Strain identifier

BacDive ID: 3911

Type strain: Yes

Species: Brachybacterium fresconis

Strain Designation: R-5509

Strain history: CIP <- 2004, JCM <- 2003, LMG <- J. Heyrman: strain R-5509

NCBI tax ID(s): 173363 (species)

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General

@ref: 5386

BacDive-ID: 3911

DSM-Number: 14564

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

description: Brachybacterium fresconis R-5509 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from mural painting.

NCBI tax id

  • NCBI tax id: 173363
  • Matching level: species

strain history

@refhistory
5386<- J. Heyrman; R-5509
67770LMG 20336 <-- J. Heyrman R-5509.
119454CIP <- 2004, JCM <- 2003, LMG <- J. Heyrman: strain R-5509

doi: 10.13145/bacdive3911.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermabacteraceae
  • genus: Brachybacterium
  • species: Brachybacterium fresconis
  • full scientific name: Brachybacterium fresconis Heyrman et al. 2002

@ref: 5386

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium fresconis

full scientific name: Brachybacterium fresconis Heyrman et al. 2002

strain designation: R-5509

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119454positiveovoid-shapedno

colony morphology

  • @ref: 119454

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5386BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
33216MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119454CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29
119454CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5386positivegrowth28mesophilic
33216positivegrowth30mesophilic
58850positivegrowth28mesophilic
67770positivegrowth28mesophilic
119454positivegrowth10-37
119454nogrowth41thermophilic
119454nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58850aerobe
119454obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.57

halophily

  • @ref: 119454
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 5386
  • murein short key: A31.02
  • type: A4gamma m-Dpm-D-Glu2; alpha-carboxyl group of D-Glu substituted by glycine

observation

  • @ref: 67770
  • observation: quinones: MK-7, MK-8, MK-7(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
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
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371L-xylose-builds acid from65328
119454citrate-carbon source16947
119454esculin+hydrolysis4853
119454hippurate+hydrolysis606565
119454nitrate+reduction17632
119454nitrite-reduction16301
119454nitrate-respiration17632

antibiotic resistance

  • @ref: 119454
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119454
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11945415688acetoin-
11945417234glucose-

enzymes

@refvalueactivityec
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
68382alpha-glucosidase-3.2.1.20
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
119454oxidase-
119454beta-galactosidase+3.2.1.23
119454alcohol dehydrogenase-1.1.1.1
119454gelatinase+/-
119454amylase+
119454DNase-
119454caseinase+3.4.21.50
119454catalase+1.11.1.6
119454tween esterase-
119454gamma-glutamyltransferase-2.3.2.2
119454lecithinase-
119454lipase-
119454lysine decarboxylase-4.1.1.18
119454ornithine decarboxylase-4.1.1.17
119454phenylalanine ammonia-lyase-4.3.1.24
119454protease+
119454tryptophan deaminase-
119454urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119454---+-+-----+++------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119454+/-+/-+/-+/-+/-+/--+/-+/-+/-+/-+/-+/--+/--+/-+/-------+/--+/---+/-+/---+/-+/----------+/----+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5386mural paintingHerberstein, St. Katharinen KapelleAustriaAUTEurope
58850Mural paintingCastle HerbersteinAustriaAUTEurope
67770Microbial biofilm damaging the mural painting at the Saint-Catherine chapel of Castle HerbersteinAustriaAUTEurope
119454Microbial biofilm damaging the mural paintingHerberstein castle, HimsdorfAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Other#Painting

taxonmaps

  • @ref: 69479
  • File name: preview.99_6771.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1217;97_1443;98_4994;99_6771&stattab=map
  • Last taxonomy: Brachybacterium
  • 16S sequence: AJ415378
  • Sequence Identity:
  • Total samples: 1142
  • soil counts: 75
  • aquatic counts: 270
  • animal counts: 767
  • plant counts: 30

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53861Risk group (German classification)
1194541Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5386
  • description: Brachybacterium fresconis partial 16S rRNA gene, type strain LMG 20336T
  • accession: AJ415378
  • length: 1471
  • database: ena
  • NCBI tax ID: 173363

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brachybacterium fresconis DSM 14564GCA_017876515contigncbi173363
66792Brachybacterium fresconis strain DSM 14564173363.3wgspatric173363
66792Brachybacterium fresconis DSM 145642918358370draftimg173363

GC content

  • @ref: 5386
  • GC-content: 70.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno89.168no
gram-positiveyes92.188no
anaerobicno99.676no
aerobicyes93.266yes
halophileyes56.925no
spore-formingno86.767no
glucose-utilyes89.863no
flagellatedno97.183no
glucose-fermentno67.012no
thermophileno99.455yes

External links

@ref: 5386

culture collection no.: DSM 14564, LMG 20336, CCUG 50350, JCM 12138, CIP 108248

straininfo link

  • @ref: 73421
  • straininfo: 19648

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361268Brachybacterium fresconis sp. nov. and Brachybacterium sacelli sp. nov., isolated from deteriorated parts of a medieval wall painting of the chapel of Castle Herberstein (Austria).Heyrman J, Balcaen A, De Vos P, Schumann P, Swings JInt J Syst Evol Microbiol10.1099/00207713-52-5-16412002Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Austria, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, History, Medieval, Molecular Sequence Data, Paintings/*history, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny14657129Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain.Buczolits S, Schumann P, Weidler G, Radax C, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.02728-02003Animals, Animals, Laboratory/microbiology, DNA, Ribosomal/genetics, Liver/*microbiology, Mice/*microbiology, Micrococcaceae/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Phenotype, *Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitle
5386Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14564)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14564
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
33216Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5849
58850Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50350)https://www.ccug.se/strain?id=50350
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
73421Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID19648.1StrainInfo: A central database for resolving microbial strain identifiers
119454Curators of the CIPCollection of Institut Pasteur (CIP 108248)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108248