Strain identifier

BacDive ID: 14664

Type strain: No

Species: Mammaliicoccus sciuri

Strain Designation: R1-33, BM 12492

Strain history: CIP <- 1999, N. El Solh, Inst. Pasteur, Paris, France: strain BM 12492 <- W. Kloos: strain R1-33

NCBI tax ID(s): 1296 (species)

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: 6619

BacDive-ID: 14664

DSM-Number: 16827

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

description: Mammaliicoccus sciuri R1-33 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from skin of a Norway rat.

NCBI tax id

  • NCBI tax id: 1296
  • Matching level: species

strain history

@refhistory
6619<- CIP <- W. E. Kloos; R1-33
122520CIP <- 1999, N. El Solh, Inst. Pasteur, Paris, France: strain BM 12492 <- W. Kloos: strain R1-33

doi: 10.13145/bacdive14664.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Mammaliicoccus
  • species: Mammaliicoccus sciuri
  • full scientific name: Mammaliicoccus sciuri (Kloos et al. 1976) Madhaiyan et al. 2020
  • synonyms

    @refsynonym
    20215Staphylococcus sciuri
    20215Staphylococcus sciuri subsp. rodentium
    20215Staphylococcus sciuri subsp. carnaticus

@ref: 6619

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Staphylococcaceae

genus: Mammaliicoccus

species: Mammaliicoccus sciuri

full scientific name: Mammaliicoccus sciuri (Kloos et al. 1976) Madhaiyan et al. 2020

strain designation: R1-33, BM 12492

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122520positivecoccus-shapedno

colony morphology

@reftype of hemolysishemolysis ability
6619gamma
1225201

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6619COLUMBIA 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
6619TRYPTICASE 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
42116MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122520CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6619positivegrowth37mesophilic
42116positivegrowth37mesophilic
53957positivegrowth37mesophilic
122520positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53957aerobe
122520facultative anaerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.63

murein

  • @ref: 6619
  • murein short key: A11.63
  • type: A3alpha L-Lys-L-Ala-Gly3, L-Ser0-1

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-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
68371methyl alpha-D-glucopyranoside-builds acid from320061
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
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
122520hippurate+hydrolysis606565
122520nitrate+reduction17632
122520nitrite-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
12252035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837515688acetoin-
12252015688acetoin-

enzymes

@refvalueactivityec
68375beta-glucuronidase+3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
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
122520oxidase-
122520beta-galactosidase-3.2.1.23
122520alcohol dehydrogenase-1.1.1.1
122520gelatinase-
122520amylase-
122520DNase-
122520caseinase+3.4.21.50
122520catalase+1.11.1.6
122520coagulase-
122520tween esterase+
122520gamma-glutamyltransferase-2.3.2.2
122520lecithinase-
122520lipase-
122520lysine decarboxylase-4.1.1.18
122520ornithine decarboxylase-4.1.1.17
122520phenylalanine ammonia-lyase-4.3.1.24
122520protease+
122520tryptophan deaminase-
122520urease-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
122520-+++-+----++--++++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122520+---+----+/-+++---+/-++--+/-+/-+++++--++------++--+/----+/---

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
6619---+++++-++-+++---+/--++++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122520++-+---+-++----+++++--+--------++++++----+---+---+----+----++------------+-+--+++-----+--++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
6619skin of a Norway ratUSAUSANorth America
53957Norway rat1992
122520Animal, Rat

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_116.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_96;98_105;99_116&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AB233332
  • Sequence Identity:
  • Total samples: 7505
  • soil counts: 269
  • aquatic counts: 251
  • animal counts: 6869
  • plant counts: 116

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
6619yes, in single casesyes1Risk group (German classification)
1225201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus sciuri subsp. rodentium strain ATCC 700061 16S ribosomal RNA gene, partial sequenceAY688096465ena147469
6619Staphylococcus sciuri subsp. rodentium gene for 16S rRNA, partial sequence, strain: GTC 844AB2333321460ena147469

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mammaliicoccus sciuri CCUG 37923GCA_003968855scaffoldncbi1296
66792Staphylococcus sciuri subsp. rodentium strain CCUG 37923147469.3wgspatric1296

GC content

  • @ref: 6619
  • GC-content: 35.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
flagellatedno94.074no
gram-positiveyes92.965no
anaerobicno99.629yes
aerobicyes94.73no
halophileyes92.618no
spore-formingno86.578no
thermophileno99.816yes
glucose-utilyes86.741no
motileno88.204no
glucose-fermentyes73.07yes

External links

@ref: 6619

culture collection no.: DSM 16827, ATCC 700061, CIP 105829, CCUG 37923, CCM 4657

straininfo link

  • @ref: 83790
  • straininfo: 45397

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6619Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16827)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16827
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
42116Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17892
53957Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37923)https://www.ccug.se/strain?id=37923
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)
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
83790Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45397.1StrainInfo: A central database for resolving microbial strain identifiers
122520Curators of the CIPCollection of Institut Pasteur (CIP 105829)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105829