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Related Experiment Video

Updated: Oct 23, 2025

Oral Biofilm Sampling for Microbiome Analysis in Healthy Children
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Strain-Level Profiling of Oral Microbiota with Targeted Sequencing.

Chiranjit Mukherjee1, Eugene J Leys2

  • 1Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA. mukherjee.55@osu.edu.

Methods in Molecular Biology (Clifton, N.J.)
|August 19, 2021
PubMed
Summary
This summary is machine-generated.

Targeted sequencing of the 16S-23S Intergenic Spacer Region (ISR) offers higher resolution for oral microbiota analysis. This method distinguishes bacterial subspecies and strains, overcoming limitations of traditional 16S rRNA gene sequencing.

Keywords:
Amplicon sequencingBacteriaDADA2High resolutionIllumina MiSeqMicrobiomeStrainsTaxonomic assignment

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • 16S rRNA gene sequencing is standard for microbial community analysis but lacks subspecies resolution.
  • Oral microbiota studies require higher resolution to differentiate closely related species and strains.

Purpose of the Study:

  • To introduce and validate a novel sequencing approach using the 16S-23S Intergenic Spacer Region (ISR).
  • To achieve subspecies- or strain-level taxonomic characterization of microbial communities, particularly in the oral cavity.

Main Methods:

  • Targeted sequencing of the bacterial 16S-23S Intergenic Spacer Region (ISR).
  • Utilizing the higher genetic diversity within the ISR for enhanced taxonomic discrimination.
  • Leveraging established advantages of 16S-based methods like simple library prep and cost-effective sequencing.

Main Results:

  • The ISR sequencing approach provides subspecies-level resolution.
  • This method successfully differentiates closely related oral bacterial species and strains.
  • The approach maintains the practical benefits of 16S sequencing.

Conclusions:

  • Sequencing the 16S-23S ISR is a powerful tool for high-resolution oral microbiota characterization.
  • This method surpasses traditional 16S rRNA gene sequencing for detailed taxonomic studies.
  • It offers a cost-effective and efficient solution for strain-level microbial analysis.