Strain identifier

BacDive ID: 14521

Type strain: Yes

Species: Staphylococcus delphini

Strain Designation: Heidy

Strain history: CIP <- 1993, P.E. Varaldo, Ancona Univ., Ancona, Italy: strain Heidy

NCBI tax ID(s): 53344 (species)

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General

@ref: 9075

BacDive-ID: 14521

DSM-Number: 20771

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe

description: Staphylococcus delphini Heidy is a facultative anaerobe bacterium that was isolated from purulent material from a dolphin living in an aquarium.

NCBI tax id

  • NCBI tax id: 53344
  • Matching level: species

strain history

@refhistory
9075<- P.E. Varaldo, Heidy
407711993, P.E. Varaldo, Microbiol. Univ., Ancona, Spain: strain Heidy
118888CIP <- 1993, P.E. Varaldo, Ancona Univ., Ancona, Italy: strain Heidy

doi: 10.13145/bacdive14521.20240916.9.1

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 delphini
  • full scientific name: Staphylococcus delphini Varaldo et al. 1988

@ref: 9075

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus delphini

full scientific name: Staphylococcus delphini Varaldo et al. 1988

strain designation: Heidy

type strain: yes

Morphology

cell morphology

  • @ref: 118888
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 9075
  • type of hemolysis: gamma

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9075COLUMBIA 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
9075TRYPTICASE 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
40771MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118888CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118888CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
9075positivegrowth37
40771positivegrowth37
49910positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 118888
  • oxygen tolerance: facultative anaerobe

murein

  • @ref: 9075
  • 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
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
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-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
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
118888nitrate+reduction17632
118888nitrite-reduction16301
68375ornithine-degradation18257
68375esculin-hydrolysis4853
68375D-glucose+fermentation17634
68375D-fructose+fermentation15824
68375D-mannose+fermentation16024
68375maltose+fermentation17306
68375trehalose-fermentation27082
68375D-mannitol+fermentation16899
68375raffinose-fermentation16634
68375D-ribose+fermentation16988
68375cellobiose-fermentation17057
68375nitrate+reduction17632
68375sucrose+fermentation17992
68375N-acetylglucosamine+fermentation59640
68375arabinose-fermentation22599

antibiotic resistance

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

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
11888835581indoleno

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
118888oxidase-
118888catalase+1.11.1.6
118888urease+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
118888-+++-+----++-+-----+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118888+---+----++++---+/-+--+/-+-----++-++---+/----+------+/---

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
9075++--+++++-+-+-+-+-++-+++--
9075++--+++++/--+-+-+-+-++-+++/---
9075----+++++-+-+--+-++/--+++/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
9075purulent material from a dolphin living in an aquariumGenoaItalyITAEurope
49910Dolphin,purulent skin lesionItalyITAEurope
118888Environment, Purulent material from aquarium dolphinsLiguriaItalyITAEurope1975

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Infection#Inflammation
#Host#Mammals#Aquatic mammal
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_1134.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_888;99_1134&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AB009938
  • Sequence Identity:
  • Total samples: 413
  • soil counts: 3
  • aquatic counts: 5
  • animal counts: 399
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
90751Risk group (German classification)
1188881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus delphini strain DSM 20771 16S ribosomal RNA gene, partial sequenceAY688050464nuccore53344
20218Staphylococcus delphini strain ATCC 49171 16S ribosomal RNA gene, partial sequenceEU157196366nuccore53344
9075Staphylococcus delphini rrn gene for 16S ribosomal RNAAB0099381493nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157195366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157197366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157198366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157199366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157200366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157201366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157202366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157203366nuccore53344
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157204366nuccore1141105
124043Staphylococcus delphini strain HT20030679 16S ribosomal RNA gene, partial sequence.EU157205366nuccore53344

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus delphini HeidyGCA_003585325contigncbi53344
66792Staphylococcus delphini strain Heidy53344.20wgspatric53344
66792Staphylococcus delphini Heidy2917461297draftimg53344

GC content

  • @ref: 9075
  • GC-content: 39.0

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes84.978no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no99.416yes
69480spore-formingspore-formingAbility to form endo- or exosporesno66.931no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no51.869yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96no
69480flagellatedmotile2+Ability to perform flagellated movementno80.025no

External links

@ref: 9075

culture collection no.: CCUG 30107, CCM 4115, DSM 20771, ATCC 49171, CIP 103732, NCIMB 13206

straininfo link

  • @ref: 83652
  • straininfo: 46869

literature

  • topic: Phylogeny
  • Pubmed-ID: 32672529
  • title: Staphylococcus ursi sp. nov., a new member of the 'Staphylococcus intermedius group' isolated from healthy black bears.
  • authors: Perreten V, Kania SA, Bemis D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004324
  • year: 2020
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcus/*classification/isolation & purification, Staphylococcus intermedius/genetics, Tennessee, Ursidae/*microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9075Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20771)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20771
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
40771Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15562
49910Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30107)https://www.ccug.se/strain?id=30107
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)
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)
83652Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46869.1StrainInfo: A central database for resolving microbial strain identifiers
118888Curators of the CIPCollection of Institut Pasteur (CIP 103732)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103732
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy