Strain identifier

BacDive ID: 1843

Type strain: No

Species: Brevibacterium ravenspurgense

Strain Designation: 5401308

Strain history: CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 5401308

NCBI tax ID(s): 479117 (species)

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General

@ref: 16665

BacDive-ID: 1843

DSM-Number: 23039

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

description: Brevibacterium ravenspurgense 5401308 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from human ankle discharge sample.

NCBI tax id

  • NCBI tax id: 479117
  • Matching level: species

strain history

@refhistory
375502006, V. Roux, Timone Hosp., Marseille, France: strain 5401308
16665<- CCUG
67770CIP 109422 <-- V. Roux 5401308.
120846CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 5401308

doi: 10.13145/bacdive1843.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Brevibacteriaceae
  • genus: Brevibacterium
  • species: Brevibacterium ravenspurgense
  • full scientific name: Brevibacterium ravenspurgense Mages et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Brevibacterium massiliense

@ref: 16665

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Brevibacteriaceae

genus: Brevibacterium

species: Brevibacterium ravenspurgense

full scientific name: Brevibacterium ravenspurgense Mages et al. 2009 emend. Bernard et al. 2016

strain designation: 5401308

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29171positive0.9 µm0.4 µmrod-shapedno
69480no92.717
69480positive100
120846positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19801Beige10-14 daysISP 2
1980110-14 daysISP 3
19801Grey white10-14 daysISP 4
19801Grey white10-14 daysISP 5
19801Green brown10-14 daysISP 6
19801Grey white10-14 daysISP 7
600361 day
1208461

multicellular morphology

@refforms multicellular complexmedium name
19801noISP 2
19801noISP 3
19801noISP 4
19801noISP 5
19801noISP 6
19801noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16665TRYPTICASE 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
19801ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19801ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19801ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19801ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19801ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19801ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37550MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120846CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
19801positiveoptimum28mesophilic
16665positivegrowth28mesophilic
29171positivegrowth25-45
29171positiveoptimum34mesophilic
37550positivegrowth37mesophilic
60036positivegrowth30-42
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29171aerobe
60036aerobe
120846facultative anaerobe

spore formation

@refspore formationconfidence
29171no
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
29171NaClpositivegrowth<15 %
29171NaClpositiveoptimum01-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1980162968cellulose-
1980116634raffinose+/-
1980126546rhamnose+/-
1980128757fructose+
1980129864mannitol+
1980117268myo-inositol+
1980118222xylose+
1980117992sucrose+
1980122599arabinose+
1980117234glucose+
29171620642,3-butanediol+carbon source
2917116449alanine+carbon source
29171286442-oxopentanoate+carbon source
2917122653asparagine+carbon source
2917129987glutamate+carbon source
2917151850methyl pyruvate+carbon source
2917117822serine+carbon source
2917130031succinate+carbon source
2917153423tween 40+carbon source
2917153426tween 80+carbon source
68371Potassium 5-ketogluconate-builds acid from
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
12084617632nitrate-reduction
12084616301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 120846
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29171catalase+1.11.1.6
29171pyrazinamidase+3.5.1.B15
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
120846oxidase-
120846catalase+1.11.1.6
120846urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19801----------+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19801+++-++-+-++--------
120846+++-++-+-++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120846-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
16665human ankle discharge sampleMarseilleFranceFRAEurope
60036Human external fixerMarseille,Timone hospitalFranceFRAEurope2005-06-01
67770Human ankle dischargeMarseilleFranceFRAEurope
120846HumanMarseilleFranceFRAEurope2005

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Limb#Foot
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_1637.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15817;96_933;97_1085;98_1294;99_1637&stattab=map
  • Last taxonomy: Brevibacterium ravenspurgense subclade
  • 16S sequence: EU868814
  • Sequence Identity:
  • Total samples: 27187
  • soil counts: 1174
  • aquatic counts: 1902
  • animal counts: 23611
  • plant counts: 500

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
16665yes, in single cases1Risk group (German classification)
1208461Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16665
  • description: Brevibacterium sp. 5401308 16S ribosomal RNA gene, partial sequence
  • accession: EU868814
  • length: 1450
  • database: ena
  • NCBI tax ID: 1176165

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevibacterium massiliense 5401308 = CCUG 538551176165.5wgspatric1176165
66792Brevibacterium ravenspurgense CCUG 538552744054970draftimg1176165
67770Brevibacterium ravenspurgense 5401308 = CCUG 53855GCA_000285915contigncbi1176165
67770Brevibacterium ravenspurgense 5401308 = CCUG 53855GCA_001584405contigncbi1176165

GC content

@refGC-contentmethod
1666562.3sequence analysis
6777062.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.181yes
gram-positiveyes92.452yes
anaerobicno98.302no
halophileyes84.549yes
spore-formingno92.46yes
flagellatedno98.296yes
glucose-utilyes81.816yes
aerobicyes87.524no
thermophileno98.814yes
glucose-fermentno88.322yes

External links

@ref: 16665

culture collection no.: DSM 23039, CCUG 53855, CIP 109422, CSUR P26, JCM 18108

straininfo link

  • @ref: 71488
  • straininfo: 364120

literature

  • topic: Phylogeny
  • Pubmed-ID: 19567570
  • title: Brevibacterium massiliense sp. nov., isolated from a human ankle discharge.
  • authors: Roux V, Raoult D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.007864-0
  • year: 2009
  • mesh: Ankle/*microbiology, Bacterial Typing Techniques, Brevibacterium/chemistry/*classification/genetics/*isolation & purification, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Exudates and Transudates/*microbiology, Fatty Acids/analysis, Gram-Positive Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16665Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23039)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23039
19801Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23039.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
29171Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2559528776041
37550Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7162
60036Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53855)https://www.ccug.se/strain?id=53855
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
71488Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364120.1StrainInfo: A central database for resolving microbial strain identifiers
120846Curators of the CIPCollection of Institut Pasteur (CIP 109422)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109422