Strain identifier

BacDive ID: 3916

Type strain: Yes

Species: Brachybacterium zhongshanense

Strain Designation: JB

Strain history: CGMCC 1.6508 <-- G. Zhang et al. strain JB.

NCBI tax ID(s): 1305859 (strain), 416230 (species)

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General

@ref: 7728

BacDive-ID: 3916

DSM-Number: 18832

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Brachybacterium zhongshanense JB is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from sediment, river Qijiang.

NCBI tax id

NCBI tax idMatching level
416230species
1305859strain

strain history

@refhistory
7728<- Guoping Sun <- Xiaowei Cai, JB
67770CGMCC 1.6508 <-- G. Zhang et al. strain JB.

doi: 10.13145/bacdive3916.20230509.8.1

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 zhongshanense
  • full scientific name: Brachybacterium zhongshanense Zhang et al. 2007

@ref: 7728

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Brachybacterium

species: Brachybacterium zhongshanense

full scientific name: Brachybacterium zhongshanense Zhang et al. 2007

strain designation: JB

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32103positiverod-shapedno
69480positive94.566

pigmentation

  • @ref: 32103
  • production: no

Culture and growth conditions

culture medium

  • @ref: 7728
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
7728positivegrowth28mesophilic
32103positivegrowth25-40
32103positiveoptimum32.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32103positivegrowth05-11alkaliphile
32103positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32103
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
32103no
69481no95
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32103NaClpositivegrowth0-10 %
32103NaClpositiveoptimum5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3210330089acetate+carbon source
3210322599arabinose+carbon source
3210317057cellobiose+carbon source
3210323652dextrin+carbon source
3210328757fructose+carbon source
3210328260galactose+carbon source
3210324175galacturonate+carbon source
321035291gelatin+carbon source
3210317234glucose+carbon source
3210317754glycerol+carbon source
3210328087glycogen+carbon source
3210317596inosine+carbon source
3210324996lactate+carbon source
3210317716lactose+carbon source
3210317306maltose+carbon source
3210337684mannose+carbon source
3210328053melibiose+carbon source
3210315361pyruvate+carbon source
3210351850methyl pyruvate+carbon source
3210316634raffinose+carbon source
3210317992sucrose+carbon source
3210327082trehalose+carbon source
3210316199urea+carbon source
3210317151xylitol+carbon source
3210318222xylose+carbon source
321034853esculin+hydrolysis
3210317632nitrate+reduction

enzymes

@refvalueactivityec
32103catalase+1.11.1.6
32103gelatinase+
32103urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7728sediment, river QijiangZhongshan CityChinaCHNAsia
67770Sediments along the Qijiang RiverZhongshan CityChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 7728
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7728
  • description: Brachybacterium zhongshanense strain JB 16S ribosomal RNA gene, partial sequence
  • accession: EF125186
  • length: 1485
  • database: ena
  • NCBI tax ID: 416230

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brachybacterium zhongshanense JCM 15471GCA_001314085contigncbi1305859
66792Brachybacterium zhongshanense JCM 154711305859.3wgspatric1305859
66792Brachybacterium zhongshanense JCM 154712681813033draftimg1305859

GC content

@refGC-contentmethod
772871.2
6777071.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno89.277no
gram-positiveyes91.537no
anaerobicno94.538yes
halophileno79.952no
spore-formingno96.815yes
thermophileno99.604yes
glucose-utilyes88.113yes
aerobicyes55.778yes
flagellatedno97.136yes
glucose-fermentyes60.211no

External links

@ref: 7728

culture collection no.: DSM 18832, CGMCC 1.6508, LMG 23926, JCM 15471

straininfo link

  • @ref: 73426
  • straininfo: 293206

literature

  • topic: Phylogeny
  • Pubmed-ID: 17978212
  • title: Brachybacterium zhongshanense sp. nov., a cellulose-decomposing bacterium from sediment along the Qijiang River, Zhongshan City, China.
  • authors: Zhang G, Zeng G, Cai X, Deng S, Luo H, Sun G
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64968-0
  • year: 2007
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cellulose/*metabolism, China, DNA Fingerprinting/methods, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S, Rivers/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7728Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18832)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18832
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
32103Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2834828776041
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/
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
73426Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293206.1StrainInfo: A central database for resolving microbial strain identifiers