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BacDive ID 3916
Type strain
Strain Designation JB
Culture col. no. DSM 18832 CGMCC 1.6508 LMG 23926 JB JCM 15471
NCBI tax ID(s) 1305859 416230
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

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/bacdive3916.20250331.9.3

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
125438no90.5
125439positive97.3

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

@refgrowthtypetemperature
7728positivegrowth28
32103positivegrowth25-40
32103positiveoptimum32.5
67770positivegrowth28

culture pH

@refabilitytypepHPH range
32103positivegrowth05-11alkaliphile
32103positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32103
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 32103
  • spore formation: no

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: nuccore
  • 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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes84.27no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no69.631yes
125438spore-formingspore-formingAbility to form endo- or exosporesno85.417no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no58.67no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.296yes
125438motile2+flagellatedAbility to perform flagellated movementno90.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno63
125439BacteriaNetmotilityAbility to perform movementno72.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive97.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe79.3

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/
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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