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

These findings indicate that a single metatranscriptomics run can complement or replace kingdom-specific approaches for profiling RNA viruses and the host transcriptome, while also identifying transcriptionally active bacteria and DNA viruses. Low-abundance or latent microorganisms may still require targeted assays. Metatranscriptomics thus provides a cost- and time-efficient strategy for integrated microbiome research and holds promise for clinical applications in acute infections and cases of diagnostic uncertainty.

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Publication Details

Journal
Frontiers in Microbiology
Published
2026-01-07
DOI
https://doi.org/10.3389/fmicb.2025.1685035
Primary Topic
Respiratory viral infections research
Type
article
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article

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

Marina Sabatier, Bruno Simon, Hussein Anani, Yves Gillet et al.
Frontiers in Microbiology
Respiratory viral infections research
article

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

Marina Sabatier, Bruno Simon, Hussein Anani, Yves Gillet, Quentin Semanas, Bruno Lina, Hadrien Regue, Laurence Josset, Theophile Boyer, Antonin Bal, Gregory Destras, Dominique Ploin
article en

Abstract

These findings indicate that a single metatranscriptomics run can complement or replace kingdom-specific approaches for profiling RNA viruses and the host transcriptome, while also identifying transcriptionally active bacteria and DNA viruses. Low-abundance or latent microorganisms may still require targeted assays. Metatranscriptomics thus provides a cost- and time-efficient strategy for integrated microbiome research and holds promise for clinical applications in acute infections and cases of diagnostic uncertainty.

Frontiers in MicrobiologyVol. 16
Université Claude Bernard Lyon 1 (FR), École Normale Supérieure de Lyon (FR), Centre National de la Recherche Scientifique (FR), Inserm (FR), Hôpital Femme Mère Enfant (FR), Hospices Civils de Lyon (FR), Laboratoire National de Référence (MA), Virologie et Pathologies Humaines (FR), Centre International de Recherche en Infectiologie (FR)
Openalex Percentile: Top 96%
Respiratory viral infections research
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Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response — Marina Sabatier, Bruno Simon, et al. · Frontiers in Microbiology (2026) | TGRS Research Map | TGRS