Strain identifier
BacDive ID: 5132
Type strain:
Species: Serratia ficaria
Strain Designation: 4024
Strain history: CIP <- 1979, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 4024
NCBI tax ID(s): 1411141 (strain), 61651 (species)
General
@ref: 1775
BacDive-ID: 5132
DSM-Number: 4569
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Serratia ficaria 4024 is a mesophilic, motile bacterium that was isolated from fig.
NCBI tax id
NCBI tax id | Matching level |
---|---|
61651 | species |
1411141 | strain |
strain history
@ref | history |
---|---|
1775 | <- CIP <- P.A.D. Grimont; 4024 |
33057 | 1979, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 4024 |
67770 | Y. Kosako 316 <-- R. Sakazaki 316 <-- ATCC 33105 <-- M. P. Starr <-- P. A. D. Grimont 4024. |
119342 | CIP <- 1979, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 4024 |
doi: 10.13145/bacdive5132.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Yersiniaceae
- genus: Serratia
- species: Serratia ficaria
- full scientific name: Serratia ficaria Grimont et al. 1981
@ref: 1775
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Yersiniaceae
genus: Serratia
species: Serratia ficaria
full scientific name: Serratia ficaria Grimont et al. 1981
strain designation: 4024
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.6 | ||
69480 | 99.93 | negative | ||
119342 | yes | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1775 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
33057 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
119342 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
119342 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1775 | positive | growth | 30 | mesophilic |
33057 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.464 |
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 | xylitol | - | builds acid from | 17151 |
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 | ribitol | + | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | + | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | D-arabinose | + | builds acid from | 17108 |
68371 | erythritol | + | builds acid from | 17113 |
68371 | glycerol | + | builds acid from | 17754 |
68368 | nitrate | + | reduction | 17632 |
68368 | L-arabinose | + | fermentation | 30849 |
68368 | amygdalin | + | fermentation | 27613 |
68368 | melibiose | + | fermentation | 28053 |
68368 | sucrose | + | fermentation | 17992 |
68368 | L-rhamnose | + | fermentation | 62345 |
68368 | sorbitol | + | fermentation | 30911 |
68368 | myo-inositol | + | fermentation | 17268 |
68368 | D-mannitol | + | fermentation | 16899 |
68368 | D-glucose | + | fermentation | 17634 |
68368 | gelatin | + | hydrolysis | 5291 |
68368 | tryptophan | - | energy source | 27897 |
68368 | urea | - | hydrolysis | 16199 |
68368 | citrate | + | assimilation | 16947 |
68368 | ornithine | - | degradation | 18257 |
68368 | lysine | - | degradation | 25094 |
68368 | arginine | - | hydrolysis | 29016 |
68372 | glycerol | + | assimilation | 17754 |
68372 | erythritol | + | assimilation | 17113 |
68372 | D-arabinose | - | assimilation | 17108 |
68372 | L-arabinose | + | assimilation | 30849 |
68372 | D-ribose | + | assimilation | 16988 |
68372 | D-xylose | + | assimilation | 65327 |
68372 | L-xylose | - | assimilation | 65328 |
68372 | ribitol | - | assimilation | 15963 |
68372 | methyl beta-D-xylopyranoside | - | assimilation | 74863 |
68372 | D-galactose | + | assimilation | 12936 |
68372 | D-glucose | + | assimilation | 17634 |
68372 | D-fructose | + | assimilation | 15824 |
68372 | D-mannose | + | assimilation | 16024 |
68372 | L-sorbose | - | assimilation | 17266 |
68372 | L-rhamnose | + | assimilation | 62345 |
68372 | galactitol | - | assimilation | 16813 |
68372 | myo-inositol | + | assimilation | 17268 |
68372 | D-mannitol | + | assimilation | 16899 |
68372 | sorbitol | + | assimilation | 30911 |
68372 | methyl alpha-D-mannoside | - | assimilation | 43943 |
68372 | methyl alpha-D-glucopyranoside | - | assimilation | 320061 |
68372 | N-acetylglucosamine | + | assimilation | 59640 |
68372 | amygdalin | - | assimilation | 27613 |
68372 | arbutin | + | assimilation | 18305 |
68372 | esculin | + | assimilation | 4853 |
68372 | salicin | + | assimilation | 17814 |
68372 | cellobiose | + | assimilation | 17057 |
68372 | maltose | + | assimilation | 17306 |
68372 | lactose | - | assimilation | 17716 |
68372 | melibiose | + | assimilation | 28053 |
68372 | sucrose | + | assimilation | 17992 |
68372 | trehalose | + | assimilation | 27082 |
68372 | inulin | - | assimilation | 15443 |
68372 | melezitose | + | assimilation | 6731 |
68372 | raffinose | + | assimilation | 16634 |
68372 | starch | - | assimilation | 28017 |
68372 | glycogen | - | assimilation | 28087 |
68372 | xylitol | - | assimilation | 17151 |
68372 | gentiobiose | + | assimilation | 28066 |
68372 | turanose | + | assimilation | 32528 |
68372 | D-lyxose | - | assimilation | 62318 |
68372 | D-tagatose | - | assimilation | 16443 |
68372 | D-fucose | - | assimilation | 28847 |
68372 | L-fucose | + | assimilation | 18287 |
68372 | D-arabitol | + | assimilation | 18333 |
68372 | L-arabitol | + | assimilation | 18403 |
68372 | gluconate | + | assimilation | 24265 |
68372 | Potassium 2-ketogluconate | + | assimilation | |
68372 | Potassium 5-ketogluconate | + | assimilation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 17997 | dinitrogen | no |
68368 | 16301 | nitrite | yes |
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | + | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX | NO2 | N2 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1775 | + | - | - | - | + | - | - | - | - | + | + | + | + | + | + | + | + | + | + | + | - | + | - |
1775 | + | - | - | - | + | - | - | - | - | + | + | + | + | + | + | + | + | + | + | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1775 | - | + | + | + | + | + | + | - | + | - | + | + | + | + | - | + | - | + | + | + | - | + | + | + | + | + | + | + | + | + | + | + | + | - | + | + | - | - | - | + | + | + | - | + | + | + | + | - | - | + |
API 50CHas
@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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1775 | - | + | + | - | + | + | + | - | - | - | + | + | + | + | - | + | - | + | + | + | - | - | + | - | + | + | + | + | + | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
1775 | fig | |||||
46119 | Calimyrna fig,Winters | 1977 | ||||
67770 | Smyrna figs | |||||
119342 | Calimyrna fig | Winters, California | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Tree |
#Host Body-Site | #Plant | #Fruit (Seed) |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1775 | 1 | Risk group (German classification) |
119342 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Serratia ficaria gene for 16S ribosomal RNA, partial sequence | AB004745 | 1449 | ena | 61651 |
20218 | Serratia ficaria gene for 16S rRNA, partial sequence, strain: NBRC 102596 | AB681873 | 1467 | ena | 61651 |
20218 | Serratia ficaria partial 16S rRNA gene, strain NCTC 12148 | AJ279054 | 1362 | ena | 61651 |
1775 | Serratia ficaria 16S rRNA gene (strain DSM 4569) | AJ233428 | 1495 | ena | 61651 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Serratia ficaria NCTC12148 | GCA_900187015 | complete | ncbi | 61651 |
66792 | Serratia ficaria NBRC 102596 | 1411141.3 | wgs | patric | 1411141 |
66792 | Serratia ficaria strain NCTC12148 | 61651.3 | complete | patric | 61651 |
66792 | Serratia ficaria NBRC 102596 | 2731957628 | draft | img | 1411141 |
66792 | Serratia ficaria NCTC 12148 | 2773857830 | complete | img | 61651 |
67770 | Serratia ficaria NBRC 102596 | GCA_001590885 | contig | ncbi | 1411141 |
GC content
- @ref: 67770
- GC-content: 59.4-59.8
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.262 | no |
flagellated | no | 54.998 | no |
gram-positive | no | 97.906 | no |
anaerobic | no | 98.404 | no |
aerobic | yes | 86.332 | no |
halophile | no | 93.31 | no |
spore-forming | no | 95.564 | no |
thermophile | no | 99.733 | no |
glucose-util | yes | 94.84 | yes |
glucose-ferment | yes | 91.175 | no |
External links
@ref: 1775
culture collection no.: DSM 4569, ATCC 33105, CIP 79.23, ICPB 4050, CCUG 14507, NCTC 12148, LMG 7881, JCM 1241, BCRC 14809, CCM 3418, IAM 13540, NBRC 102596
straininfo link
- @ref: 74624
- straininfo: 389412
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25281728 | Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves. | Garcia-Fraile P, Chudickova M, Benada O, Pikula J, Kolarik M | Int J Syst Evol Microbiol | 10.1099/ijs.0.066407-0 | 2014 | Animals, Bacterial Typing Techniques, Base Composition, Caves, Chiroptera/*microbiology, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/isolation & purification | Genetics |
Phylogeny | 31089912 | Serratia microhaemolytica sp. nov., isolated from an artificial lake in Southern China. | Wang J, Zheng ML, Jiao JY, Wang WJ, Li S, Xiao M, Chen C, Qu PH, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01273-9 | 2019 | Anaerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Hydrogen-Ion Concentration, Lakes/*microbiology, Locomotion, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/*isolation & purification/physiology, Sodium Chloride/metabolism, Temperature | Transcriptome |
Phylogeny | 31971498 | Serratia vespertilionis (Garcia-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981). | Garcia-Fraile P, Sproer C, Chesneau O, Criscuolo A, Lang E, Clermont D | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003996 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification, Whole Genome Sequencing | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1775 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4569) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4569 | |||
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 | |
33057 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11049 | ||||
46119 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 14507) | https://www.ccug.se/strain?id=14507 | |||
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/ | ||||
68368 | Automatically annotated from API 20E | |||||
68371 | Automatically annotated from API 50CH acid | |||||
68372 | Automatically annotated from API 50CH assim | |||||
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 | |||
74624 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389412.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119342 | Curators of the CIP | Collection of Institut Pasteur (CIP 79.23) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2079.23 |