Strain identifier

BacDive ID: 14632

Type strain: Yes

Species: Staphylococcus condimenti

Strain Designation: F-2

Strain history: CIP <- 1998, C. Hertel, Univ. Hohenheim, Stuttgart, Germany: strain F-2 <- 1991, Tanasupawat

NCBI tax ID(s): 70255 (species)

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

@ref: 4438

BacDive-ID: 14632

DSM-Number: 11674

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Staphylococcus condimenti F-2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soy sauce mash.

NCBI tax id

  • NCBI tax id: 70255
  • Matching level: species

strain history

@refhistory
4438<- A.J. Probst <- ? <- JCM <- Tanasupawat (Staphylococcus carnosus) <- T. Ueno, F-8 (Tetracoccus soyae)
67770S. Tanasupawat F2.
118723CIP <- 1998, C. Hertel, Univ. Hohenheim, Stuttgart, Germany: strain F-2 <- 1991, Tanasupawat

doi: 10.13145/bacdive14632.20230509.8.1

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 condimenti
  • full scientific name: Staphylococcus condimenti Probst et al. 1998

@ref: 4438

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus condimenti

full scientific name: Staphylococcus condimenti Probst et al. 1998

strain designation: F-2

type strain: yes

Morphology

cell morphology

  • @ref: 118723
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@reftype of hemolysis
4438gamma
118723

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4438COLUMBIA 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
4438TRYPTICASE 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
38579MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118723CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29
118723CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4438positivegrowth37mesophilic
38579positivegrowth30mesophilic
54986positivegrowth37mesophilic
67770positivegrowth30mesophilic
118723positivegrowth22-41
118723nogrowth10psychrophilic
118723nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54986aerobe
118723facultative anaerobe

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
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
118723hippurate-hydrolysis606565
118723nitrate+reduction17632
118723nitrite-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
68375N-acetylglucosamine+fermentation59640
68375turanose-fermentation32528
68375arabinose-fermentation22599

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
11872335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837515688acetoin-
11872315688acetoin-

enzymes

@refvalueactivityec
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
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
118723oxidase-
118723beta-galactosidase+3.2.1.23
118723alcohol dehydrogenase+1.1.1.1
118723gelatinase-
118723amylase-
118723DNase+
118723caseinase-3.4.21.50
118723catalase+1.11.1.6
118723coagulase-
118723tween esterase+
118723gamma-glutamyltransferase-2.3.2.2
118723lecithinase+
118723lipase-
118723lysine decarboxylase-4.1.1.18
118723ornithine decarboxylase-4.1.1.17
118723phenylalanine ammonia-lyase-4.3.1.24
118723protease-
118723tryptophan deaminase-
118723urease+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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118723-+++------++-+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118723+/----+----+/-+++----++--+------+--+-----------------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
4438++--+++-+++---+-+-+-+-+---
4438++--+++-+++---+-+-+-+-+---
4438++--+++-+++---+-+-+-+-+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118723++-++------+-------+-----------+-+--+------------+---------++------------+-+----+---+-+---+++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
4438soy sauce mashJapanJPNAsia
54986Soy sauce mash
67770Soy-sauce mash
118723Food, Soy sauce mash1991

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Food

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44381Risk group (German classification)
1187231Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus condimenti strain DSM 11674 16S ribosomal RNA gene, partial sequenceAY688048464ena70255
4438Staphylococcus condimenti 16S rRNA gene, strain F-2 T, DSM 11674 TY157501545ena70255

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus condimenti DSM 11674GCA_001618885completencbi70255
66792Staphylococcus condimenti NCTC13827GCA_900637235completencbi70255
66792Staphylococcus condimenti strain DSM 1167470255.17wgspatric70255
66792Staphylococcus condimenti strain DSM 1167470255.13completepatric70255
66792Staphylococcus condimenti strain DSM 1167470255.10wgspatric70255
66792Staphylococcus condimenti strain FDAARGOS_114870255.23completepatric70255
66792Staphylococcus condimenti strain NCTC1382770255.18completepatric70255
66792Staphylococcus condimenti DSM 116742645727505draftimg70255
66792Staphylococcus condimenti DSM 116742687453551completeimg70255
66792Staphylococcus condimenti DSM 116742917450786draftimg70255
67770Staphylococcus condimenti DSM 11674GCA_001014685contigncbi70255
67770Staphylococcus condimenti DSM 11674GCA_002902505scaffoldncbi70255

GC content

  • @ref: 67770
  • GC-content: 35.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno85.601no
gram-positiveyes88.994no
anaerobicno98.969yes
aerobicyes90.012no
halophileyes92.1no
spore-formingno92.133no
glucose-utilyes88.334no
motileno86.011no
thermophileno99.749yes
glucose-fermentyes81.695no

External links

@ref: 4438

culture collection no.: DSM 11674, JCM 6074, CCUG 39902, CCM 4753, CIP 105760, NCIMB 13559, NCTC 13827

straininfo link

  • @ref: 83760
  • straininfo: 49151

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734019Staphylococcus condimenti sp. nov., from soy sauce mash, and Staphylococcus carnosus (Schleifer and Fischer 1982) subsp. utilis subsp. nov.Probst AJ, Hertel C, Richter L, Wassill L, Ludwig W, Hammes WPInt J Syst Bacteriol10.1099/00207713-48-3-6511998Base Sequence, Food Microbiology, Molecular Sequence Data, Oligonucleotide Probes, Phylogeny, *Soybeans, Staphylococcus/*classification/isolation & purificationBiotechnology
Genetics27257207First Draft Genome Sequence of Staphylococcus condimenti F-2T.Zheng B, Hu X, Jiang X, Li A, Yao J, Li LGenome Announc10.1128/genomeA.00499-162016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4438Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11674)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11674
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
38579Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17815
54986Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39902)https://www.ccug.se/strain?id=39902
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)
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
83760Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49151.1StrainInfo: A central database for resolving microbial strain identifiers
118723Curators of the CIPCollection of Institut Pasteur (CIP 105760)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105760