Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment

TL;DR

This study characterizes bacterial communities in Drosophila, revealing that natural microbiota are mainly influenced by food source and host species, while lab environments show more stochastic effects and no host species influence.

Contribution

It provides a comprehensive comparison of bacterial communities in wild and laboratory Drosophila, highlighting environmental and host effects on microbiota composition and identifying a potential core microbiome.

Findings

Natural microbiota shaped mainly by food substrate

Lab microbiota influenced by stochastic effects

Identification of a core genus Gluconobacter in wild flies

Abstract

The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory reared Drosophila species. We find no evidence for host species effects in lab reared flies, instead lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore we were able to identify candidate pathogens in natural fly isolates.