Strain identifier

BacDive ID: 14657

Type strain: Yes

Species: Staphylococcus hominis subsp. novobiosepticus

Strain Designation: R22

Strain history: CIP <- 1998, C. George, North Carolina State Univ., Raleigh, NC, USA: strain R22 <- W. Kloos

NCBI tax ID(s): 145393 (subspecies)

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General

@ref: 5932

BacDive-ID: 14657

DSM-Number: 15614

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

description: Staphylococcus hominis subsp. novobiosepticus R22 is an aerobe, Gram-positive bacterium that was isolated from human blood.

NCBI tax id

  • NCBI tax id: 145393
  • Matching level: subspecies

strain history

@refhistory
5932<- ATCC <- W. E. Kloos; R22
119951CIP <- 1998, C. George, North Carolina State Univ., Raleigh, NC, USA: strain R22 <- W. Kloos

doi: 10.13145/bacdive14657.20240916.9.1

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 hominis subsp. novobiosepticus
  • full scientific name: Staphylococcus hominis subsp. novobiosepticus Kloos et al. 1998

@ref: 5932

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus hominis subsp. novobiosepticus

full scientific name: Staphylococcus hominis subsp. novobiosepticus Kloos et al. 1998

strain designation: R22

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119951positivecoccus-shapedno
69480positive90.578

colony morphology

@reftype of hemolysisincubation period
5932gamma1-2 days
119951

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5932COLUMBIA 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
5932TRYPTICASE 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
34064MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119951CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
5932positivegrowth37
34064positivegrowth30
55419positivegrowth30
119951positivegrowth22-41
119951nogrowth10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55419aerobe
119951facultative anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

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
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
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
119951hippurate+hydrolysis606565
119951nitrate+reduction17632
119951nitrite-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
6837515688acetoinyes
11995135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837515688acetoin+
11995115688acetoin-

enzymes

@refvalueactivityec
5932catalase+1.11.1.6
5932cytochrome-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
119951oxidase-
119951beta-galactosidase+3.2.1.23
119951alcohol dehydrogenase-1.1.1.1
119951gelatinase+/-
119951amylase-
119951DNase-
119951caseinase-3.4.21.50
119951catalase+1.11.1.6
119951coagulase-
119951tween esterase-
119951gamma-glutamyltransferase-2.3.2.2
119951lecithinase+
119951lipase-
119951lysine decarboxylase-4.1.1.18
119951ornithine decarboxylase-4.1.1.17
119951phenylalanine ammonia-lyase-4.3.1.24
119951protease-
119951tryptophan deaminase-
119951urease+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
119951-+++------++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119951+--------+++---------------++-+--+/------+---------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
5932+---++-++-----++----++-+--
5932+---++-++-----++----++-+-
5932+---++-++-----++----++-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119951+++----+-+++++-----------------+---+------------------------+--------------+------------------+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
5932human bloodNew JerseyUSAUSANorth America
55419Human bloodUSAUSANorth America1992
119951BloodUnited States of AmericaUSANorth America1992

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59322Risk group (German classification)
1199511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Staphylococcus hominis subsp. novobiosepticus strain ATCC 700236 16S ribosomal RNA gene, partial sequence
  • accession: AY688065
  • length: 464
  • database: nuccore
  • NCBI tax ID: 145393

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus hominis subsp. novobiosepticus CCUG 42399GCA_002902465scaffoldncbi145393
66792Staphylococcus hominis subsp. novobiosepticus strain CCUG 42399145393.3wgspatric145393

GC content

  • @ref: 5932
  • GC-content: 35

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.578no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.861yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes64.081no
69480spore-formingspore-formingAbility to form endo- or exosporesno74.078no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.192no
69480flagellatedmotile2+Ability to perform flagellated movementno81.034no

External links

@ref: 5932

culture collection no.: DSM 15614, ATCC 700236, CCUG 42399, CIP 105719

straininfo link

  • @ref: 83783
  • straininfo: 45414

literature

  • topic: Pathogenicity
  • Pubmed-ID: 9734034
  • title: Staphylococcus hominis subsp. novobiosepticus subsp. nov., a novel trehalose- and N-acetyl-D-glucosamine-negative, novobiocin- and multiple-antibiotic-resistant subspecies isolated from human blood cultures.
  • authors: Kloos WE, George CG, Olgiate JS, Van Pelt L, McKinnon ML, Zimmer BL, Muller E, Weinstein MP, Mirrett S
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-3-799
  • year: 1998
  • mesh: Acetylglucosamine/analysis, Bacteremia/*microbiology, Bacterial Proteins/genetics, Base Composition, Base Sequence, DNA, Bacterial/analysis, Drug Resistance, Microbial, Humans, Molecular Sequence Data, Novobiocin/pharmacology, Phenotype, Plasmids, Restriction Mapping, Staphylococcus/chemistry/*classification/drug effects, Trehalose/analysis
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5932Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15614)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15614
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
34064Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17770
55419Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42399)https://www.ccug.se/strain?id=42399
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
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
83783Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45414.1StrainInfo: A central database for resolving microbial strain identifiers
119951Curators of the CIPCollection of Institut Pasteur (CIP 105719)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105719