Abstract
Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.
Highlights
Interactions between hosts and microorganisms are increasingly recognized as a ubiquitous principle in nature[1], capable of modulating animal physiology, fitness, and host social behaviour[2]
We have investigated 116 microbiomes by whole-genome shotgun (WGS) sequencing of 63 samples of blowflies of the species Chrysomya megacephala and 53 individual houseflies of the species Musca domestica, describing the complexity of the pan-microbiomes of both mechanical vectors at the species level
The genomes of M. domestica and C. megacephala were sequenced to a depth of 3.2-fold and 6.6-fold respectively, the host mitochondrial DNA was sequenced to a depth of 7000-fold[15], and the Wolbachia spp. endosymbiont genome was covered to a depth of >2000-fold
Summary
Interactions between hosts and microorganisms are increasingly recognized as a ubiquitous principle in nature[1], capable of modulating animal physiology, fitness, and host social behaviour[2]. The microbiomes of termites, bees, ants, flies, mosquitoes, and the triatome bug[6] have recently been analysed Many of these studies have been restricted to 16S sequencing[7], which generally limits the identification of microbial taxa by the experimental shortcomings and biases of PCR-based and/or cultivation-based methods, yet providing a record of the phylum- and genus-level diversity. To depict the microbiomes of both fly species, we analysed the entire dataset using three approaches with different degrees of stringency, which we combined for high confidence of taxa assignment This allowed us to reach a species-level identification of the microbial communities in these mechanical vectors and provide a better understanding of the roles of these flies as potential agents of pathogen transmission
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