Strain identifier

BacDive ID: 1869

Type strain: Yes

Species: Brevibacterium ravenspurgense

Strain Designation: 20

Strain history: CCUG 56047 <-- G. Funke 20.

NCBI tax ID(s): 479117 (species)

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General

@ref: 15500

BacDive-ID: 1869

DSM-Number: 21258

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

description: Brevibacterium ravenspurgense 20 is a microaerophile, mesophilic, Gram-positive human pathogen that forms irregular colonies and was isolated from wound swab, 45-year-old male patient.

NCBI tax id

  • NCBI tax id: 479117
  • Matching level: species

strain history

@refhistory
15500<- G. Funke, Gärtner & Colleagues Laboratories, Ravensburg, Germany; 20
67770CCUG 56047 <-- G. Funke 20.

doi: 10.13145/bacdive1869.20230509.8.1

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: 15500

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: 20

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24964positive0.4-1.4 µm0.3-0.5 µmrod-shapedno
69480no92.865
69480positive100

colony morphology

  • @ref: 24964
  • type of hemolysis: CAMP test
  • hemolysis ability: 1
  • colony size: 0.2-2.0 mm
  • colony color: greyish-white or beige
  • colony shape: irregular
  • medium used: air supplemented with 5 % CO 2

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15500TRYPTICASE 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
24964tryptic soy, brain–heart infusion and nutrient brothyes
24964air supplemented with 5 % CO 2yes

culture temp

@refgrowthtypetemperaturerange
15500positivegrowth35mesophilic
24964positivegrowth25-42
60844positivegrowth37mesophilic
67770positivegrowth35mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60844
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

  • @ref: 24964
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10.0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
24964739183-O-methyl-D-glucose-respiration
2496440585alpha-cyclodextrin-respiration
2496436219alpha-lactose-respiration
2496427613amygdalin-respiration
2496418305arbutin-respiration
24964495055beta-cyclodextrin-respiration
2496415903beta-d-glucose-respiration
2496417057cellobiose-respiration
2496418333D-arabitol-respiration
2496415824D-fructose-respiration
2496412936D-galactose-respiration
2496418024D-galacturonic acid-respiration
249648391D-gluconate-respiration
2496416899D-mannitol-respiration
2496416024D-mannose-respiration
2496427605D-psicose-respiration
2496417924D-sorbitol-respiration
2496423652dextrin-respiration
2496428066gentiobiose-respiration
2496428087glycogen-respiration
2496417268myo-inositol-respiration
2496430849L-arabinose-respiration
2496418287L-fucose-respiration
2496462345L-rhamnose-respiration
249646359lactulose-respiration
2496417306maltose-respiration
2496461993maltotriose-respiration
2496428808mannan-respiration
249646731melezitose-respiration
2496428053melibiose-respiration
2496455507methyl alpha-D-galactoside-respiration
24964320061methyl alpha-D-glucopyranoside-respiration
2496443943methyl alpha-D-mannoside-respiration
2496417540methyl beta-D-galactoside-respiration
24964320055methyl beta-D-glucopyranoside-respiration
24964506227N-acetylglucosamine-respiration
2496417632nitrate-reduction
2496416301nitrite-reduction
2496418394palatinose-respiration
2496416634raffinose-respiration
2496417814salicin-respiration
2496432488sedoheptulosan-respiration
2496417164stachyose-respiration
24964645522-hydroxybutyrate+respiration
24964286442-oxopentanoate+respiration
24964620642,3-butanediol+respiration
2496430089acetate+respiration
2496415570D-alanine+respiration
249644853esculin+hydrolysis
249645291gelatin+hydrolysis
2496421217L-alaninamide+respiration
2496416977L-alanine+respiration
2496473786L-alanylglycine+respiration
2496417196L-asparagine+respiration
2496429985L-glutamate+respiration
2496417115L-serine+respiration
2496424996lactate+respiration
2496451850methyl pyruvate+respiration
2496475146monomethyl succinate+respiration
2496444337N-acetyl-L-glutamate+respiration
2496473784glycyl-l-glutamate+respiration
2496417272propionate+respiration
2496415361pyruvate+respiration
2496453423tween 40+respiration
2496453426tween 80+respiration

enzymes

@refvalueactivityec
249646-phospho-beta-galactosidase-3.2.1.85
24964acid phosphatase-3.1.3.2
24964alanine arylamidase+3.4.11.2
24964alkaline phosphatase-3.1.3.1
24964alpha-arabinosidase-3.2.1.55
24964alpha-chymotrypsin-3.4.21.1
24964alpha-fucosidase-3.2.1.51
24964alpha-galactosidase-3.2.1.22
24964alpha-glucosidase-3.2.1.20
24964alpha-mannosidase-3.2.1.24
24964arginine arylamidase+
24964arginine dihydrolase-3.5.3.6
24964beta-galactosidase-3.2.1.23
24964beta-glucosidase-3.2.1.21
24964beta-glucuronidase-3.2.1.31
24964catalase+1.11.1.6
24964cystine arylamidase-3.4.11.3
24964cytochrome oxidase-1.9.3.1
24964esterase (C 4)+
24964esterase lipase (C 8)+
24964glutamyl-glutamate arylamidase-
24964glycin arylamidase+
24964histidine arylamidase+
24964leucine arylamidase+3.4.11.1
24964leucyl glycin arylamidase+3.4.11.1
24964lipase (C 14)-
24964N-acetyl-beta-glucosaminidase-3.2.1.52
24964naphthol-AS-BI-phosphohydrolase+/-
24964phenylalanine arylamidase+
24964proline-arylamidase+3.4.11.5
24964pyrazinamidase+3.5.1.B15
24964pyroglutamic acid arylamidase-
24964pyrrolidonyl arylamidase-3.4.19.3
24964serine arylamidase+
24964trypsin-3.4.21.4
24964tyrosine arylamidase+
24964urease-3.5.1.5
24964valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture durationenrichment culture temperaturesampling date
15500wound swab, 45-year-old male patientRavensburgGermanyDEUEurope
249642 days35
60844Human wound,45-yr-old maleRavensburgGermanyDEUEurope1998
67770Wound swab (45-year-old male)

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Infection#Patient#Swab
#Host Body-Site#Other#Wound
#Host#Human#Male

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: EU086793
  • Sequence Identity:
  • Total samples: 27187
  • soil counts: 1174
  • aquatic counts: 1902
  • animal counts: 23611
  • plant counts: 500

Safety information

risk assessment

  • @ref: 15500
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15500
  • description: Brevibacterium ravenspurgense strain 20 16S ribosomal RNA gene, partial sequence
  • accession: EU086793
  • length: 1470
  • database: ena
  • NCBI tax ID: 479117

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevibacterium ravenspurgense strain CCUG56047479117.4wgspatric479117
66792Brevibacterium ravenspurgense CCUG 560472744054563draftimg479117
67770Brevibacterium ravenspurgense CCUG56047GCA_001584615contigncbi479117

GC content

@refGC-contentmethod
2496462.3
2496462.4
1550062.4sequence analysis
6777062.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes92.085no
anaerobicno98.079yes
halophileyes79.633no
spore-formingno93.722no
glucose-utilyes80.46no
aerobicyes89.05no
thermophileno99.016yes
motileno92.577yes
flagellatedno98.043yes
glucose-fermentno88.837no

External links

@ref: 15500

culture collection no.: DSM 21258, CCUG 56047, JCM 19110

straininfo link

  • @ref: 71514
  • straininfo: 406356

literature

  • topic: Phylogeny
  • Pubmed-ID: 27498845
  • title: Brevibacterium massiliense (Roux and Raoult 2009) is a later heterotypic synonym of Brevibacterium ravenspurgense (Mages, Frodl, Bernard and Funke 2009), using whole-genome sequence analysis as a comparative tool.
  • authors: Bernard KA, Pacheco AL, Burdz T, Wiebe D, Huynh C, Bonner C, German GJ, Bernier AM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001371
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Brevibacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Urine/*microbiology
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15500Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21258)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21258
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
24964K. A. P. Bernard, Ana Luisa,Burdz, Tamara,Wiebe, Deborah,Huynh, Chris,Bonner, Christine,German, Greg J.,Bernier, Anne-Marie10.1099/ijsem.0.001371Brevibacterium massiliense (Roux and Raoult 2009) is a later heterotypic synonym of Brevibacterium ravenspurgense (Mages, Frodl, Bernard and Funke 2009), using whole-genome sequence analysis as a comparative toolIJSEM 66: 4440-4444 201627498845
60844Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56047)https://www.ccug.se/strain?id=56047
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
71514Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406356.1StrainInfo: A central database for resolving microbial strain identifiers