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Microbiota Modulation by Antibiotics01:21

Microbiota Modulation by Antibiotics

Antibiotics have revolutionized modern medicine by saving countless lives from bacterial infections. However, their widespread use has inadvertently harmed the delicate balance of the human gut microbiota. The gut microbiota, a complex community of bacteria, archaea, viruses, and fungi, plays a vital role in regulating metabolism, immune responses, and maintaining intestinal health. Antibiotics, especially broad-spectrum types, disrupt this ecosystem by eradicating both harmful and beneficial...
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Updated: May 28, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Published on: October 15, 2019

Probiotic-Induced Gut Microbiota Modulation: A Comparative Analysis Using 16S rRNA V3-V4 and Targeted Sequencing.

Han Lee1, Gaeun Kim1, Jungeun Kim1

  • 1Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu 11759, Republic of Korea.

Microorganisms
|May 27, 2026
PubMed
Summary
This summary is machine-generated.

Standard 16S rRNA V3-V4 sequencing shows bias in quantifying specific microbes like probiotics. High-resolution targeted species sequencing (TSS) offers better accuracy for probiotic efficacy studies.

Keywords:
16S rRNAgut microbiotaprobioticstarget species

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Area of Science:

  • Microbiome research
  • Gut microbiota analysis
  • Probiotic efficacy studies

Background:

  • Standard 16S rRNA V3-V4 sequencing has limitations in taxonomic resolution and primer mismatch.
  • Accurate quantification of specific low-abundance taxa, such as probiotic strains, is challenging with current methods.
  • Reliable assessment of probiotic efficacy requires precise microbial quantification.

Purpose of the Study:

  • To compare the bias and reliability of standard 16S rRNA V3-V4 sequencing versus high-resolution targeted species sequencing (TSS).
  • To establish reliability metrics for probiotic efficacy assessments using different sequencing methods.
  • To evaluate the suitability of 16S rRNA V3-V4 sequencing for monitoring specific probiotic strains.

Main Methods:

  • A longitudinal pilot study involving older participants receiving synbiotic supplementation.
  • Collection and analysis of fecal samples over a nine-week period.
  • Comparison of outcomes between standard 16S rRNA V3-V4 sequencing and high-resolution TSS.

Main Results:

  • V3-V4 analysis revealed transient alpha-diversity reduction and genus-level fluctuations.
  • Taxonomic overlap between V3-V4 and TSS was high at the phylum level but decreased to 6.7% at the species level.
  • TSS successfully quantified administered *Bifidobacterium animalis*, unlike V3-V4 sequencing.

Conclusions:

  • 16S rRNA V3-V4 sequencing introduces significant quantitative bias, limiting its use for specific probiotic strain monitoring.
  • The reliability of clinical probiotic efficacy assessments is compromised by V3-V4 sequencing limitations.
  • A dual-sequencing approach combining V3-V4 and TSS is recommended for rigorous probiotic efficacy evaluation.