Strain identifier

BacDive ID: 133714

Type strain: Yes

Species: Knoellia locipacati

Strain Designation: DMZ1

Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; DMZ1.

NCBI tax ID(s): 882824 (species)

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General

@ref: 30256

BacDive-ID: 133714

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

description: Knoellia locipacati DMZ1 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 882824
  • Matching level: species

strain history

  • @ref: 67770
  • history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; DMZ1.

doi: 10.13145/bacdive133714.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Knoellia
  • species: Knoellia locipacati
  • full scientific name: Knoellia locipacati Shin et al. 2012

@ref: 30256

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Intrasporangiaceae

genus: Knoellia

species: Knoellia locipacati

strain designation: DMZ1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30256positiverod-shapedno
69480no92.003
69480positive100

pigmentation

  • @ref: 30256
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30256positivegrowth10-37
30256positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30256positivegrowth6.0-9.0alkaliphile
30256positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 30256
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
30256NaClpositivegrowth0-5 %
30256NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3025622599arabinose+carbon source
3025618403L-arabitol+carbon source
3025617057cellobiose+carbon source
3025628757fructose+carbon source
3025628260galactose+carbon source
3025617716lactose+carbon source
3025617306maltose+carbon source
3025629864mannitol+carbon source
3025637684mannose+carbon source
3025617814salicin+carbon source
3025630911sorbitol+carbon source
3025617992sucrose+carbon source
3025627082trehalose+carbon source
3025617151xylitol+carbon source
3025618222xylose+carbon source

enzymes

@refvalueactivityec
30256acid phosphatase+3.1.3.2
30256alkaline phosphatase+3.1.3.1
30256catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
30256soil
67770soil of the Demilitarized ZoneRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_10555.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1391;97_1657;98_2108;99_10555&stattab=map
  • Last taxonomy: Knoellia locipacati
  • 16S sequence: HQ171909
  • Sequence Identity:
  • Total samples: 3761
  • soil counts: 727
  • aquatic counts: 682
  • animal counts: 2228
  • plant counts: 124

Sequence information

16S sequences

  • @ref: 30256
  • description: Knoellia locipacati strain DMZ1 16S ribosomal RNA gene, partial sequence
  • accession: HQ171909
  • length: 1448
  • database: nuccore
  • NCBI tax ID: 882824

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Knoellia locipacati NBRC 109775GCA_007992835contigncbi882824
66792Knoellia locipacati strain NBRC 109775882824.3wgspatric882824

GC content

@refGC-contentmethod
3025672.6
6777072.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno94.538yes
flagellatedno97.864yes
gram-positiveyes90.635yes
anaerobicno98.839yes
halophileno96.645no
spore-formingno89.664no
thermophileno97.295yes
glucose-utilyes88.245no
aerobicyes92.708yes
glucose-fermentno92.099no

External links

@ref: 30256

culture collection no.: KACC 15114, JCM 17313, NBRC 109775

literature

  • topic: Phylogeny
  • Pubmed-ID: 21421930
  • title: Knoellia locipacati sp. nov., from soil of the Demilitarized Zone in South Korea.
  • authors: Shin NR, Roh SW, Kim MS, Jung MJ, Whon TW, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.031880-0
  • year: 2011
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Lipids/analysis, *Military Facilities, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30256Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172659828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1