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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

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

Insights

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.

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.

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