< Back to previous page

Project

Microbiota profiling of the house fly, Musca Domestica

We share our living spaces with a variety of insects – some of them can be nuisance pests, others can be beneficial, and some insects we do not even notice. These insects carry with them an abundance of microbes, that can be either beneficial (sometimes even crucial) or pathogenic for them, serve as a food source or be part of the transient microbiota. While insects can introduce valuable diversity to the niches they inhabit, they can also transport unwanted microbes to our indoor environments. There have only been a few studies looking at the microbiome of synanthropic insect species (i.e. living in close association with humans), with the most attention given to the vinegar fly Drosophila melanogaster.

In this study we chose to focus on the common house fly Musca domestica and characterize its microbiota in detail. Firstly, we set in place the methodology to efficiently analyze both bacteria and fungi in the internal and external compartments of the fly. Subsequently, we collected more than 400 house flies from two distinct geographical locations – Belgium and Rwanda. The sampling was carried out in three different human related habitats, namely in homes, farms and hospitals. The microbes inside and on the outer surface of the collected flies were analyzed using culture-dependent and culture-independent methods. A subset of cultured isolates was identified to the species level and screened for anti-microbial resistance, as it has been proposed that insects can act as environmental reservoirs for anti-microbial resistance genes.

Using targeted amplicon sequencing of partial bacterial 16S ribosomal RNA genes and the fungal internal transcribed spacer (ITS) region, we portrayed a detailed picture of house fly microbiota in a variety of habitats. Interestingly, the bacterial communities were more diverse on the outer surface of the flies compared to the internal compartment. This was not the case for fungi, which were equally diverse in both compartments in all habitats. In general, geography and habitat had a stronger influence on the composition of M. domestica external microbial communities than on internal microbiota. The bacterial subset of the internal microbiota, while varying among individuals, was rather stable with similar patterns between flies from different locations. On the other hand, the external bacteria clustered according to the fly’s country and habitat of origin, resulting in location specific microbial signatures. For example, Planococcaceae, Ruminococcaceae, Acinetobacter, and Flavobacterium were significantly enriched in fly samples from Belgian farms, whereas Massilia, Carnobacteriaceae and Corynebacterium were enriched in samples from Rwandan farms. Furthermore, the fungal communities were highly dependent on the fly sampling country and less on the habitat.

The most abundant bacterial genus detected both with targeted amplicon sequencing and with the culturing method was Staphylococcus. Identification based on β subunit of bacterial RNA polymerase (rpoB) and chaperone DnaJ of isolated strains revealed that at least 17 different Staphylococcus species were present in the house fly samples, among which S. xylosus was most abundant. These isolates were additionally tested for their anti-microbial resistance, which showed high variation between species and slight tendency for more severely resistant strains in flies from Rwandan hospitals. However, for firm conclusions in this regard more isolates from flies from more habitats are needed to be analyzed.

Among the cultured isolates we discovered a novel species that we formally described as Apibacter muscae. The genus already included two species that were isolated from bees, suggesting that this is potentially an insect specific genus.

Taken together, our study took an in depth look at microbes harbored by one of the most common synanthropic insects, the house fly. We showed that they carry very diverse bacterial and fungal communities that depend on the geographical location and habitat of the flies. However, the internal bacterial communities are more stable compared to the external ones, suggesting that their composition is under a tighter control of the fly physiology. We saw extensive overlap between microbial species found in the flies and the ones reported indoors, but the extent to which house flies influence microbial communities we encounter in our living spaces, remains to be further investigated. 

Date:20 Oct 2015 →  2 Apr 2020
Keywords:Microbial volatile organic compounds, Insects, Microbe transmission
Disciplines:Biomaterials engineering, Biological system engineering, Biomechanical engineering, Other (bio)medical engineering, Environmental engineering and biotechnology, Industrial biotechnology, Other biotechnology, bio-engineering and biosystem engineering, Microbiology, Systems biology, Laboratory medicine, Genetics, Molecular and cell biology, Scientific computing, Bioinformatics and computational biology, Public health care, Public health services
Project type:PhD project