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Updated: Oct 6, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Respiratory tract infections and gut microbiome modifications: A systematic review

Claire A Woodall1, Luke J McGeoch2, Alastair D Hay1

  • 1Centre for Academic Primary Care, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom.

Plos One
|January 13, 2022
PubMed

Insights

Respiratory tract infections (RTIs) significantly reduce gut microbiome diversity and abundance. This systematic review highlights a depletion of beneficial bacteria and an enrichment of others, underscoring the need for further research.

Area of Science:

  • Microbiology
  • Gastroenterology
  • Infectious Diseases

Background:

  • Respiratory tract infections (RTIs) are common and can impact the gut microbiome, but this relationship is not well understood.
  • Changes in gut microbiota may contribute to gastrointestinal symptoms associated with RTIs.

Purpose of the Study:

  • To systematically review and evaluate evidence on gut microbiome alterations in patients with RTIs compared to healthy controls.
  • To synthesize findings from human cohort studies investigating the impact of viral and bacterial respiratory infections on gut microbial composition.

Main Methods:

  • Systematic literature search of Medline, Embase, Web of Science, Cochrane, and Clinical Trial Database (Jan 2015-June 2021).
  • Inclusion of human cohort studies comparing gut microbiome in RTI patients versus controls.
  • Narrative synthesis of data from eligible studies, including meta-analysis of Shannon diversity.

Main Results:

  • Eleven studies were included, focusing on SARS-CoV-2, influenza, Tuberculosis, Community-Acquired Pneumonia, and recurrent RTIs.
  • A significant decrease in gut microbiome diversity (Shannon index: -1.45 units, p < 0.0001) and overall taxa abundance (p = 0.0086) was observed in RTI patients.
  • Meta-analysis revealed depletion of Lachnospiraceae, Ruminococcaceae, and Ruminococcus, with enrichment of Enterococcus.

Conclusions:

  • RTIs are associated with significant gut microbiome dysbiosis, characterized by reduced diversity and altered bacterial populations.
  • High heterogeneity among studies suggests variations in methodology and confounding factors.
  • Further well-designed human cohort studies are essential to elucidate the complex interplay between respiratory infections and gut microbial ecology.

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