Strain identifier

BacDive ID: 132634

Type strain: Yes

Species: Yimella radicis

Strain Designation: py1292

Strain history: <- Shu-Kun Tang, Yunnan Univ.

NCBI tax ID(s): 1847819 (species)

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General

@ref: 24423

BacDive-ID: 132634

DSM-Number: 100721

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

description: Yimella radicis py1292 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root of Paris polyphylla Smith var. yunnanensis.

NCBI tax id

  • NCBI tax id: 1847819
  • Matching level: species

strain history

@refhistory
24423<- S.-K. Tang, YIM <- L.-L. Yang, Yunnan Institute of Microbiology (YIM), Kunming, P.R. China; py1292
67770LMG 29070 <-- S.-K. Tang and L.-L. Yang; Yunnan Inst. of Microbiol., Yunnan Univ., China; py1292.
67771<- Shu-Kun Tang, Yunnan Univ.

doi: 10.13145/bacdive132634.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Yimella
  • species: Yimella radicis
  • full scientific name: Yimella radicis Yang et al. 2016

@ref: 24423

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Yimella

species: Yimella radicis

full scientific name: Yimella radicis Yang et al. 2016

strain designation: py1292

type strain: yes

Morphology

cell morphology

  • @ref: 24900
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

  • @ref: 24900
  • colony size: 0.5-1.5 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 4 days
  • medium used: TSA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24900Trypticase Soy Agar (TSA)yes
24423TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24900positivegrowth20-45
24900positiveoptimum28mesophilic
24423positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
24900positivegrowth6.0-8.0
24900positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
24900aerobe
67771aerobe

spore formation

  • @ref: 24900
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
24900NaClpositivegrowth0-9.0 %
24900NaClpositiveoptimum0-3.0 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2490062968cellulose-hydrolysis
249005291gelatin-hydrolysis
2490017234glucose-fermentation
2490017632nitrate-reduction
2490027897tryptophan-energy source
2490053424tween 20-hydrolysis
2490053426tween 80-hydrolysis
2490016199urea-hydrolysis
24900645522-hydroxybutyrate+respiration
24900370543-hydroxybutyrate+respiration
2490030089acetate+respiration
2490013705acetoacetate+respiration
2490015895D-galactonic acid lactone+respiration
2490023652dextrin+respiration
249004853esculin+hydrolysis
249004853esculin+builds acid from
2490015740formate+respiration
2490016537galactarate+respiration
2490016865gamma-aminobutyric acid+respiration
2490029985L-glutamate+respiration
2490062345L-rhamnose+respiration
2490017115L-serine+respiration
2490017306maltose+respiration
2490028053melibiose+respiration
2490074611methyl (R)-lactate+respiration
24900320061methyl alpha-D-glucopyranoside+builds acid from
2490017272propionate+respiration
2490016634raffinose+builds acid from
2490016634raffinose+respiration
2490028017starch+hydrolysis
2490017992sucrose+respiration
2490053423tween 40+hydrolysis
2490053425tween 60+hydrolysis

metabolite production

  • @ref: 24900
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 24900
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
24900acid phosphatase+3.1.3.2
24900alkaline phosphatase+3.1.3.1
24900alpha-chymotrypsin-3.4.21.1
24900alpha-fucosidase-3.2.1.51
24900alpha-galactosidase+3.2.1.22
24900alpha-glucosidase+3.2.1.20
24900alpha-mannosidase+3.2.1.24
24900beta-galactosidase+3.2.1.23
24900beta-glucosidase-3.2.1.21
24900beta-glucuronidase-3.2.1.31
24900catalase+1.11.1.6
24900cystine arylamidase-3.4.11.3
24900cytochrome oxidase+1.9.3.1
24900esterase (C 4)+
24900esterase lipase (C 8)+
24900leucine arylamidase+3.4.11.1
24900lipase (C 14)-
24900N-acetyl-beta-glucosaminidase-3.2.1.52
24900naphthol-AS-BI-phosphohydrolase+
24900trypsin-3.4.21.4
24900tryptophan deaminase-4.1.99.1
24900valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
24423surface-sterilized root of Paris polyphylla Smith var. yunnanensisParis polyphylla Smith var. yunnanensisYunnan Province, ZhongdianChinaCHNAsia
67770Surface-sterilized root of Paris polyphylla Smith var. yunnanensisParis polyphyllaZhongdian, Yunnan Province, southwest ChinaChinaCHNAsia
67771From the rhizome of `Paris polyphylla var.yunnanensis`ChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 24423
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24423
  • description: Yimella radicis strain py1292 16S ribosomal RNA gene, partial sequence
  • accession: KU517232
  • length: 1434
  • database: ena
  • NCBI tax ID: 1847819

GC content

@refGC-contentmethod
2490065.5high performance liquid chromatography (HPLC)
2442365.6high performance liquid chromatography (HPLC)

External links

@ref: 24423

culture collection no.: DSM 100721, KCTC 39612, LMG 29070, JCM 32439

straininfo link

  • @ref: 90948
  • straininfo: 407290

literature

  • topic: Phylogeny
  • Pubmed-ID: 27469463
  • title: Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis.
  • authors: Yang LL, Jiang Z, Tang SK, Chu X, Xu LH, Zhi XY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001334
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Melanthiaceae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24423Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100721Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100721)
24900L.-L. J. Yang, Zhao,Tang, Shu-Kun,Chu, Xiao,Xu, Li-Hua,Zhi, Xiao-YangYimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis10.1099/ijsem.0.001334IJSEM 66: 4191-4196 201627469463
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
90948Reimer, 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-ID407290.1