Strain identifier

BacDive ID: 3906

Type strain: Yes

Species: Brachybacterium conglomeratum

Strain Designation: 5-2

Strain history: CIP <- 1995, IFO <- CCM <- K. Komagata: strain 5-2

NCBI tax ID(s): 47846 (species)

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General

@ref: 3862

BacDive-ID: 3906

DSM-Number: 10241

keywords: 16S sequence, Bacteria, mesophilic

description: Brachybacterium conglomeratum 5-2 is a mesophilic bacterium that was isolated from oil brine.

NCBI tax id

  • NCBI tax id: 47846
  • Matching level: species

strain history

@refhistory
3862<- IFO <- CCM <- K. Komagata, 5-2 (Micrococcus conglomeratus)
67770CCM 2589 <-- K. Komagata 5-2.
118732CIP <- 1995, IFO <- CCM <- K. Komagata: strain 5-2

doi: 10.13145/bacdive3906.20230509.8.1

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 conglomeratum
  • full scientific name: Brachybacterium conglomeratum (ex Migula 1900) Takeuchi et al. 1995

@ref: 3862

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium conglomeratum

full scientific name: Brachybacterium conglomeratum (ex Migula 1900) Takeuchi et al. 1995

strain designation: 5-2

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18352Beige (1001)10-14 daysISP 2
18352Beige (1001)10-14 daysISP 3
18352Beige (1001)10-14 daysISP 4
18352Beige (1001)10-14 daysISP 5
18352Beige (1001)10-14 daysISP 6
18352Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18352noISP 2
18352noISP 3
18352noISP 4
18352noISP 5
18352noISP 6
18352noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3862TRYPTICASE 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
18352ISP 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
18352ISP 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:
18352ISP 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
18352ISP 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
18352ISP 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
18352ISP 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
34701MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118732CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18352positiveoptimum28mesophilic
3862positivegrowth28mesophilic
34701positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

murein

  • @ref: 3862
  • 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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

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
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
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18352--++/--+++++---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18352-++-++-+-+-++-+++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3862oil brineJapanJPNAsia
67770Oil brine
118732Oil brineJapanJPNAsia1965

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Condition#Saline
#Engineered#Food production#Oil (Food)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5012.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1217;97_1443;98_1761;99_5012&stattab=map
  • Last taxonomy: Brachybacterium
  • 16S sequence: AB537169
  • Sequence Identity:
  • Total samples: 19744
  • soil counts: 1884
  • aquatic counts: 2613
  • animal counts: 14166
  • plant counts: 1081

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183521German classification
38621Risk group (German classification)
1187321Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Brachybacterium conglomeratum gene for 16S ribosomal RNA, partial sequence
  • accession: AB537169
  • length: 1458
  • database: ena
  • NCBI tax ID: 47846

GC content

@refGC-contentmethod
386271high performance liquid chromatography (HPLC)
6777070.6high performance liquid chromatography (HPLC)

External links

@ref: 3862

culture collection no.: DSM 10241, AJ 1015, CCM 2589, IFO 15472, NBRC 15472, JCM 11608, CCUG 50160, CCUG 50354, CIP 104400, IAM 14580, KCTC 9915, LMG 19849, NCIMB 13395, VKM Ac-1975

straininfo link

  • @ref: 73416
  • straininfo: 13707

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21216918Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential.Gontia I, Kavita K, Schmid M, Hartmann A, Jha BInt J Syst Evol Microbiol10.1099/ijs.0.023176-02011Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Chenopodiaceae/growth & development/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolismMetabolism
Phylogeny27514821Brachybacterium aquaticum sp. nov., a novel actinobacterium isolated from seawater.Kaur G, Kumar N, Mual P, Kumar A, Kumar RM, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0014142016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3862Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10241)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10241
18352Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10241.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
34701Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16304
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
73416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13707.1StrainInfo: A central database for resolving microbial strain identifiers
118732Curators of the CIPCollection of Institut Pasteur (CIP 104400)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104400