Strain identifier

BacDive ID: 140582

Type strain: Yes

Species: Kibdelosporangium kanagawaense

Strain Designation: K08-0175

Strain history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K8-0175 <- A. Fukada; K8-0175

NCBI tax ID(s): 1882231 (species)

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General

@ref: 64851

BacDive-ID: 140582

DSM-Number: 103925

keywords: 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

description: Kibdelosporangium kanagawaense K08-0175 is an aerobe, spore-forming, Gram-positive bacterium that builds a substrate mycelium and was isolated from plant root sample of Ophiopogon japonicus.

NCBI tax id

  • NCBI tax id: 1882231
  • Matching level: species

strain history

  • @ref: 64851
  • history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K8-0175 <- A. Fukada; K8-0175

doi: 10.13145/bacdive140582.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Kibdelosporangium
  • species: Kibdelosporangium kanagawaense
  • full scientific name: Kibdelosporangium kanagawaense Mingma et al. 2017

@ref: 64851

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Kibdelosporangium

species: Kibdelosporangium kanagawaense

full scientific name: Kibdelosporangium kanagawaense Mingma et al. 2017

strain designation: K08-0175

type strain: yes

Morphology

cell morphology

  • @ref: 43258
  • gram stain: positive
  • motility: no

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
43258yessubstrate myceliumwhite to pale yellow
43258yesaerial myceliumwhite
43258yessubstrate myceliumpale yellowISP2
43258yessubstrate myceliumwhiteISP3
43258yessubstrate myceliumpale yellowISP4
43258yessubstrate myceliumpale yellowISP5
43258yessubstrate myceliumpale yellowpotato dextrose agar
43258yessubstrate myceliumpale yellownutrient agar
43258yessubstrate myceliumpale yellowCzapek's agar

pigmentation

@refproductionname
43258noSoluble pigments
43258noMelanin

multimedia

  • @ref: 64851
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_103925.jpg
  • caption: Medium 547 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43258ISP2yes
43258ISP3yes
43258ISP4yes
43258ISP5yes
43258potato dextrose agaryes
43258Nutrient agar (NA)yes
43258Czapek's agaryes
64851ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
64851STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43258positiveoptimum24-32
43258positivegrowth16-38
64851positivegrowth28mesophilic

culture pH

  • @ref: 43258
  • ability: positive
  • type: growth
  • pH: 5.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43258
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43258
  • spore description: Long straight chains of rod-shaped spores (more than 20 spores per chain) with smooth surfaces
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 43258
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4325817234glucose+carbon source
4325830849L-arabinose+carbon source
4325812936D-galactose+carbon source
4325817268myo-inositol+carbon source
4325836218beta-lactose+carbon source
4325817306maltose+carbon source
4325816024D-mannose+carbon source
4325828053melibiose+carbon source
4325816634raffinose+carbon source
4325833942ribose+carbon source
4325817992sucrose+carbon source
4325818222xylose+carbon source
4325827922sorbose-carbon source
4325817151xylitol-carbon source
4325830849L-arabinose+builds acid from
4325812936D-galactose+builds acid from
4325817234glucose+builds acid from
4325817268myo-inositol+builds acid from
4325836218beta-lactose+builds acid from
4325816024D-mannose+builds acid from
4325828053melibiose+builds acid from
4325817992sucrose+builds acid from
4325818222xylose+builds acid from
4325817057cellobiose+carbon source
4325848095(-)-D-fructose+carbon source
4325816899D-mannitol+carbon source
43258(-)-D-rhamnose+carbon source
4325817057cellobiose+builds acid from
4325848095(-)-D-fructose+builds acid from
4325816899D-mannitol+builds acid from
43258(-)-D-rhamnose+builds acid from
4325817151xylitol-builds acid from
4325816634raffinose-builds acid from
4325817632nitrate-reduction

enzymes

@refvalueactivityec
43258catalase+1.11.1.6
43258cytochrome oxidase-1.9.3.1
43258alkaline phosphatase+3.1.3.1
43258esterase (C 4)+
43258esterase Lipase (C 8)+
43258leucine aminopeptidase+3.4.1.1
43258valine arylamidase+
43258cystine arylamidase+3.4.11.3
43258trypsin+3.4.21.4
43258acid phosphatase+3.1.3.2
43258phosphoamidase+3.9.1.1
43258alpha-glucosidase+3.2.1.20
43258alpha-mannosidase+3.2.1.24
43258alpha-galactosidase+/-3.2.1.22
43258beta-galactosidase+/-3.2.1.23
43258lipase (C 14)-
43258alpha-chymotrypsin-3.4.21.1
43258beta-glucuronidase-3.2.1.31
43258beta-glucosidase-3.2.1.21
43258glucosaminidase-
43258alpha-fucosidase-3.2.1.51
43258urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43258plant root sample of Ophiopogon japonicusKanagawa, JapanJapanJPNAsia
64851root of Ophiopogon japonicusKanagawa prefectureJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_121494.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_415;97_14873;98_18401;99_121494&stattab=map
  • Last taxonomy: Kibdelosporangium kanagawaense
  • 16S sequence: LC169780
  • Sequence Identity:
  • Total samples: 16
  • soil counts: 14
  • animal counts: 2

Safety information

risk assessment

  • @ref: 64851
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64851
  • description: Kibdelosporangium kanagawaense gene for 16S ribosomal RNA, partial sequence
  • accession: LC169780
  • length: 1424
  • database: ena
  • NCBI tax ID: 1882231

GC content

  • @ref: 64851
  • GC-content: 64.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64851

culture collection no.: DSM 103925, TBRC 6786, NBRC 112388

straininfo link

  • @ref: 96747
  • straininfo: 400701

literature

  • topic: Phylogeny
  • Pubmed-ID: 28598312
  • title: Three novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangiumrhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov.
  • authors: Mingma R, Duangmal K, Omura S, Takahashi Y, Matsumoto A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001861
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Nucleic Acid Hybridization, Ophiopogon/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43258Ratchanee Mingma, Kannika Duangmal, Satoshi Omura, Yoko Takahashi and Atsuko MatsumotoThree novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangium rhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov.10.1099/ijsem.0.001861IJSEM 67: 1758-1765 201728598312
64851Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103925Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103925)
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/
96747Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400701.1