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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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[Microbiotes and metagenomics].

Jean Weissenbach1, Abdelghani Sghir1

  • 1CEA ; Institut de Génomique ; Genoscope, 2, rue Gaston Crémieux, 91057 Évry, France.

Medecine Sciences : M/S
|December 24, 2016
PubMed
Summary

Twenty years after major advances in microbial community analysis, impressive progress has been made in microbial monitoring and diagnosis. However, understanding the functions and interactions of these microorganisms remains a significant challenge.

Area of Science:

  • Microbiology
  • Genomics
  • Systems Biology

Background:

  • The 1990s saw significant technical advancements in the study of microflora and microbial communities, primarily through analytical, often brute-force, approaches.
  • Despite these advances, fundamental questions about microbial functions, interactions, and the factors maintaining microbial associations persist.

Purpose of the Study:

  • To evaluate the conclusions that can be drawn from microbial community analyses conducted twenty years after major technical advances.
  • To assess the progress in understanding microbial functions and the mechanisms underlying microbial community dynamics.

Main Methods:

  • Retrospective analysis of data generated by major technical advances in microbial community studies from the 1990s.
  • Review of gene inventories and physiological process insights.

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  • Examination of the current state of microbiota manipulation.

    • Main Results:

    • Impressive results have been achieved in microbial composition, monitoring, and diagnosis.
    • Gene inventories are nearing completion, deepening understanding of some physiological processes but offering limited functional insights.
    • Microbiota manipulation has begun, demonstrating practical applications but lacking a deep mechanistic understanding.

    Conclusions:

    • While microbial composition and monitoring have seen remarkable progress, the functional roles and ecological interactions of microorganisms remain largely enigmatic.
    • Current knowledge, including near-complete gene inventories, provides some physiological insights but falls short of explaining microbial community assembly and maintenance.
    • Practical manipulation of microbiota is emerging, yet the underlying principles governing these interventions are not yet fully understood.