Strain identifier

BacDive ID: 14673

Type strain: Yes

Species: Staphylococcus massiliensis

Strain Designation: 5402776

Strain history: <- CCUG <- V. Roux, Timone Hospital, Marseille, France

NCBI tax ID(s): 1189613 (strain), 555791 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17364

BacDive-ID: 14673

DSM-Number: 23764

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

description: Staphylococcus massiliensis 5402776 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human brain abscess.

NCBI tax id

NCBI tax idMatching level
555791species
1189613strain

strain history

  • @ref: 17364
  • history: <- CCUG <- V. Roux, Timone Hospital, Marseille, France

doi: 10.13145/bacdive14673.20230509.8.1

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 massiliensis
  • full scientific name: Staphylococcus massiliensis Al Masalma et al. 2010

@ref: 17364

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus massiliensis

full scientific name: Staphylococcus massiliensis Al Masalma et al. 2010

strain designation: 5402776

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
29110positive0.65 µmcoccus-shapedno
69480positive100

colony morphology

  • @ref: 17364
  • type of hemolysis: gamma

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17364COLUMBIA 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
17364TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
17364positivegrowth37mesophilic
29110positivegrowth25-45
29110positiveoptimum33.5mesophilic
60797positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29110aerobe
60797microaerophile

spore formation

@refspore formationconfidence
29110no
69481no100
69480no99.864

halophily

  • @ref: 29110
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-15 %

observation

  • @ref: 29110
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2911016449alanine+carbon source
29110286442-oxopentanoate+carbon source
2911022599arabinose+carbon source
2911017234glucose+carbon source
2911029987glutamate+carbon source
2911017754glycerol+carbon source
2911017596inosine+carbon source
2911024996lactate+carbon source
2911015361pyruvate+carbon source
2911051850methyl pyruvate+carbon source
2911033942ribose+carbon source
2911017822serine+carbon source
2911017632nitrate+reduction
6837516199urea-hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose-fermentation
6837515824D-fructose-fermentation
6837516024D-mannose-fermentation
6837517306maltose-fermentation
6837517716lactose-fermentation
6837527082trehalose-fermentation
6837516899D-mannitol-fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate+reduction
6837517992sucrose-fermentation
6837559640N-acetylglucosamine-fermentation
6837532528turanose-fermentation
6837522599arabinose-fermentation

antibiotic resistance

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

metabolite production

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
17364catalase+1.11.1.6
17364cytochrome-c oxidase-1.9.3.1
29110catalase+1.11.1.6
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

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
17364--------------+-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17364human brain abscessMarseilleFranceFRAEurope
60797Human brain abscess (or contamination ?)Marseille,Timone hospitalFranceFRAEurope2005-12-01

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Brain
#Host Body-Site#Other#Abscess
#Infection#Patient

Safety information

risk assessment

  • @ref: 17364
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17364
  • description: Staphylococcus massiliensis strain CCUG 55927 16S ribosomal RNA gene, partial sequence
  • accession: EU707796
  • length: 1477
  • database: ena
  • NCBI tax ID: 1189613

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus massiliensis CCUG 55927GCA_000298075scaffoldncbi1189613
66792Staphylococcus massiliensis CCUG 55927GCA_002902705scaffoldncbi1189613
66792Staphylococcus massiliensis CCUG 559271189613.4wgspatric1189613
66792Staphylococcus massiliensis CCUG 559271189613.3wgspatric1189613
66792Staphylococcus massiliensis CCUG 559272551306057draftimg1189613
66792Staphylococcus massiliensis CCUG 559272917458906draftimg1189613

GC content

@refGC-contentmethod
1736436.6high performance liquid chromatography (HPLC)
2911036.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.583yes
flagellatedno93.055yes
gram-positiveyes92.135yes
anaerobicno99.399yes
aerobicyes91.032no
halophileyes95.927no
spore-formingno90.941yes
glucose-utilyes85.782no
thermophileno99.402no
glucose-fermentyes66.447no

External links

@ref: 17364

culture collection no.: DSM 23764, CCUG 55927, CSUR P23, CCM 7895

straininfo link

  • @ref: 83799
  • straininfo: 369641

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19666814Staphylococcus massiliensis sp. nov., isolated from a human brain abscess.Al Masalma M, Raoult D, Roux VInt J Syst Evol Microbiol10.1099/ijs.0.006486-02009Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Brain Abscess/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Humans, Male, Middle Aged, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Staphylococcal Infections/*microbiology, Staphylococcus/*classification/genetics/*isolation & purification/physiologyGenetics
Genetics23209235Draft genome sequence of Staphylococcus massiliensis strain 5402776T.Roux V, Robert C, Gimenez G, Raoult DJ Bacteriol10.1128/JB.01909-122012Base Composition, Base Sequence, Brain Abscess/microbiology, DNA, Bacterial/genetics, *Genome, Bacterial, Humans, Inverted Repeat Sequences/genetics, Molecular Sequence Data, Proviruses/genetics, RNA, Bacterial/genetics, Sequence Analysis, DNA, Staphylococcal Infections/microbiology, Staphylococcus/*genetics/isolation & purification, Transposases/geneticsPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17364Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23764)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23764
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
29110Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2553828776041
60797Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55927)https://www.ccug.se/strain?id=55927
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)
68375Automatically annotated from API ID32STA
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
83799Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID369641.1StrainInfo: A central database for resolving microbial strain identifiers