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Microbiota of the Respiratory Tract01:29

Microbiota of the Respiratory Tract

The human respiratory tract, comprising the upper and lower segments, serves as a critical interface with the external environment. The upper respiratory tract (URT)—including the nostrils, sinuses, pharynx, and oropharynx—is heavily colonized by microbes, while the lower respiratory tract (LRT), composed of the larynx, trachea, bronchi, and lungs, was long thought to be sterile. However, recent molecular studies have revealed that the lungs are not devoid of microbes but act more like...
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Related Experiment Video

Updated: Jul 4, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Published on: December 22, 2014

Pharyngeal Microenvironment Associated with Human Rhinovirus Infection in Children: Insights from Metatranscriptomic

Muhammad Noman1,2, Ying Li1,2,3,4, Jiaming Huang1,2

  • 1State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

NPJ Biofilms and Microbiomes
|July 2, 2026
PubMed
Summary
This summary is machine-generated.

Human rhinovirus (HRV) infections in children with acute low respiratory tract infections (ALRTIs) alter pharyngeal microbiome and host gene expression. HRV-positive children showed higher microbial diversity and distinct gene expression patterns, linked to antibiotic resistance genes.

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Absorption of Nasal and Bronchial Fluids: Precision Sampling of the Human Respiratory Mucosa and Laboratory Processing of Samples
11:54

Absorption of Nasal and Bronchial Fluids: Precision Sampling of the Human Respiratory Mucosa and Laboratory Processing of Samples

Published on: January 21, 2018

Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Human rhinovirus (HRV) is a frequent cause of acute low respiratory tract infections (ALRTIs) in children.
  • HRV infection significantly impacts host gene expression and the respiratory tract microbiome.

Purpose of the Study:

  • To determine HRV prevalence in children with ALRTI in Wuhan.
  • To investigate the interactions between HRV, host gene expression, and the pharyngeal microbiome.

Main Methods:

  • Collected 1,790 samples from children with ALRTI and screened for HRV using qPCR and targeted next-generation sequencing (tNGS).
  • Analyzed 47 HRV-positive, 29 healthy control, and 27 HRV-negative ALRTI samples using meta-transcriptomic sequencing.
  • Compared microbiota dynamics, gene expression, and antimicrobial resistance genes (ARGs) between infected and healthy individuals.

Main Results:

  • HRV prevalence was 13.8%, with HRV-A and HRV-C strains dominant.
  • HRV-positive samples exhibited higher microbial diversity (Haemophilus, Neisseria, Streptococcus).
  • Identified 22,321 differentially expressed genes (DEGs) linked to immune activation and cellular processes.
  • ARGs were more prevalent in healthy individuals; significant concordance found between microbial composition and ARG profiles.

Conclusions:

  • HRV infection induces distinct shifts in pharyngeal microbial communities and host transcriptional responses.
  • Pharyngeal microbiome variations are closely associated with resistome composition.