Strain identifier

BacDive ID: 140635

Type strain: Yes

Species: Phytohabitans kaempferiae

Strain Designation: KK1-3

NCBI tax ID(s): 1620943 (species)

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General

@ref: 67663

BacDive-ID: 140635

DSM-Number: 111731

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

description: Phytohabitans kaempferiae KK1-3 is a spore-forming, thermophilic, Gram-positive bacterium that has a Pale yellow pigmentation and was isolated from the leaf of Kaempferia larsenii.

NCBI tax id

  • NCBI tax id: 1620943
  • Matching level: species

doi: 10.13145/bacdive140635.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Phytohabitans
  • species: Phytohabitans kaempferiae
  • full scientific name: Phytohabitans kaempferiae Niemhom et al. 2016

@ref: 67663

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micromonosporales

family: Micromonosporaceae

genus: Phytohabitans

species: Phytohabitans kaempferiae

full scientific name: Phytohabitans kaempferiae Niemhom et al. 2016

strain designation: KK1-3

type strain: yes

Morphology

cell morphology

  • @ref: 43067
  • gram stain: positive

multicellular morphology

  • @ref: 43067
  • forms multicellular complex: yes

pigmentation

  • @ref: 43067
  • production: yes
  • color: Pale yellow
  • name: soluble pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43067ISP2yes
67663GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
67663ISP2 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

culture temp

@refgrowthtypetemperaturerange
43067positivemaximum40thermophilic
43067positiveoptimum30-37mesophilic
67663positivegrowth28mesophilic

culture pH

  • @ref: 43067
  • ability: positive
  • type: growth
  • pH: 6-10
  • PH range: alkaliphile

Physiology and metabolism

spore formation

  • @ref: 43067
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 43067
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4306717057cellobiose+carbon source
4306717634D-glucose+carbon source
4306716024D-mannose+carbon source
4306765327D-xylose+carbon source
4306730849L-arabinose+carbon source
4306762345L-rhamnose+carbon source
4306717992sucrose+carbon source
4306715824D-fructose+/-carbon source
4306712936D-galactose+/-carbon source
4306717716lactose+/-carbon source
4306728053melibiose-carbon source
4306716988D-ribose-carbon source
4306717814D-salicin-carbon source
4306717754glycerol-carbon source
4306729864mannitol-carbon source
4306717268myo-inositol-carbon source
43067milk+degradation
4306728017starch+hydrolysis
430675291gelatin-degradation
4306717632nitrate-reduction

enzymes

@refvalueactivityec
43067alkaline phosphatase+3.1.3.1
43067leucine arylamidase+3.4.11.1
43067trypsin+3.4.21.4
43067acid phosphatase+3.1.3.2
43067naphthol-AS-BI-phosphohydrolase+
43067beta-galactosidase+3.2.1.23
43067alpha-mannosidase+3.2.1.24
43067alpha-glucosidase+3.2.1.20
43067N-acetyl-beta-glucosaminidase+3.2.1.52
43067beta-glucosidase+/-3.2.1.21
43067esterase (C 4)-
43067esterase Lipase (C 8)-
43067lipase (C 14)-
43067valine arylamidase-
43067cystine arylamidase-3.4.11.3
43067alpha-chymotrypsin-3.4.21.1
43067alpha-galactosidase-3.2.1.22
43067beta-glucuronidase-3.2.1.31
43067alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43067the leaf of Kaempferia larseniiUbon Ratchathani province, ThailandThailandTHAAsia
67663Leaf, Kaempferia larseniiUbon RatchathaniThailandTHAAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 67663
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4306716S rRNA gene sequencesLC0317741485ena1620943
6766349_DSM_111731_900Rena

GC content

  • @ref: 43067
  • GC-content: 71
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 67663

culture collection no.: BCC 66360, NBRC 110005, DSM 111731

straininfo link

  • @ref: 96762
  • straininfo: 407629

literature

  • topic: Phylogeny
  • Pubmed-ID: 27126122
  • title: Phytohabitans kaempferiae sp. nov., an endophytic actinomycete isolated from the leaf of Kaempferia larsenii.
  • authors: Niemhom N, Chutrakul C, Suriyachadkun C, Thawai C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001121
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistry, Zingiberaceae/*microbiology
  • 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
43067Nantawan Niemhom, Chanikul Chutrakul, Chanwit Suriyachadkun and Chitti ThawaiPhytohabitans kaempferiae sp. nov., an endophytic actinomycete isolated from the leaf of Kaempferia larsenii10.1099/ijsem.0.001121IJSEM 66: 2917-2922 201627126122
67663Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-111731Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 111731)
96762Reimer, 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-ID407629.1