# Microbiome composition modulates the lethal outcome of Drosophila A virus infection

## TL;DR

This study shows that changes in gut bacteria can affect how deadly a virus is in fruit flies, even without changing immune responses or gut damage.

## Contribution

The study reveals that microbiome composition modulates viral pathogenesis independently of immune responses, viral evolution, and intestinal damage.

## Key findings

- Lactiplantibacillus plantarum reduces lifespan in Drosophila A virus-infected flies despite lower viral protein accumulation.
- Tolerance reduction requires live bacteria and is specific to Drosophila A virus.
- Microbiome changes do not alter transcriptional immune responses or select for more pathogenic viral variants.

## Abstract

Host-associated microbiomes can strongly influence viral infection outcomes, yet how minor variations in commensal bacterial composition modulate viral pathogenesis remain poorly understood. Here, we used Drosophila melanogaster to investigate how bacterial microbiome composition affects pathogenesis of enteric RNA viruses. Lactiplantibacillus plantarum supplementation increased bacterial microbiome diversity without altering total bacterial load, while Acetobacter pomorum supplementation had minimal impact on the bacterial microbiome. L. plantarum-enriched flies exhibited an additional ~ 15% reduction in lifespan from Drosophila A virus (DAV) infection despite showing reduced viral protein accumulation and similar viral RNA levels. The reduction in tolerance to viral infection required live bacteria and was observed only for DAV, as no change in mortality was observed with Nora virus or Drosophila C virus infections. Mechanistic investigations revealed that tolerance reduction occurs independently of transcriptional immune responses, as DAV-infected flies showed similar transcriptional profiles regardless of bacterial microbiome composition. Intestinal barrier function assays demonstrated that a large number of L. plantarum-supplemented flies died before developing signs of gut barrier disruption, suggesting that extra-intestinal mechanisms contribute to mortality; this interpretation is further supported by similar levels of intestinal damage markers observed in virus-infected flies under both microbiome conditions. Viral genomic sequencing ruled out microbiome-driven selection of more pathogenic viral variants, as no adaptive mutations were observed between microbiome conditions that could account for the differential pathogenesis. These findings describe how subtle shifts in microbiome composition modulate viral infection outcomes through pathways that operate independently of canonical immune responses, viral evolution, and intestinal damage.

The online version contains supplementary material available at 10.1007/s00018-025-06042-8.