Strain identifier

BacDive ID: 3905

Type strain: Yes

Species: Brachybacterium paraconglomeratum

Strain Designation: 7-11

Strain history: NCIMB 9861 <-- H. E. Schefferle 7-11.

NCBI tax ID(s): 173362 (species)

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General

@ref: 12531

BacDive-ID: 3905

DSM-Number: 46341

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

description: Brachybacterium paraconglomeratum 7-11 is a mesophilic bacterium that was isolated from poultry deep litter.

NCBI tax id

  • NCBI tax id: 173362
  • Matching level: species

strain history

@refhistory
12531<- IMET (Brachybacterium faecium) <- IMV, Kiew <- NCIB <- H.E. Schefferle, 7-11
67770NCIMB 9861 <-- H. E. Schefferle 7-11.

doi: 10.13145/bacdive3905.20230509.8.1

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

@ref: 12531

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium paraconglomeratum

full scientific name: Brachybacterium paraconglomeratum Takeuchi et al. 1995

strain designation: 7-11

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.653
6948099.999positive

colony morphology

@refcolony colorincubation periodmedium used
20194Beige (1001)10-14 daysISP 2
20194Beige (1001)10-14 daysISP 3
20194Beige (1001)10-14 daysISP 4
20194Beige (1001)10-14 daysISP 5
20194Beige (1001)10-14 daysISP 6
20194Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20194noISP 2
20194noISP 3
20194noISP 4
20194noISP 5
20194noISP 6
20194noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12531TRYPTICASE 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
20194ISP 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
20194ISP 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:
20194ISP 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
20194ISP 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
20194ISP 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
20194ISP 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

culture temp

@refgrowthtypetemperaturerange
20194positiveoptimum28mesophilic
12531positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.934

murein

  • @ref: 12531
  • 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
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20194--++-++-+++------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20194+++-++++-+-++-+++++

Isolation, sampling and environmental information

isolation

@refsample type
12531poultry deep litter
67770Poultry deep litter

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste
#Host#Birds
#Host#Other#Decomposing animal

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
125311Risk group (German classification)
201941German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Brachybacterium paraconglomeratum partial 16S rRNA gene, type strain LMG 19861TAJ4153771472ena173362
67770Brachybacterium paraconglomeratum gene for 16S rRNA, partial sequence, strain: JCM 17781AB6457611473ena173362

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brachybacterium paraconglomeratum KCTC 9916GCA_003994255scaffoldncbi173362
66792Brachybacterium paraconglomeratum strain KCTC 9916173362.3wgspatric173362

GC content

@refGC-contentmethod
1253168.0
6777068.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
motileno91.224no
flagellatedno97.406no
gram-positiveyes92.54no
anaerobicno99.561no
aerobicyes88.476no
halophileyes52.348no
spore-formingno91.136no
thermophileno99.022yes
glucose-utilyes88.749no
glucose-fermentno79.673yes

External links

@ref: 12531

culture collection no.: DSM 46341, ATCC 51843, IFO 15224, IMET 11353, NBRC 15224, NCIB 9861, JCM 17781, CIP 103334, IAM 14583, JCM 11649, KCTC 9916, LMG 19861, NCIMB 9861, VKM Ac-1425, VKM Ac-1977

straininfo link

  • @ref: 73415
  • straininfo: 92221

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
Phylogeny34170217Brachybacterium subflavum sp. nov., a novel actinobacterium isolated from the foregut of grass carp.Ming H, Cheng LJ, Yi BF, Xia TT, Niu MM, Zhao ZY, Liu BB, Nie GX, Cui CXInt J Syst Evol Microbiol10.1099/ijsem.0.0048392021Actinobacteria/*classification/genetics/*isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Carps/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis/chemistry, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12531Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46341)https://www.dsmz.de/collection/catalogue/details/culture/DSM-46341
20194Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM46341.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
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/
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)
73415Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92221.1StrainInfo: A central database for resolving microbial strain identifiers