Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.

ABSTRACT:

Introduction

Omics-based studies focusing on a single kingdom, such as bacterial 16S gene sequencing, viral metagenomics, and human mRNA sequencing, are commonly used to explore the microbiome and its association with host responses. But combining these approaches is often expensive and time-consuming. Metatranscriptomics provides a snapshot of the entire active microbiome through bulk RNA sequencing in a single test, yet its performance relative to kingdom-specific methods has not been systematically assessed.

Methods

We compared metatranscriptomics with three kingdom-specific sequencing approaches in 20 nasopharyngeal aspirates from infants 7 months of age hospitalized for bronchiolitis at the Hospices Civils de Lyon.

Results

Applying specific sequencing depth thres

SUBMITTER: Destras G 

PROVIDER: S-EPMC12819617 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature