Strain identifier

BacDive ID: 3903

Type strain: Yes

Species: Brachybacterium nesterenkovii

Strain Designation: 35, IMV-Ac 752

Strain history: CIP <- 1996, K. Schubert, Inst. für Genetik und Mikrobiol., München, Germany <- DSM <- Gvozdyak

NCBI tax ID(s): 47847 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3641

BacDive-ID: 3903

DSM-Number: 9573

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic

description: Brachybacterium nesterenkovii 35 is a facultative anaerobe, mesophilic bacterium that was isolated from milk.

NCBI tax id

  • NCBI tax id: 47847
  • Matching level: species

strain history

@refhistory
3641<- O.R. Gvozdyak, 35 (= IMV Ac-752)
67770IFO 15384 <-- IMV Ac-752 (=T. M. Nogina 34).
121275CIP <- 1996, K. Schubert, Inst. für Genetik und Mikrobiol., München, Germany <- DSM <- Gvozdyak

doi: 10.13145/bacdive3903.20230509.8.1

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 nesterenkovii
  • full scientific name: Brachybacterium nesterenkovii Gvozdyak et al. 1992

@ref: 3641

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium nesterenkovii

full scientific name: Brachybacterium nesterenkovii Gvozdyak et al. 1992

strain designation: 35, IMV-Ac 752

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.385
69480100positive
121275nopositivecoccus-shaped

colony morphology

@refcolony colorincubation periodmedium used
20212Lemon yellow (1012)10-14 daysISP 2
20212Lemon yellow (1012)10-14 daysISP 3
20212Lemon yellow (1012)10-14 daysISP 4
20212Lemon yellow (1012)10-14 daysISP 5
20212Lemon yellow (1012)10-14 daysISP 6
20212Lemon yellow (1012)10-14 daysISP 7
121275

multicellular morphology

@refforms multicellular complexmedium name
20212noISP 2
20212noISP 3
20212noISP 4
20212noISP 5
20212noISP 6
20212noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3641TRYPTICASE 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
20212ISP 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
20212ISP 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:
20212ISP 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
20212ISP 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
20212ISP 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
20212ISP 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
34053MEDIUM 111 - for ClavibacteryesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
121275CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111

culture temp

@refgrowthtypetemperaturerange
20212positiveoptimum28mesophilic
3641positivegrowth28mesophilic
34053positivegrowth30mesophilic
67770positivegrowth28mesophilic
121275positivegrowth22-41
121275nogrowth10psychrophilic
121275nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121275
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
121275NaClpositivegrowth0-8 %
121275NaClnogrowth10 %

murein

  • @ref: 3641
  • murein short key: A31.01
  • type: A4gamma m-Dpm-D-Glu2

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
121275citrate-carbon source16947
121275esculin+hydrolysis4853
121275hippurate-hydrolysis606565
121275nitrate-reduction17632
121275nitrite-reduction16301
121275nitrate+respiration17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379lactose+fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 121275
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121275
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12127515688acetoin-
12127517234glucose+

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-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
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
121275oxidase-
121275beta-galactosidase+3.2.1.23
121275alcohol dehydrogenase-1.1.1.1
121275gelatinase-
121275amylase-
121275DNase-
121275caseinase-3.4.21.50
121275catalase+1.11.1.6
121275tween esterase-
121275gamma-glutamyltransferase-2.3.2.2
121275lecithinase-
121275lipase-
121275lysine decarboxylase-4.1.1.18
121275ornithine decarboxylase-4.1.1.17
121275phenylalanine ammonia-lyase-4.3.1.24
121275protease-
121275tryptophan deaminase-
121275urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20212+/-----++++--++/---+/-+--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20212-++-+--+---++++++--
121275-++-+----+-++-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121275+--+++/----++++/--------+/-+/-+/-+++++++++/---+---+/-+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121275++++---+++++++---++------------+---+------------------------+------------------------------+-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3641milkUkraineUKREurope
67770Milk product
121275Food, MilkUkraineUKREurope1984

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Engineered#Food production#Dairy product

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
36411Risk group (German classification)
202121German classification
1212751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3641
  • description: B.nesterenkovii 16S ribosomal RNA gene
  • accession: X91033
  • length: 1514
  • database: ena
  • NCBI tax ID: 47847

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brachybacterium nesterenkovii strain CIP10481347847.3wgspatric47847
66792Brachybacterium nesterenkovii CIP1048132865174459draftimg47847
67770Brachybacterium nesterenkovii CIP104813GCA_900163655contigncbi47847

GC content

@refGC-contentmethod
364170thermal denaturation, midpoint method (Tm)
6777072high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes95.273no
anaerobicno98.583no
halophileno69.858no
spore-formingno93.615no
glucose-utilyes83.798no
aerobicyes66.085no
flagellatedno97.394no
thermophileno95.664no
motileno92.353no
glucose-fermentno50.839yes

External links

@ref: 3641

culture collection no.: DSM 9573, IMV Ac-752, JCM 11648, CIP 104813, IAM 14582, IFO 15384, LMG 19549, NBRC 15384

straininfo link

  • @ref: 73413
  • straininfo: 13201

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1736971Taxonomic study of the genus Brachybacterium: Brachybacterium nesterenkovii sp. nov.Gvozdyak OR, Nogina TM, Schumann PInt J Syst Bacteriol10.1099/00207713-42-1-741992Arthrobacter/*classification/growth & development/metabolism, DNA, Bacterial/analysis, Sequence Homology, Nucleic AcidMetabolism
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
Phylogeny17978239Brachybacterium phenoliresistens sp. nov., isolated from oil-contaminated coastal sand.Chou JH, Lin KY, Lin MC, Sheu SY, Wei YH, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65019-02007Actinomycetales/chemistry/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, *Petroleum, Phenols/pharmacology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Pollutants, Species Specificity, TaiwanGenetics
Phylogeny24532648Brachybacterium huguangmaarense sp. nov., isolated from Lake sediment.Liu Y, Xie QY, Shi W, Li L, An JY, Zhao YM, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.052464-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Lakes/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny26311250Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch.Liu Y, Zhai L, Yao S, Cao Y, Cao Y, Zhang X, Su J, Ge Y, Zhao R, Cheng CInt J Syst Evol Microbiol10.1099/ijsem.0.0005592015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Morinda/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3641Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9573)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9573
20212Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM9573.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
34053Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16763
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/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
73413Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13201.1StrainInfo: A central database for resolving microbial strain identifiers
121275Curators of the CIPCollection of Institut Pasteur (CIP 104813)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104813