Strain identifier

BacDive ID: 14554

Type strain: Yes

Species: Staphylococcus hyicus

Strain Designation: 1

Strain history: CIP <- 1981, CCM <- ATCC <- D. Sompolinsky: strain 1, Micrococcus hyicus

NCBI tax ID(s): 1284 (species)

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General

@ref: 8830

BacDive-ID: 14554

DSM-Number: 20459

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, animal pathogen

description: Staphylococcus hyicus 1 is a mesophilic, Gram-positive animal pathogen that was isolated from pig with exudative epidermitis.

NCBI tax id

  • NCBI tax id: 1284
  • Matching level: species

strain history

@refhistory
8830<- K.H. Schleifer <- NCTC <- ATCC <- D. Sompolinsky, 1 (Micrococcus hyicus)
67770R. Sakazaki <-- ATCC 11249 <-- D. Sompolinsky 1.
120021CIP <- 1981, CCM <- ATCC <- D. Sompolinsky: strain 1, Micrococcus hyicus

doi: 10.13145/bacdive14554.20230509.8.1

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 hyicus
  • full scientific name: Staphylococcus hyicus (Sompolinsky 1953) Devriese et al. 1978 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus hyicus

@ref: 8830

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus hyicus subsp. hyicus

full scientific name: Staphylococcus hyicus subsp. hyicus (Sompolinsky 1953) Devriese et al. 1978

strain designation: 1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120021positivecoccus-shapedno

colony morphology

@reftype of hemolysisincubation periodhemolysis ability
8830gamma1-2 days
1200211

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8830COLUMBIA 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
8830TRYPTICASE 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
37621MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120021CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
8830positivegrowth37mesophilic
37621positivegrowth37mesophilic
67770positivegrowth26mesophilic
120021positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no92
69480no99.684

murein

  • @ref: 8830
  • murein short key: A11.02
  • type: A3alpha L-Lys-Gly5-6

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
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
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120021nitrate+reduction17632
120021nitrite+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

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistant
6837528368novobiocinyesyes1.8 µg
1200210129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesnoyes

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12002135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
8830catalase+1.11.1.6
8830cytochrome-c oxidase-1.9.3.1
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
120021oxidase-
120021beta-galactosidase+3.2.1.23
120021alcohol dehydrogenase+1.1.1.1
120021gelatinase+
120021DNase+
120021catalase+1.11.1.6
120021coagulase-
120021lecithinase-
120021lysine decarboxylase-4.1.1.18
120021ornithine decarboxylase-4.1.1.17
120021urease-3.5.1.5

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120021----+----++++--------+------+/--++-----------------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
8830-+--+++-++--+-+---+--++--+
8830-+--+++-++--+-+---+--++--+
8830-+--+++-++--+-+---+--++--+

Isolation, sampling and environmental information

isolation

@refsample type
8830pig with exudative epidermitis
67770Pig with exudative epidermitis
120021Animal, Pig with exudative epidermitis

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_2789.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_888;99_2789&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: D83368
  • Sequence Identity:
  • Total samples: 74
  • soil counts: 1
  • aquatic counts: 1
  • animal counts: 72

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
8830yes2Risk group (German classification)
1200211Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus hyicus strain DSM 20459 16S ribosomal RNA gene, partial sequenceAY688066464ena1284
8830Staphylococcus hyicus gene for 16S rRNA, partial sequence, strain: ATCC 11249D833681476ena1284

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus hyicus ATCC 11249GCA_000816085completencbi1284
66792Staphylococcus hyicus NCTC10350GCA_900474585completencbi1284
66792Staphylococcus hyicus CCUG 6509GCA_003970475scaffoldncbi1284
66792Staphylococcus hyicus ATCC 112491284.6completepatric1284
66792Staphylococcus hyicus strain CCUG 65091284.37wgspatric1284
66792Staphylococcus hyicus strain NCTC103501284.32completepatric1284
66792Staphylococcus hyicus NCTC 103502811995276completeimg1284
66792Staphylococcus hyicus ATCC 112492645727708completeimg1284

GC content

@refGC-contentmethod
883034.8
883032.9
6777032.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno92.041no
flagellatedno93.978no
gram-positiveyes91.479no
anaerobicno99.107no
aerobicyes90.201no
halophileyes91.121no
spore-formingno85.905no
thermophileno99.699yes
glucose-utilyes85.999no
glucose-fermentyes80.927yes

External links

@ref: 8830

culture collection no.: DSM 20459, ATCC 11249, CCM 2368, NCTC 10350, JCM 2423, BCRC 12925, CCUG 15602, CCUG 6509, CIP 81.58, LMG 13352, MTCC 6153, NBIMCC 1094, PCM 2192

straininfo link

  • @ref: 83685
  • straininfo: 264337

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2139423Isolation and characterization of staphyloferrin A, a compound with siderophore activity from Staphylococcus hyicus DSM 20459.Meiwes J, Fiedler HP, Haag H, Zahner H, Konetschny-Rapp S, Jung GFEMS Microbiol Lett10.1111/j.1574-6968.1990.tb13863.x1990Chromatography, High Pressure Liquid, Citrates/*isolation & purification, Iron Chelating Agents/*isolation & purification, Molecular Structure, Ornithine/*analogs & derivatives/isolation & purification, Siderophores, Species Specificity, Staphylococcus/*analysisEnzymology
Enzymology2379505Staphyloferrin A: a structurally new siderophore from staphylococci.Konetschny-Rapp S, Jung G, Meiwes J, Zahner HEur J Biochem10.1111/j.1432-1033.1990.tb19094.x1990Amino Acids/analysis, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Circular Dichroism, Citrates/*isolation & purification, Culture Media/analysis, Ferric Compounds/*isolation & purification, Magnetic Resonance Spectroscopy, Molecular Structure, Ornithine/*analogs & derivatives/isolation & purification, Staphylococcus/*analysis, StereoisomerismPhylogeny
Enzymology3630477Isolation and characterization of a staphylococcal enzyme bacteriolytic on streptococci.Muller HP, Blobel HZentralbl Bakteriol Mikrobiol Hyg A10.1016/s0176-6724(87)80123-21987*Bacteriolysis, Cell Wall/drug effects, Chromatography, DEAE-Cellulose, Chromatography, High Pressure Liquid, Enzymes/analysis/*isolation & purification/metabolism, Isoelectric Focusing, Sodium Chloride/metabolism, Staphylococcus/*enzymology, Streptococcus/*drug effectsPhylogeny
6639273Chemical composition and structure of cell wall teichoic acids of staphylococci.Endl J, Seidl HP, Fiedler F, Schleifer KHArch Microbiol10.1007/BF004144831983Acetylglucosamine/analysis, Cell Wall/analysis, Chemical Phenomena, Chemistry, Glycerophosphates/analysis, Polysaccharides/analysis, Staphylococcus/*analysis/ultrastructure, Staphylococcus aureus/*analysis, Staphylococcus epidermidis/*analysis, Teichoic Acids/*analysis
Metabolism8138126Isolation and biological characterization of staphyloferrin B, a compound with siderophore activity from staphylococci.Haag H, Fiedler HP, Meiwes J, Drechsel H, Jung G, Zahner HFEMS Microbiol Lett10.1111/j.1574-6968.1994.tb06626.x1994Biological Assay, Biological Transport, Citrates/analysis/*chemistry/metabolism, Iron/*metabolism, Ornithine/analogs & derivatives/analysis, Picolinic Acids/pharmacology, Polyamines/*chemistry/metabolism, Siderophores/*chemistry/metabolism, Species Specificity, Spectrophotometry, Ultraviolet, Staphylococcus/*chemistry/drug effectsPhylogeny
Enzymology8400765Purification and chemical characterization of staphyloferrin B, a hydrophilic siderophore from staphylococci.Drechsel H, Freund S, Nicholson G, Haag H, Jung O, Zahner H, Jung GBiometals10.1007/BF002058581993Citrates/chemistry/*isolation & purification, Ketoglutaric Acids/chemistry/*isolation & purification, Molecular Structure, Siderophores/chemistry/*isolation & purification, Solubility, Staphylococcus/*metabolism, Water/chemistryPhylogeny
Phylogeny9626935Differentiation and distribution of three types of exfoliative toxin produced by Staphylococcus hyicus from pigs with exudative epidermitis.Andresen LOFEMS Immunol Med Microbiol10.1111/j.1574-695X.1998.tb01140.x1998Animals, Antibodies, Bacterial, Antibodies, Monoclonal, Bacteriophage Typing, Epidermitis, Exudative, of Swine/*microbiology, Exfoliatins/chemistry/classification/immunology/*isolation & purification, Species Specificity, Staphylococcus/*chemistry/classification/growth & development/isolation & purification, SwineEnzymology
Cultivation10225289Studies on the effect of divalent metal ions on exfoliative toxins from Staphylococcus hyicus: indications of ExhA and ExhB being metalloproteins.Andresen LOFEMS Immunol Med Microbiol10.1111/j.1574-695X.1999.tb01251.x1999Bacterial Proteins/*analysis, Bacterial Toxins/*analysis, Cations, Divalent, Chelating Agents, Cobalt, Copper, Culture Media, Metalloproteins/*analysis, *Metals, *Staphylococcus/growth & development, ZincPathogenicity
Transcriptome21111546An IgG-binding protein A homolog in Staphylococcus hyicus.Rosander A, Guss B, Pringle MVet Microbiol10.1016/j.vetmic.2010.10.0112010Amino Acid Motifs, Animals, Binding Sites, DNA, Bacterial/genetics, Peptide Library, Polymerase Chain Reaction/veterinary, Protein Sorting Signals/genetics, Sequence Analysis, DNA, Staphylococcal Infections/microbiology/veterinary, Staphylococcal Protein A/*genetics, Staphylococcus aureus/genetics, Staphylococcus hyicus/*genetics, Swine/microbiology, Swine Diseases/microbiology
Phylogeny21335502Staphylococcus agnetis sp. nov., a coagulase-variable species from bovine subclinical and mild clinical mastitis.Taponen S, Supre K, Piessens V, Van Coillie E, De Vliegher S, Koort JMKInt J Syst Evol Microbiol10.1099/ijs.0.028365-02011Amplified Fragment Length Polymorphism Analysis, Animals, Asymptomatic Diseases, Bacterial Typing Techniques, Cattle, Cluster Analysis, Coagulase/*metabolism, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Mastitis, Bovine/*microbiology, Milk/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptide Elongation Factor Tu/genetics, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcal Infections/microbiology/*veterinary, Staphylococcus/*classification/genetics/*isolation & purification/metabolismMetabolism
Transcriptome25700402Sequence Analysis of Staphylococcus hyicus ATCC 11249T, an Etiological Agent of Exudative Epidermitis in Swine, Reveals a Type VII Secretion System Locus and a Novel 116-Kilobase Genomic Island Harboring Toxin-Encoding Genes.Calcutt MJ, Foecking MF, Hsieh HY, Adkins PR, Stewart GC, Middleton JRGenome Announc10.1128/genomeA.01525-142015
Pathogenicity31900561A new high-yielding antimicrobial peptide NZX and its antibacterial activity against Staphylococcus hyicus in vitro/vivo.Liu H, Yang N, Mao R, Teng D, Hao Y, Wang X, Wang JAppl Microbiol Biotechnol10.1007/s00253-019-10313-32020Animals, Anti-Bacterial Agents/*pharmacology, Antimicrobial Cationic Peptides/*pharmacology, Bacterial Translocation/drug effects, Cell Line, Cytokines/immunology, Female, Fermentation, Gram-Positive Bacteria/drug effects, Humans, Mice, Mice, Inbred ICR, Microbial Sensitivity Tests, Pichia/genetics/metabolism, Specific Pathogen-Free Organisms, Staphylococcal Infections/drug therapy, Staphylococcus hyicus/*drug effectsBiotechnology
Pathogenicity34063982Design and Pharmacodynamics of Recombinant Fungus Defensin NZL with Improved Activity against Staphylococcus hyicus In Vitro and In Vivo.Liu H, Yang N, Teng D, Mao R, Hao Y, Ma X, Wang JInt J Mol Sci10.3390/ijms221154352021Animals, Anti-Bacterial Agents/*pharmacology, Cells, Cultured, Defensins/*pharmacology, Humans, Mice, Microbial Sensitivity Tests/methods, Saccharomycetales/*metabolism, Staphylococcal Infections/*drug therapy, Staphylococcus hyicus/*drug effectsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8830Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20459)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20459
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
37621Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11221
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83685Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264337.1StrainInfo: A central database for resolving microbial strain identifiers
120021Curators of the CIPCollection of Institut Pasteur (CIP 81.58)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.58