Strain identifier

BacDive ID: 14606

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
3129<- JCM <- S. Tanasupawat, SK03
67770S. Tanasupawat SK-03.
121841CIP <- 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

@refgram stainconfidencemotility
69480positive100
121841no

colony morphology

  • @ref: 3129
  • type of hemolysis: gamma

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3129COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
3129TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
40888MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121841CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121841CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3129positivegrowth37mesophilic
40888positivegrowth37mesophilic
52542positivegrowth18psychrophilic
52542positivegrowth42thermophilic
67770positivegrowth30mesophilic

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

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
121841nitrate+reduction17632
121841nitrite-reduction16301
68375urea+hydrolysis16199
68375arginine+hydrolysis29016
68375ornithine-degradation18257
68375esculin-hydrolysis4853
68375D-glucose+fermentation17634
68375D-fructose+fermentation15824
68375D-mannose-fermentation16024
68375maltose+fermentation17306
68375lactose+fermentation17716
68375trehalose+fermentation27082
68375D-mannitol-fermentation16899
68375raffinose-fermentation16634
68375D-ribose-fermentation16988
68375cellobiose-fermentation17057
68375nitrate+reduction17632
68375sucrose+fermentation17992
68375arabinose-fermentation22599

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12184135581indoleno

metabolite tests

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68375beta-glucuronidase-3.2.1.31
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase+3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase+3.5.3.6
68375urease+3.5.1.5
121841oxidase-
121841catalase+1.11.1.6
121841urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • @reffatty acidpercentageECL
    52542C14:00.314
    52542C15:00.315
    52542C16:0216
    52542C17:00.417
    52542C18:02.518
    52542C20:00.720
    52542C14:0 ISO1.313.618
    52542C15:0 ANTEISO49.414.711
    52542C15:0 ISO14.314.621
    52542C16:0 iso1.715.626
    52542C17:0 anteiso15.616.722
    52542C17:0 iso7.716.629
    52542C18:0 ISO0.317.632
    52542C18:1 ω9c0.417.769
    52542C18:2 ω6,9c/C18:0 ANTE117.724
    52542C19:0 ANTEISO1.118.729
    52542C19:0 ISO0.818.633
    52542C20:2 ω6,9c0.319.735
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    52542C14:00.314
    52542C15:00.315
    52542C16:0216
    52542C17:00.417
    52542C18:02.518
    52542C20:00.720
    52542C14:0 ISO1.313.618
    52542C15:0 ANTEISO49.414.711
    52542C15:0 ISO14.314.621
    52542C16:0 iso1.715.626
    52542C17:0 anteiso15.616.722
    52542C17:0 iso7.716.629
    52542C18:0 ISO0.317.632
    52542C18:1 ω9c0.417.769
    52542C18:2 ω6,9c/C18:0 ANTE117.724
    52542C19:0 ANTEISO1.118.729
    52542C19:0 ISO0.818.633
    52542C20:2 ω6,9c0.319.735
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121841--++-+----+--+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121841+/----+/-----+++---------+-----++-++-+-----+---------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
3129++--++-+++----+-+--+/-++++--
3129++--++-+++----+-+----++/----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3129Kung-chom (fermented shrimp)ThailandTHAAsia
52542Shrimp,fermented (Kung-chom)ThailandTHAAsia
67770Kung-chom (fermented shrimp)
121841Fermented shrimpThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
31291Risk group (German classification)
1218411Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus piscifermentans rrn gene for 16S ribosomal RNAAB0099431493ena70258
20218Staphylococcus piscifermentans strain DSM 7373 16S ribosomal RNA gene, partial sequenceAY688085464ena70258
3129Staphylococcus piscifermentans 16S rRNA gene, strain SK03 TY157541544ena70258
67770Staphylococcus piscifermentans CIP103958 16S ribosomal RNA gene, partial sequenceEU7271841516ena70258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus piscifermentans NBRC 109625GCA_007992655contigncbi70258
66792Staphylococcus piscifermentans DSM 7373GCA_003970555scaffoldncbi70258
66792Staphylococcus piscifermentans strain DSM 737370258.7wgspatric70258
66792Staphylococcus piscifermentans strain NBRC 10962570258.8wgspatric70258
66792Staphylococcus piscifermentans strain NCTC1383670258.6completepatric70258
66792Staphylococcus piscifermentans NCTC 138362772190616completeimg70258
67770Staphylococcus piscifermentans NCTC13836GCA_900186985completencbi70258

GC content

@refGC-contentmethod
312937.0high performance liquid chromatography (HPLC)
6777036.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
gram-positiveyes88.461no
anaerobicno99.173no
halophileyes91.954no
spore-formingno89.746no
glucose-utilyes87.193no
flagellatedno86.736no
thermophileno99.668no
aerobicyes87.449no
glucose-fermentyes80.067yes
motileno85.517no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1390108Staphylococcus piscifermentans sp. nov., from fermented fish in Thailand.Tanasupawat S, Hashimoto Y, Ezaki T, Kozaki M, Komagata KInt J Syst Bacteriol10.1099/00207713-42-4-5771992Animals, 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, ThailandBiotechnology
Metabolism26256665Improvement of Fish Sauce Quality by Strain CMC5-3-1: A Novel Species of Staphylococcus sp.Udomsil N, Rodtong S, Tanasupawat S, Yongsawatdigul JJ Food Sci10.1111/1750-3841.129862015Aldehydes/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/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3129Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7373)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7373
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40888Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15813
52542Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35133)https://www.ccug.se/strain?id=35133
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68375Automatically annotated from API ID32STA
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
83736Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46137.1StrainInfo: A central database for resolving microbial strain identifiers
121841Curators of the CIPCollection of Institut Pasteur (CIP 103958)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103958