Data from: Microbial communities of the house fly Musca domestica vary with geographical location and habitat

House flies (Musca domestica) are widespread, synanthropic filth flies
commonly found on decaying matter, garbage, and feces as well as human
food. They have been shown to vector microbes, including clinically
relevant pathogens. Previous studies have demonstrated that house flies
carry a complex and variable prokaryotic microbiota, but the main drivers
underlying this variability and the influence of habitat on the microbiota
remain understudied. Moreover, the differences between the external and
internal microbiota and the eukaryotic components have not been examined.
To obtain a comprehensive view of the fly microbiota and its environmental
drivers, we sampled over 400 flies from two geographically distinct
countries (Belgium and Rwanda) and three different environments – farms,
homes and hospitals. Both the internal as well as external microbiota of
the house flies were studied, using amplicon sequencing targeting both
bacteria and fungi. Results show that the house fly’s internal bacterial
community is very diverse yet relatively consistent across geographic
location and habitat, dominated by genera Staphylococcus and Weissella.
The external bacterial community, however, varies with geographic location
and habitat. The fly fungal microbiota carries a distinct signature
correlating with the country of sampling, with order Capnodiales and genus
Wallemia dominating Belgian flies and genus Cladosporium dominating
Rwandan fly samples. Together, our results reveal an intricate country
specific pattern for fungal communities, a relatively stable internal
bacterial microbiota and a variable external bacterial microbiota that
depends on geographical location and habitat. These findings suggest that
vectoring of a wide spectrum of environmental microbes occurs principally
through the external fly body surface, while the internal microbiome is
likely more limited by fly physiology.