Strain identifier

BacDive ID: 3908

Type strain: Yes

Species: Brachybacterium rhamnosum

Strain Designation: H-6S

Strain history: CIP <- 1995, IFO <- K. Kishimoto, Takeda Chemical Industries Ltd., Hikari plant, Japan

NCBI tax ID(s): 173361 (species)

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General

@ref: 3861

BacDive-ID: 3908

DSM-Number: 10240

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, coccus-shaped

description: Brachybacterium rhamnosum H-6S is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from corn steep liquor.

NCBI tax id

  • NCBI tax id: 173361
  • Matching level: species

strain history

@refhistory
3861<- IFO. Strain H-6S
67770IFO 15203 <-- Takeda Chem. Ind., Ltd. (K. Kishimoto H-6S).
122182CIP <- 1995, IFO <- K. Kishimoto, Takeda Chemical Industries Ltd., Hikari plant, Japan

doi: 10.13145/bacdive3908.20230509.8.1

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 rhamnosum
  • full scientific name: Brachybacterium rhamnosum Takeuchi et al. 1995

@ref: 3861

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium rhamnosum

full scientific name: Brachybacterium rhamnosum Takeuchi et al. 1995

strain designation: H-6S

type strain: yes

Morphology

cell morphology

  • @ref: 122182
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18315Beige (1001)10-14 daysISP 2
18315Beige (1001)10-14 daysISP 3
18315Beige (1001)10-14 daysISP 4
18315Colorless10-14 daysISP 5
18315Beige (1001)10-14 daysISP 6
18315Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18315noISP 2
18315noISP 3
18315noISP 4
18315noISP 5
18315noISP 6
18315noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3861TRYPTICASE 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
18315ISP 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
18315ISP 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:
18315ISP 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
18315ISP 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
18315ISP 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
18315ISP 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
34698MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122182CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122182CIP Medium 251yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=251
122182CIP Medium 99yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=99

culture temp

@refgrowthtypetemperaturerange
18315positiveoptimum28mesophilic
3861positivegrowth28mesophilic
34698positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122182
  • oxygen tolerance: obligate aerobe

murein

  • @ref: 3861
  • 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

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
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
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
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-xylose+builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
122182nitrate-reduction17632
122182nitrite-reduction16301
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen+fermentation28087

metabolite production

  • @ref: 122182
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
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
122182oxidase+
122182catalase+1.11.1.6
122182urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18315--+--++-++-+------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18315-+++++++---++-+++--
122182-++-++++---++-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122182+/-+/--+-+---++++/----+/-+/-+/----+++++++/-+++-+/-++++/-+/-+/----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
3861corn steep liquorJapanJPNAsia
67770Corn steep liquor
122182Corn steep liquorJapanJPNAsiaHikari, Yamaguchi1991

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Beverage
#Engineered#Food production#Fermented
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183151German classification
38611Risk group (German classification)
1221821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Brachybacterium rhamnosum partial 16S rRNA gene, type strain LMG 19848T
  • accession: AJ415376
  • length: 1471
  • database: ena
  • NCBI tax ID: 173361

GC content

@refGC-contentmethod
386172high performance liquid chromatography (HPLC)
6777071.5high performance liquid chromatography (HPLC)

External links

@ref: 3861

culture collection no.: DSM 10240, ATCC 51844, IFO 15203, NBRC 15203, JCM 11650, CIP 104398, IAM 14584, KCTC 9917, LMG 19848, NCIMB 13338, VKM Ac-1976

straininfo link

  • @ref: 73418
  • straininfo: 92765

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny20543157Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood.Park SK, Kim MS, Jung MJ, Nam YD, Park EJ, Roh SW, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.022517-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Fermentation, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sodium Chloride/metabolismMetabolism
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
Phylogeny26476895Brachybacterium horti sp. nov., isolated from garden soil.Singh H, Du J, Yang JE, Shik Yin C, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0006962015Actinomycetales/*classification/genetics/isolation & purification, *Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3861Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10240)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10240
18315Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10240.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34698Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16302
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
73418Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92765.1StrainInfo: A central database for resolving microbial strain identifiers
122182Curators of the CIPCollection of Institut Pasteur (CIP 104398)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104398