453 | ena | 28094 |
12714 | Burkholderia caryophylli gene for 16S rRNA, strain: ATCC 25418 | AB021423 | 1448 | ena | 28094 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Trinickia caryophylli LMG 2155 | GCA_902833925 | scaffold | ncbi | 28094 |
66792 | Paraburkholderia caryophylli strain Ballard 720 | 28094.5 | wgs | patric | 28094 |
66792 | Trinickia caryophylli strain DSM 50341 | 28094.8 | wgs | patric | 28094 |
66792 | Trinickia caryophylli strain LMG 2155 | 28094.9 | wgs | patric | 28094 |
67770 | Trinickia caryophylli DSM 50341 | GCA_007097545 | contig | ncbi | 28094 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 85.656 | no |
gram-positive | no | 98.477 | no |
anaerobic | no | 97.837 | no |
aerobic | yes | 83.967 | no |
halophile | no | 94.905 | no |
spore-forming | no | 93.84 | no |
thermophile | no | 98.964 | no |
glucose-util | yes | 93.386 | yes |
motile | yes | 87.894 | no |
glucose-ferment | no | 89.923 | yes |
External links
@ref: 12714
culture collection no.: DSM 50341, ATCC 25418, CCUG 20834, CFBP 2429, CFBP 3818, CIP 105770, HAMBI 2159, ICMP 512, NCPPB 2151, LMG 2155, JCM 10488, BCRC 12862, BCRC 13908, CCEB 861, CCM 4971, ICPB PC113, JCM 9310, KCTC 2965, VKM B-1295, VTT E-991296
straininfo link
- @ref: 71549
- straininfo: 3944
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17220453 | Burkholderia soli sp. nov., isolated from soil cultivated with Korean ginseng. | Yoo SH, Kim BY, Weon HY, Kwon SW, Go SJ, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.64471-0 | 2007 | Agriculture, Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 22081715 | Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil. | Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, James EK, Sprent JI, Young JPW, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.037408-0 | 2011 | Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Mimosa/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA | Genetics |
Pathogenicity | 31605027 | Structure elucidation and biosynthetic locus of trinickiabactin from the plant pathogenic bacterium Trinickia caryophylli. | Jiao J, Du J, Frediansyah A, Jahanshah G, Gross H | J Antibiot (Tokyo) | 10.1038/s41429-019-0246-0 | 2019 | Anti-Bacterial Agents/*biosynthesis/*chemistry/pharmacology, Computer Simulation, Drug Discovery, Gram-Negative Bacteria/drug effects, Magnetic Resonance Spectroscopy, Microbial Sensitivity Tests, Multigene Family, Plant Diseases/*microbiology, Proteobacteria/*chemistry/genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
12714 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50341) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-50341 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
47209 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 20834) | https://www.ccug.se/strain?id=20834 | |||
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
71549 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3944.1 | StrainInfo: A central database for resolving microbial strain identifiers |