Strain identifier
BacDive ID: 14606
Type strain:
Species: Staphylococcus piscifermentans
Strain Designation: SK03, SK 03
Strain history: CIP <- 1994, Komagata, Tokyo Univ., Tokyo, Japan: strain SK 03 <- S. Tanasupawat, Japan
NCBI tax ID(s): 70258 (species)
General
@ref: 3129
BacDive-ID: 14606
DSM-Number: 7373
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive
description: Staphylococcus piscifermentans SK03 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from Kung-chom .
NCBI tax id
- NCBI tax id: 70258
- Matching level: species
strain history
@ref | history |
---|---|
3129 | <- JCM <- S. Tanasupawat, SK03 |
67770 | S. Tanasupawat SK-03. |
121841 | CIP <- 1994, Komagata, Tokyo Univ., Tokyo, Japan: strain SK 03 <- S. Tanasupawat, Japan |
doi: 10.13145/bacdive14606.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Staphylococcaceae
- genus: Staphylococcus
- species: Staphylococcus piscifermentans
- full scientific name: Staphylococcus piscifermentans Tanasupawat et al. 1992
@ref: 3129
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Staphylococcaceae
genus: Staphylococcus
species: Staphylococcus piscifermentans
full scientific name: Staphylococcus piscifermentans Tanasupawat et al. 1992
strain designation: SK03, SK 03
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | motility |
---|---|---|---|
69480 | positive | 100 | |
121841 | no |
colony morphology
- @ref: 3129
- type of hemolysis: gamma
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3129 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
3129 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
40888 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
121841 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
121841 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3129 | positive | growth | 37 | mesophilic |
40888 | positive | growth | 37 | mesophilic |
52542 | positive | growth | 18 | psychrophilic |
52542 | positive | growth | 42 | thermophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 52542
- ability: positive
- type: growth
- pH: 6.8-9.0
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 121841
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.405
halophily
- @ref: 52542
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 6-10 %
murein
- @ref: 3129
- murein short key: A11.02
- type: A3alpha L-Lys-Gly5-6
observation
- @ref: 67770
- observation: quinones: MK-7
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 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
121841 | nitrate | + | reduction | 17632 |
121841 | nitrite | - | reduction | 16301 |
68375 | urea | + | hydrolysis | 16199 |
68375 | arginine | + | hydrolysis | 29016 |
68375 | ornithine | - | degradation | 18257 |
68375 | esculin | - | hydrolysis | 4853 |
68375 | D-glucose | + | fermentation | 17634 |
68375 | D-fructose | + | fermentation | 15824 |
68375 | D-mannose | - | fermentation | 16024 |
68375 | maltose | + | fermentation | 17306 |
68375 | lactose | + | fermentation | 17716 |
68375 | trehalose | + | fermentation | 27082 |
68375 | D-mannitol | - | fermentation | 16899 |
68375 | raffinose | - | fermentation | 16634 |
68375 | D-ribose | - | fermentation | 16988 |
68375 | cellobiose | - | fermentation | 17057 |
68375 | nitrate | + | reduction | 17632 |
68375 | sucrose | + | fermentation | 17992 |
68375 | arabinose | - | fermentation | 22599 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68375 | 15688 | acetoin | no |
121841 | 35581 | indole | no |
metabolite tests
- @ref: 68375
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68375 | beta-glucuronidase | - | 3.2.1.31 |
68375 | alkaline phosphatase | - | 3.1.3.1 |
68375 | L-arginine arylamidase | - | |
68375 | beta-galactosidase | + | 3.2.1.23 |
68375 | beta-glucosidase | - | 3.2.1.21 |
68375 | ornithine decarboxylase | - | 4.1.1.17 |
68375 | arginine dihydrolase | + | 3.5.3.6 |
68375 | urease | + | 3.5.1.5 |
121841 | oxidase | - | |
121841 | catalase | + | 1.11.1.6 |
121841 | 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 |
fatty acid profile
@ref fatty acid percentage ECL 52542 C14:0 0.3 14 52542 C15:0 0.3 15 52542 C16:0 2 16 52542 C17:0 0.4 17 52542 C18:0 2.5 18 52542 C20:0 0.7 20 52542 C14:0 ISO 1.3 13.618 52542 C15:0 ANTEISO 49.4 14.711 52542 C15:0 ISO 14.3 14.621 52542 C16:0 iso 1.7 15.626 52542 C17:0 anteiso 15.6 16.722 52542 C17:0 iso 7.7 16.629 52542 C18:0 ISO 0.3 17.632 52542 C18:1 ω9c 0.4 17.769 52542 C18:2 ω6,9c/C18:0 ANTE 1 17.724 52542 C19:0 ANTEISO 1.1 18.729 52542 C19:0 ISO 0.8 18.633 52542 C20:2 ω6,9c 0.3 19.735 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
@ref fatty acid percentage ECL 52542 C14:0 0.3 14 52542 C15:0 0.3 15 52542 C16:0 2 16 52542 C17:0 0.4 17 52542 C18:0 2.5 18 52542 C20:0 0.7 20 52542 C14:0 ISO 1.3 13.618 52542 C15:0 ANTEISO 49.4 14.711 52542 C15:0 ISO 14.3 14.621 52542 C16:0 iso 1.7 15.626 52542 C17:0 anteiso 15.6 16.722 52542 C17:0 iso 7.7 16.629 52542 C18:0 ISO 0.3 17.632 52542 C18:1 ω9c 0.4 17.769 52542 C18:2 ω6,9c/C18:0 ANTE 1 17.724 52542 C19:0 ANTEISO 1.1 18.729 52542 C19:0 ISO 0.8 18.633 52542 C20:2 ω6,9c 0.3 19.735 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121841 | - | - | + | + | - | + | - | - | - | - | + | - | - | + | - | + | + | - | - | - |
API 50CHac
@ref | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121841 | +/- | - | - | - | +/- | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | + | + | - | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
API ID32STA
@ref | URE | ADH Arg | ODC | ESC | GLU | FRU | MNE | MAL | LAC | TRE | MAN | RAF | RIB | CEL | NIT | VP | beta GAL | ArgA | PAL | PyrA | NOVO | SAC | NAG | TUR | ARA | beta GUR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3129 | + | + | - | - | + | + | - | + | + | + | - | - | - | - | + | - | + | - | - | +/- | + | + | + | + | - | - |
3129 | + | + | - | - | + | + | - | + | + | + | - | - | - | - | + | - | + | - | - | - | - | + | +/- | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
3129 | Kung-chom (fermented shrimp) | Thailand | THA | Asia |
52542 | Shrimp,fermented (Kung-chom) | Thailand | THA | Asia |
67770 | Kung-chom (fermented shrimp) | |||
121841 | Fermented shrimp | Thailand | THA | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Seafood |
#Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_1206.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_955;99_1206&stattab=map
- Last taxonomy: Staphylococcus
- 16S sequence: EU727184
- Sequence Identity:
- Total samples: 22504
- soil counts: 1443
- aquatic counts: 1299
- animal counts: 19130
- plant counts: 632
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3129 | 1 | Risk group (German classification) |
121841 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Staphylococcus piscifermentans rrn gene for 16S ribosomal RNA | AB009943 | 1493 | ena | 70258 |
20218 | Staphylococcus piscifermentans strain DSM 7373 16S ribosomal RNA gene, partial sequence | AY688085 | 464 | ena | 70258 |
3129 | Staphylococcus piscifermentans 16S rRNA gene, strain SK03 T | Y15754 | 1544 | ena | 70258 |
67770 | Staphylococcus piscifermentans CIP103958 16S ribosomal RNA gene, partial sequence | EU727184 | 1516 | ena | 70258 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Staphylococcus piscifermentans NBRC 109625 | GCA_007992655 | contig | ncbi | 70258 |
66792 | Staphylococcus piscifermentans DSM 7373 | GCA_003970555 | scaffold | ncbi | 70258 |
66792 | Staphylococcus piscifermentans strain DSM 7373 | 70258.7 | wgs | patric | 70258 |
66792 | Staphylococcus piscifermentans strain NBRC 109625 | 70258.8 | wgs | patric | 70258 |
66792 | Staphylococcus piscifermentans strain NCTC13836 | 70258.6 | complete | patric | 70258 |
66792 | Staphylococcus piscifermentans NCTC 13836 | 2772190616 | complete | img | 70258 |
67770 | Staphylococcus piscifermentans NCTC13836 | GCA_900186985 | complete | ncbi | 70258 |
GC content
@ref | GC-content | method |
---|---|---|
3129 | 37.0 | high performance liquid chromatography (HPLC) |
67770 | 36.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 88 | no |
gram-positive | yes | 88.461 | no |
anaerobic | no | 99.173 | no |
halophile | yes | 91.954 | no |
spore-forming | no | 89.746 | no |
glucose-util | yes | 87.193 | no |
flagellated | no | 86.736 | no |
thermophile | no | 99.668 | no |
aerobic | yes | 87.449 | no |
glucose-ferment | yes | 80.067 | yes |
motile | no | 85.517 | no |
External links
@ref: 3129
culture collection no.: CCUG 35133, TISTR 824, NRIC 1817, DSM 7373, ATCC 51136, JCM 6057, NCIMB 13277, CCM 4345, CIP 103958, LMG 22178, NBRC 109625, NCTC 13836
straininfo link
- @ref: 83736
- straininfo: 46137
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 1390108 | Staphylococcus piscifermentans sp. nov., from fermented fish in Thailand. | Tanasupawat S, Hashimoto Y, Ezaki T, Kozaki M, Komagata K | Int J Syst Bacteriol | 10.1099/00207713-42-4-577 | 1992 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry, Fatty Acids/analysis, Fermentation, Fishes/*microbiology, *Food Microbiology, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phenotype, Staphylococcus/chemistry/*classification/isolation & purification/physiology, Thailand | Biotechnology |
Metabolism | 26256665 | Improvement of Fish Sauce Quality by Strain CMC5-3-1: A Novel Species of Staphylococcus sp. | Udomsil N, Rodtong S, Tanasupawat S, Yongsawatdigul J | J Food Sci | 10.1111/1750-3841.12986 | 2015 | Aldehydes/metabolism, Animals, DNA, Bacterial/analysis, *Fermentation, Fish Products/*analysis/standards, Fishes, Flavoring Agents/*analysis, Glutamic Acid/*metabolism, Histamine/metabolism, Humans, *Odorants, Phylogeny, RNA, Ribosomal, 16S, Sodium Chloride/metabolism, Species Specificity, Staphylococcus/genetics/growth & development/*metabolism, *Taste, Volatile Organic Compounds/metabolism | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3129 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7373) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7373 | |||
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 | |
40888 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15813 | ||||
52542 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 35133) | https://www.ccug.se/strain?id=35133 | |||
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/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68375 | Automatically annotated from API ID32STA | |||||
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) | |||
83736 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46137.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121841 | Curators of the CIP | Collection of Institut Pasteur (CIP 103958) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103958 |