Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner

Area of Science:

• Microbiome research
• Virology
• Molecular biology

Background:

• Emerging viral pathogens necessitate high biosafety levels for sample processing.
• Inactivating viruses simplifies safety protocols but may impact other biological components.
• The effect of inactivation methods on host-associated microbiomes is largely unknown.

Purpose of the Study:

• To investigate the impact of five common inactivation methods on microbiome composition and diversity.
• To compare these effects across four distinct human body sites (gut, nasal, oral, skin).
• To guide the selection of appropriate inactivation methods for microbiome research.

Main Methods:

• Samples from gut, nasal, oral, and skin sites were treated with heat, ethanol, formaldehyde, psoralen, or TRIzol.
• Untreated samples served as controls.
• 16S rRNA gene sequencing was used to analyze bacterial taxa abundance and diversity.

Main Results:

• Nasal and skin microbiomes were most sensitive to inactivation, with ethanol and TRIzol causing major compositional shifts.
• Heat, formaldehyde, TRIzol, and psoralen significantly altered microbiome diversity across sample types.
• Oral and gut microbiomes showed greater resilience, with minimal diversity changes and moderate compositional shifts.

Conclusions:

• Inactivation methods can introduce significant, tissue-specific biases into microbiome data.
• Bacterial taxa like Firmicutes were least affected, while Bacteroidetes, Actinobacteria, and Proteobacteria showed variable responses.
• Method selection must be tailored to the specific sample type to ensure accurate microbiome analysis.