Strain identifier

BacDive ID: 14830

Type strain: Yes

Species: Streptococcus massiliensis

Strain Designation: 4401825

Strain history: CIP <- 2004, V. Roux, Hosp. La Timone, Marseille, France: strain 4401825

NCBI tax ID(s): 1123307 (strain), 313439 (species)

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General

@ref: 7628

BacDive-ID: 14830

DSM-Number: 18628

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped, human pathogen

description: Streptococcus massiliensis 4401825 is a microaerophile, mesophilic, Gram-positive human pathogen that was isolated from patient blood culture.

NCBI tax id

NCBI tax idMatching level
313439species
1123307strain

strain history

@refhistory
7628<- CCUG <- V. Roux
343242004, V. Roux, Hosp. La Timone, Marseille, France: strain 4401825
120855CIP <- 2004, V. Roux, Hosp. La Timone, Marseille, France: strain 4401825

doi: 10.13145/bacdive14830.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Streptococcaceae
  • genus: Streptococcus
  • species: Streptococcus massiliensis
  • full scientific name: Streptococcus massiliensis Glazunova et al. 2006

@ref: 7628

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus massiliensis

full scientific name: Streptococcus massiliensis Glazunova et al. 2006

strain designation: 4401825

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31667positive03-0.7 µmcoccus-shapedno
69480no97.293
69480positive100
120855positivecoccus-shapedno

colony morphology

@refincubation period
76281-2 days
120855

pigmentation

  • @ref: 31667
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7628COLUMBIA 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
34324MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120855CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
7628positivegrowth37mesophilic
31667positivegrowth25-37mesophilic
31667positiveoptimum37mesophilic
34324positivegrowth37mesophilic
58657positivegrowth37mesophilic
120855positivegrowth25-41
120855nogrowth10psychrophilic
120855nogrowth45thermophilic

culture pH

@refabilitytypepH
31667positivegrowth7
31667positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7628microaerophile
31667facultative anaerobe
58657anaerobe
58657microaerophile
120855facultative anaerobe

spore formation

@refspore formationconfidence
31667no
69481no99
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
31667NaClpositivegrowth2 %
31667NaClpositiveoptimum2 %
120855NaClnogrowth6.5 %

observation

  • @ref: 31667
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3166717306maltose+carbon source
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1208554853esculin-hydrolysis
120855606565hippurate+hydrolysis
12085517632nitrate-reduction
12085516301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine+hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838129016arginine+hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838117992sucrose-builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate+hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

antibiotic resistance

  • @ref: 120855
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-
12085515688acetoin-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase+3.5.3.6
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase+3.5.3.6
68380urease-3.5.1.5
120855oxidase-
120855beta-galactosidase-3.2.1.23
120855alcohol dehydrogenase+1.1.1.1
120855catalase-1.11.1.6
120855gamma-glutamyltransferase-2.3.2.2
120855lysine decarboxylase-4.1.1.18
120855ornithine decarboxylase-4.1.1.17
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
120855-+++-++---++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120855------------------------------------------------+/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7628-+--------+-----++--++-++++-+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
7628+----+-----------+---++---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7628patient blood cultureMarseilleFranceFRAEurope
58657Human wound,cranianMarseilleFranceFRAEurope2004-07-02
120855Human, Crane wound2004

isolation source categories

  • Cat1: #Infection
  • Cat2: #Patient
  • Cat3: #Blood culture

taxonmaps

  • @ref: 69479
  • File name: preview.99_2732.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4;96_1453;97_1734;98_2119;99_2732&stattab=map
  • Last taxonomy: Streptococcus massiliensis subclade
  • 16S sequence: AY769997
  • Sequence Identity:
  • Total samples: 6944
  • soil counts: 92
  • aquatic counts: 729
  • animal counts: 6051
  • plant counts: 72

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
7628yes, in single cases1Risk group (German classification)
1208552Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7628
  • description: Streptococcus massiliensis strain 4401825 16S ribosomal RNA gene, partial sequence
  • accession: AY769997
  • length: 1470
  • database: ena
  • NCBI tax ID: 313439

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus massiliensis 4401825GCA_000341525contigncbi1194208
66792Streptococcus massiliensis DSM 18628GCA_000380065scaffoldncbi1123307
66792Streptococcus massiliensis 44018251194208.3wgspatric1194208
66792Streptococcus massiliensis DSM 186281123307.3wgspatric1123307
66792Streptococcus massiliensis DSM 186282515154013draftimg1123307
66792Streptococcus massiliensis 44018252551306662draftimg1194208

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno95.396yes
flagellatedno95.99yes
gram-positiveyes92.59yes
anaerobicno91.871no
aerobicno98.002yes
halophileyes81.952no
spore-formingno93.933yes
thermophileno99.07no
glucose-utilyes86.429no
glucose-fermentyes86.319no

External links

@ref: 7628

culture collection no.: DSM 18628, CCUG 49690, CIP 108498

straininfo link

  • @ref: 83946
  • straininfo: 291009

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627666Streptococcus massiliensis sp. nov., isolated from a patient blood culture.Glazunova OO, Raoult D, Roux VInt J Syst Evol Microbiol10.1099/ijs.0.64009-02006Bacterial Proteins/genetics, Bacterial Typing Techniques, Blood/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Genes, rRNA, Humans, Male, Middle Aged, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Streptococcal Infections/*microbiology, Superoxide Dismutase/genetics, Viridans Streptococci/*classification/genetics/*isolation & purification/physiologyPathogenicity
Phylogeny26651833Streptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin.Saito M, Shinozaki-Kuwahara N, Hirasawa M, Takada KInt J Syst Evol Microbiol10.1099/ijsem.0.0008342015Animals, Bacterial Typing Techniques, Base Composition, Cebus/*microbiology, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Genes, Bacterial, Mouth/*microbiology, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptococcus/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7628Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18628)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18628
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
31667Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2794728776041
34324Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6126
58657Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49690)https://www.ccug.se/strain?id=49690
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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
83946Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291009.1StrainInfo: A central database for resolving microbial strain identifiers
120855Curators of the CIPCollection of Institut Pasteur (CIP 108498)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108498