Strain identifier

BacDive ID: 7512

Type strain: Yes

Species: Herbiconiux flava

Strain history: <- NBRC; NBRC 16403

NCBI tax ID(s): 881268 (species)

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General

@ref: 18237

BacDive-ID: 7512

DSM-Number: 26474

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

description: Herbiconiux flava DSM 26474 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Phyllosphere Carex sp..

NCBI tax id

  • NCBI tax id: 881268
  • Matching level: species

strain history

  • @ref: 18237
  • history: <- NBRC; NBRC 16403

doi: 10.13145/bacdive7512.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Herbiconiux
  • species: Herbiconiux flava
  • full scientific name: Herbiconiux flava Hamada et al. 2012

@ref: 18237

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Herbiconiux

species: Herbiconiux flava

full scientific name: Herbiconiux flava Hamada et al. 2012

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30227positive01-02 µm0.5-0.7 µmrod-shapedno
69480no93.896
69480positive100

pigmentation

  • @ref: 30227
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18237
  • name: PP-MEDIUM (DSMZ Medium 513)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/513
  • composition: Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18237positivegrowth28mesophilic
30227positivegrowth05-37
30227positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
30227positivegrowth05-09alkaliphile
30227positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30227
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30227no
69480no99.997

halophily

  • @ref: 30227
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

murein

  • @ref: 18237
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3022717057cellobiose+carbon source
3022728757fructose+carbon source
3022728260galactose+carbon source
3022717234glucose+carbon source
3022717754glycerol+carbon source
3022717306maltose+carbon source
3022729864mannitol+carbon source
3022737684mannose+carbon source
3022717814salicin+carbon source
3022717992sucrose+carbon source
3022718222xylose+carbon source
302274853esculin+hydrolysis

enzymes

  • @ref: 30227
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 18237
  • sample type: Phyllosphere Carex sp.
  • host species: Carex
  • geographic location: Belgorod region
  • country: Russia
  • origin.country: RUS
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

  • @ref: 18237
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Curtobacterium sp. VKM Ac-2058 gene for 16S ribosomal RNA, partial sequenceAB0420931510ena123319
18237Herbiconiux flava gene for 16S rRNA, partial sequenceAB5839211480ena881268

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbiconiux flava DSM 26474GCA_013409865contigncbi881268
66792Herbiconiux flava strain DSM 26474881268.3wgspatric881268
66792Herbiconiux flava DSM 264742844852863draftimg881268

GC content

@refGC-content
1823771.0
3022771

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno71no
motileno91.605yes
flagellatedno97.619no
gram-positiveyes94.144yes
anaerobicno99.659no
halophileno90.921no
spore-formingno93.406yes
thermophileno99.74yes
glucose-utilyes87.174no
aerobicyes94.749no
glucose-fermentno91.953no

External links

@ref: 18237

culture collection no.: DSM 26474, NBRC 16403, VKM Ac-2058

literature

  • topic: Phylogeny
  • Pubmed-ID: 21571941
  • title: Description of Herbiconiux flava sp. nov. and emended description of the genus Herbiconiux.
  • authors: Hamada M, Komukai C, Tamura T, Evtushenko LI, Vinokurova NG, Suzuki KI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.031260-0
  • year: 2011
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Carex Plant/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
18237Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26474)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26474
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
30227Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126570
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)
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)