Strain identifier

BacDive ID: 2908

Type strain: Yes

Species: Brachymonas denitrificans

Strain Designation: AS-P1

Strain history: A. Hiraishi AS-P1.

NCBI tax ID(s): 1121117 (strain), 28220 (species)

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General

@ref: 5622

BacDive-ID: 2908

DSM-Number: 15123

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Brachymonas denitrificans AS-P1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soybean curd waste sludge.

NCBI tax id

NCBI tax idMatching level
1121117strain
28220species

strain history

@refhistory
5622<- JCM <- A. Hiraishi; AS-P1
67770A. Hiraishi AS-P1.

doi: 10.13145/bacdive2908.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Brachymonas
  • species: Brachymonas denitrificans
  • full scientific name: Brachymonas denitrificans Hiraishi et al. 1995

@ref: 5622

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Brachymonas

species: Brachymonas denitrificans

full scientific name: Brachymonas denitrificans Hiraishi et al. 1995

strain designation: AS-P1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 100

colony morphology

  • @ref: 56744
  • incubation period: 3 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15123_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15123_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15123_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15123_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 5622
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5622positivegrowth30mesophilic
56744positivegrowth30
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 56744
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

observation

  • @ref: 67770
  • observation: quinones: Q-8, RQ-8

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    56744C12:0912
    56744C14:00.414
    56744C16:02416
    56744C17:00.317
    56744C18:00.718
    56744C10:0 3OH1.411.423
    56744C12:0 3OH1.913.455
    56744C16:0 2OH0.717.233
    56744C16:1 ω7c41.715.819
    56744C18:1 ω7c /12t/9t15.817.824
    56744C18:1 ω9c0.417.769
    56744C18:2 ω6,9c/C18:0 ANTE1.817.724
    56744C19:0 CYCLO ω9c0.418.87
    56744Unidentified0.69.979
    56744Unidentified0.410.459
    56744Unidentified0.518.073
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5622soybean curd waste sludgeJapanJPNAsia
56744Sludge,soybean curd waste
67770Soybean curd waste sludge

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Food
#Engineered#Waste#Solid plant waste
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_11728.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_5918;97_7122;98_8796;99_11728&stattab=map
  • Last taxonomy: Brachymonas denitrificans subclade
  • 16S sequence: D14320
  • Sequence Identity:
  • Total samples: 2225
  • soil counts: 132
  • aquatic counts: 1459
  • animal counts: 598
  • plant counts: 36

Safety information

risk assessment

  • @ref: 5622
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5622
  • description: Brachymonas denitrificans gene for 16S rRNA
  • accession: D14320
  • length: 1452
  • database: ena
  • NCBI tax ID: 28220

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brachymonas denitrificans DSM 151231121117.3wgspatric1121117
66792Brachymonas denitrificans DSM 151232599185145draftimg1121117
67770Brachymonas denitrificans DSM 15123GCA_900110225scaffoldncbi1121117

GC content

  • @ref: 5622
  • GC-content: 64.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno82.553no
flagellatedno88.241no
gram-positiveno98.821no
anaerobicno96.467yes
aerobicyes88.571yes
halophileno90.005no
spore-formingno97.658no
thermophileno93.198no
glucose-utilno79.069no
glucose-fermentno89.92no

External links

@ref: 5622

culture collection no.: DSM 15123, JCM 9216, CCUG 45365, CGMCC 1.7100

straininfo link

  • @ref: 72431
  • straininfo: 65713

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism17391334Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii.Halet D, Defoirdt T, Van Damme P, Vervaeren H, Forrez I, Van de Wiele T, Boon N, Sorgeloos P, Bossier P, Verstraete WFEMS Microbiol Ecol10.1111/j.1574-6941.2007.00305.x2007Animals, Aquaculture/methods, Artemia/*microbiology, Bacteria/growth & development/isolation & purification/*metabolism, Bioreactors, *Germ-Free Life, Hydroxybutyrates/*metabolism, Polyesters/*metabolism, Survival Analysis, Vibrio/*pathogenicity, Vibrio Infections/microbiology/*prevention & controlEnzymology
Phylogeny19643891Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas.Halpern M, Shaked T, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.007211-02009Animals, Chironomidae/*microbiology, Comamonadaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Ovum/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5622Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15123)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15123
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
56744Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45365)https://www.ccug.se/strain?id=45365
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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
72431Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID65713.1StrainInfo: A central database for resolving microbial strain identifiers