Strain identifier
BacDive ID: 11315
Type strain:
Species: Janthinobacterium agaricidamnosum
Strain Designation: W1R3
Strain history: CIP <- 1999, S.P. Lincoln, Hort. Research Int., Warwickshire, UK: strain W1r3
NCBI tax ID(s): 1349767 (strain), 55508 (species)
General
@ref: 3651
BacDive-ID: 11315
DSM-Number: 9628
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Janthinobacterium agaricidamnosum W1R3 is an aerobe, mesophilic, motile bacterium that was isolated from diseased Agaricoccus bisporus tissue.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1349767 | strain |
55508 | species |
strain history
@ref | history |
---|---|
3651 | <- S. P. Lincoln, Horticultural Reasearch Institute, Wellesbourne, Warwickshire, UK |
40289 | 1999, S.P. Lincoln, Hort. Research Int., Warwickshire, UK: strain W1r3 |
67770 | IAM 14973 <-- DSM 9628 <-- S. P. Lincoln W1R3. |
116149 | CIP <- 1999, S.P. Lincoln, Hort. Research Int., Warwickshire, UK: strain W1r3 |
doi: 10.13145/bacdive11315.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Janthinobacterium
- species: Janthinobacterium agaricidamnosum
- full scientific name: Janthinobacterium agaricidamnosum Lincoln et al. 1999
@ref: 3651
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Janthinobacterium
species: Janthinobacterium agaricidamnosum
full scientific name: Janthinobacterium agaricidamnosum Lincoln et al. 1999
strain designation: W1R3
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.158 | ||
69480 | 99.997 | negative | ||
116149 | yes | negative | rod-shaped |
colony morphology
- @ref: 116149
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3651 | OXOID NUTRIENT BROTH (DSMZ Medium 948) | yes | https://mediadive.dsmz.de/medium/948 | Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water |
3651 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
3651 | NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) | yes | https://mediadive.dsmz.de/medium/605 | Name: NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l Distilled water |
40289 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
116149 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3651 | positive | growth | 28 | mesophilic |
40289 | positive | growth | 25 | mesophilic |
55687 | positive | growth | 22 | psychrophilic |
67770 | positive | growth | 25 | mesophilic |
116149 | positive | growth | 5-30 | |
116149 | no | growth | 37 | mesophilic |
116149 | no | growth | 41 | thermophilic |
116149 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
55687 | aerobe |
116149 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116149 | NaCl | positive | growth | 0 % |
116149 | NaCl | no | growth | 4 % |
116149 | NaCl | no | growth | 6 % |
116149 | NaCl | no | growth | 8 % |
116149 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116149 | 16947 | citrate | + | carbon source |
116149 | 4853 | esculin | - | hydrolysis |
116149 | 606565 | hippurate | + | hydrolysis |
116149 | 17632 | nitrate | - | builds gas from |
116149 | 17632 | nitrate | - | reduction |
116149 | 16301 | nitrite | - | builds gas from |
116149 | 16301 | nitrite | - | reduction |
116149 | 15792 | malonate | + | assimilation |
116149 | 17234 | glucose | +/- | degradation |
116149 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 116149
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 116149
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
116149 | 15688 | acetoin | - | |
116149 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
116149 | oxidase | + | |
116149 | beta-galactosidase | + | 3.2.1.23 |
116149 | alcohol dehydrogenase | - | 1.1.1.1 |
116149 | gelatinase | +/- | |
116149 | amylase | - | |
116149 | DNase | - | |
116149 | caseinase | - | 3.4.21.50 |
116149 | catalase | + | 1.11.1.6 |
116149 | tween esterase | + | |
116149 | gamma-glutamyltransferase | + | 2.3.2.2 |
116149 | lecithinase | - | |
116149 | lipase | - | |
116149 | lysine decarboxylase | - | 4.1.1.18 |
116149 | ornithine decarboxylase | - | 4.1.1.17 |
116149 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116149 | protease | - | |
116149 | tryptophan deaminase | - | |
116149 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116149 | - | + | + | + | - | + | + | + | - | - | + | + | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116149 | + | + | - | + | + | - | - | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | + | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | + | + | - | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | + | - | + | - | + | - | - | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|---|
3651 | diseased Agaricoccus bisporus tissue | Agaricoccus bisporus | Littlehampton | United Kingdom | GBR | Europe | |
55687 | Diseased Agaricoccus bisporus tissue | Littlehampton | United Kingdom | GBR | Europe | ||
67770 | Rotting Agaricus bisporus | Agaricus bisporus | United Kingdom | GBR | Europe | ||
116149 | Agaricus bisporus | United Kingdom | GBR | Europe | 1992 |
isolation source categories
- Cat1: #Host
- Cat2: #Fungi
- Cat3: #Mushroom
taxonmaps
- @ref: 69479
- File name: preview.99_781.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_429;97_540;98_623;99_781&stattab=map
- Last taxonomy: Janthinobacterium agaricidamnosum
- 16S sequence: Y08845
- Sequence Identity:
- Total samples: 226
- soil counts: 47
- aquatic counts: 72
- animal counts: 29
- plant counts: 78
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3651 | 1 | Risk group (German classification) |
116149 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 3651
- description: J.agaricidamnosum 16S rRNA gene
- accession: Y08845
- length: 1469
- database: ena
- NCBI tax ID: 55508
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 | GCA_000723165 | complete | ncbi | 1349767 |
66792 | Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 | 1349767.10 | wgs | patric | 1349767 |
66792 | Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 | 1349767.4 | complete | patric | 1349767 |
66792 | Janthinobacterium agaricidamnosum W1R3 | 2731957621 | draft | img | 1349767 |
66792 | Janthinobacterium agaricidamnosum W1R3 | 2585427668 | complete | img | 1349767 |
67770 | Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 | GCA_001571185 | contig | ncbi | 1349767 |
GC content
@ref | GC-content | method |
---|---|---|
3651 | 64.2 | thermal denaturation, midpoint method (Tm) |
67770 | 64.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 91.931 | no |
flagellated | yes | 83.991 | no |
gram-positive | no | 98.48 | no |
anaerobic | no | 99.259 | yes |
aerobic | yes | 92.997 | yes |
halophile | no | 93.841 | no |
spore-forming | no | 93.034 | no |
glucose-util | yes | 88.324 | no |
thermophile | no | 99.52 | yes |
glucose-ferment | no | 86.73 | no |
External links
@ref: 3651
culture collection no.: CCUG 43140, CIP 106332, DSM 9628, NCPPB 3945, JCM 21444, IAM 14973, NBRC 102515
straininfo link
- @ref: 80548
- straininfo: 48653
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10555339 | Janthinobacterium agaricidamnosum sp. nov., a soft rot pathogen of Agaricus bisporus. | Lincoln SP, Fermor TR, Tindall BJ | Int J Syst Bacteriol | 10.1099/00207713-49-4-1577 | 1999 | *Agaricus/physiology, Bacterial Typing Techniques, Betaproteobacteria/chemistry/*classification/isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humidity, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA | Genetics |
Genetics | 25883287 | Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum. | Graupner K, Lackner G, Hertweck C | Genome Announc | 10.1128/genomeA.00277-15 | 2015 | ||
Phylogeny | 32176602 | Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China. | Lu H, Deng T, Cai Z, Liu F, Yang X, Wang Y, Xu M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004097 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
36514532 | Scalable downstream method for the cyclic lipopetide jagaricin. | Stein J, Schlosser N, Bardl B, Peschel G, Meyer F, Kloss F, Rosenbaum MA, Regestein L | Eng Life Sci | 10.1002/elsc.202100079 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3651 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9628) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9628 | |||
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 | |||
40289 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18451 | ||||
55687 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 43140) | https://www.ccug.se/strain?id=43140 | |||
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/ | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
80548 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48653.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116149 | Curators of the CIP | Collection of Institut Pasteur (CIP 106332) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106332 |