DOI: 10.5061/dryad.cj212m6
title: Data from: Microbial communities of the house fly Musca domestica vary with geographical location and habitat

description: 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.
description: Bac_metadataMetadata related to samples (controls and individual fly samples) with bacterial 16S V4 readsBac_otu_tableBacterial 16S V4 region ASV/sample table (from dada2)Bac_taxonomyTaxonomy file linking bacterial ASVs to the taxonomic IDs (silva database)table_Bac1246Qiime2 file, ASV/sample table of 16S V4 region, before filtering. Provenance can be viewed in https://view.qiime2.orgfilt_tab_Bac1246Qiime2 file. ASV/sample table (16S V4 region) after filtering. Provenance can be viewed on https://view.qiime2.orgrep-seqs_Bac1246Qiime2 file. Representative sequences (16S V4).taxonomy_Bac1246Qiime2 file. Taxonomy file linking the bacterial features to taxonomic assignments.Fungi_metadataMetadata related to samples (controls and individual fly samples) with fungal ITS2 readsFungi_otu_tableFungal ITS2 region ASV/sample table (from dada2)Fungi_taxonomyTaxonomy file linking fungal ASVs to the taxonomic IDs (UNITE database)table_Q10_Fun35Qiime2 file, ASV/sample table of ITS2 region, before filtering. Provenance can be viewed in https://view.qiime2.orgfilt_tab_Q10_Fun35Qiime2 file. ASV/sample table (ITS2 region) after filtering. Provenance can be viewed on https://view.qiime2.orgrep-seqs_Q10_Fun35Qiime2 file. Representative sequences (ITS2).tax_Q10_Fun35Qiime2 file. Taxonomy file linking the fungal features to taxonomic assignments.