Strain identifier

BacDive ID: 14555

Type strain: Yes

Species: Staphylococcus intermedius

Strain Designation: H11, H11/68

Strain history: CIP <- 1981, CCM <- V. Hajek: strain H11/68

NCBI tax ID(s): 1141106 (strain), 1285 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8627

BacDive-ID: 14555

DSM-Number: 20373

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive

description: Staphylococcus intermedius H11 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from pigeon nares.

NCBI tax id

NCBI tax idMatching level
1141106strain
1285species

strain history

@refhistory
8627<- K.H. Schleifer <- V. Hajek, H11
67770R. Sakazaki <-- ATCC 29663 <-- V. Hajek H11/68.
120154CIP <- 1981, CCM <- V. Hajek: strain H11/68

doi: 10.13145/bacdive14555.20230509.8.1

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 intermedius
  • full scientific name: Staphylococcus intermedius Hájek 1976 (Approved Lists 1980)

@ref: 8627

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus intermedius

full scientific name: Staphylococcus intermedius Hájek 1976

strain designation: H11, H11/68

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120154positivecoccus-shapedno

colony morphology

@reftype of hemolysishemolysis ability
8627beta1
120154

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8627COLUMBIA 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
8627TRYPTICASE 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
37296MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120154CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8627positivegrowth37mesophilic
37296positivegrowth37mesophilic
67770positivegrowth37mesophilic
120154positivegrowth22-41
120154nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120154
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.806

murein

  • @ref: 8627
  • murein short key: A11.03
  • type: A3alpha L-Lys-Gly2-4-L-Ser1-2-Gly

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
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
68371amygdalin-builds acid from27613
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
120154hippurate-hydrolysis606565
120154nitrate+reduction17632
120154nitrite-reduction16301
120154tributyrin+hydrolysis35020
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

  • @ref: 120154
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120154
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
8627catalase+1.11.1.6
8627cytochrome-c oxidase-1.9.3.1
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
120154oxidase-
120154beta-galactosidase+3.2.1.23
120154alcohol dehydrogenase-1.1.1.1
120154gelatinase+
120154amylase-
120154DNase+
120154caseinase+3.4.21.50
120154catalase+1.11.1.6
120154coagulase+
120154tween esterase+
120154gamma-glutamyltransferase-2.3.2.2
120154lecithinase-
120154lipase-
120154lysine decarboxylase-4.1.1.18
120154ornithine decarboxylase-4.1.1.17
120154phenylalanine ammonia-lyase-4.3.1.24
120154tryptophan deaminase-
120154urease+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
120154-+++------++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120154+---+----++++----+---+/--+/----++/--++------+-------+/---

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
8627+---+++++++-+-+-+-++/--++---
8627+---+++++++-+-+-+-++-++---
8627+---+++++++-+-+-+-+++/-+++--
8627+---+++++++-+-+++-+++++---
8627+---+++++++-+-+-+-++/--++---
8627+---+++++++-+-+++-++-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120154++-++--+-+++----++-+------+----+-+----------------------+--++--------------+---------------+--+----

Isolation, sampling and environmental information

isolation

@refsample type
8627pigeon nares
67770Pigeon nares
120154Animal, Pigeon, nares

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body-Site#Organ#Nose

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: D83369
  • 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
86272Risk group (German classification)
1201541Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus intermedius strain DSM 20373 16S ribosomal RNA gene, partial sequenceAY688070464ena1141106
20218Staphylococcus intermedius strain NCTC11048 16S ribosomal RNA gene, partial sequenceEU157207366ena1141106
20218S.intermedius gene for 16S ribosomal RNAZ26897771ena1141106
8627Staphylococcus intermedius gene for 16S rRNA, partial sequence, strain: ATCC 29663 (= MAFF 911388)D833691476ena1141106

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus intermedius NCTC 110481141106.7wgspatric1141106
66792Staphylococcus intermedius NCTC 110481141106.9wgspatric1141106
66792Staphylococcus intermedius NCTC 11048 strain NCTC110481141106.10wgspatric1141106
66792Staphylococcus intermedius NCTC 110482548876980draftimg1141106
66792Staphylococcus intermedius NCTC 110482917485323draftimg1141106
66792Staphylococcus intermedius NCTC 110482917445263draftimg1141106
67770Staphylococcus intermedius NCTC 11048GCA_000308095contigncbi1141106
67770Staphylococcus intermedius NCTC 11048GCA_002902385scaffoldncbi1141106
67770Staphylococcus intermedius NCTC 11048GCA_900458545contigncbi1141106

GC content

  • @ref: 8627
  • GC-content: 36.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
motileno91.165no
flagellatedno89.828no
gram-positiveyes89.972no
anaerobicno99.293no
aerobicyes90.158no
halophileyes90.074no
spore-formingno83.679no
glucose-utilyes87.631no
thermophileno99.724no
glucose-fermentyes83.445yes

External links

@ref: 8627

culture collection no.: DSM 20373, ATCC 29663, CCM 5739, NCTC 11048, JCM 2422, BCRC 12157, CCUG 27191, CCUG 6520, CECT 7205, CIP 81.60, CNCTC M16/75, KCTC 3344, LMG 13351, MTCC 6152, NRRL B-14754, GIFU 8781

straininfo link

  • @ref: 83686
  • straininfo: 7371

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity2007645Phage typing of Staphylococcus intermedius.Overturf GD, Talan DA, Singer K, Anderson N, Miller JI, Greene RT, Froman SJ Clin Microbiol10.1128/jcm.29.2.373-375.19911991Animals, *Bacterial Typing Techniques, Bacteriophages/*genetics, Dogs, Gingiva/microbiology, Humans, Lysogeny, Staphylococcal Infections/microbiology, Staphylococcus/*classification/genetics/isolation & purification, Wound Infection/microbiologyPhylogeny
Phylogeny17596353Reclassification of phenotypically identified staphylococcus intermedius strains.Sasaki T, Kikuchi K, Tanaka Y, Takahashi N, Kamata S, Hiramatsu KJ Clin Microbiol10.1128/JCM.00360-072007Animal Diseases/microbiology, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cats, Chaperonin 60/genetics, Cluster Analysis, Columbidae, DNA, Bacterial/chemistry/*genetics, Disaccharides/metabolism, Dogs, Endonucleases/genetics, Horses, Humans, Hydrolases/analysis, Mannitol/metabolism, Micrococcal Nuclease/genetics, Mink, Nucleic Acid Hybridization, *Phylogeny, Sequence Analysis, DNA, Staphylococcal Infections/microbiology/veterinary, Staphylococcus/*classification/*genetics/isolation & purification/metabolism, Superoxide Dismutase/geneticsMetabolism
Phylogeny32672529Staphylococcus ursi sp. nov., a new member of the 'Staphylococcus intermedius group' isolated from healthy black bears.Perreten V, Kania SA, Bemis DInt J Syst Evol Microbiol10.1099/ijsem.0.0043242020Animals, 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8627Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20373)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20373
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
37296Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11224
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
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)
83686Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7371.1StrainInfo: A central database for resolving microbial strain identifiers
120154Curators of the CIPCollection of Institut Pasteur (CIP 81.60)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.60