Skip to main content
Premium Trial:

Request an Annual Quote

Metagenomic Sequencing Finds Flies May Transport Pathogenic Bacteria


SAN FRANCISCO (GenomeWeb) – While flies have never been touted for their cleanliness, a new study has found that they may even play a role in transporting pathogenic bacteria.

An international research team from Nanyang Technical University in Singapore, the Federal University of Rio de Janeiro in Brazil, the European Molecular Biology Laboratory, the microbial genomics firm CosmosID, and more, used metagenomic sequencing to study the microbiomes of houseflies and blowflies, finding that they picked up bacteria from one location and deposited it at another. In addition, the team said that metagenomic sequencing could be used in public health monitoring.

Stephan Schuster, senior author of the study that was published earlier this month in Scientific Reports, also said that the metagenomic sequencing approach could replace 16S sequencing as the standard for environmental sequencing, since it can identify microbes down to the species level.

In the study, the researchers sequenced the microbiomes of 116 flies — 63 blowflies and 53 houseflies — using a shotgun whole-genome sequencing approach. The flies were collected from three countries — the US, Brazil, and Singpore — and from a variety of urban and rural sites, including a food market, the entrance to a hospital, a public city park, a landfill, a city food market, the rainforest, and a farm.  The researchers analyzed the sequence datasets using three different bioinformatics approaches and combined the results to achieve higher confidence in identifying the various microbial species.

A key part of the method was being able to capture and sample the flies without contaminating them by touching them, Schuster said. To do this, he said they came up with a way to essentially freeze them when they landed on a surface by shooting a cold stream of carbon dioxide at them. That froze them in place and then a carefully positioned tube caught them when they fell. "The fly hasn't been touched, so it's a sterile way to sample," Schuster said. Then the entire fly is mashed up and DNA is extracted.

The researchers generated an average of 70 million sequence reads per blowfly and 45 million reads per housefly. After removing the host reads, they used bioinformatics tools to classify the reads from the microbiomes of the flies. Overall, they found that Proteobacteria, Bacteroidetes,and Firmicutes were the most abundant phyla, with most of the Proteobacteria in blowflies being attributed to a known endosymbiont.

The team used alignment-based methods Rapsearch2, dbAssign, and SpecI to identify the species of bacteria in the microbiomes. All three tools found that the prevalent species on the blowfly were the known endosymbionts, representing more than 60 percent of the reads.

The most abundant bacteria in the houseflies' microbiomes was Psychrobacter, which was found in around 74 percent of the individuals and represented between 2 percent and 10 percent of the total reads, depending on which alignment tool was used. The most abundant strain of Psychrobacter that the researchers found has been associated with food spoilage.

In total, they were able to identify 431 different bacterial taxa from the flies, and the two different fly species shared just over half of their microbiomes. The researchers also identified bacterial species known to be pathogenic to plants, animals, and humans. For instance, they found three species of Pectobacterium, a pathogen that liquefies plants. The Petcobacterium species the researchers identified tend to be mostly associated with potato infections and were found on flies from Brazil, the second largest potato producer in South America. The team also found a known animal pathogen on flies collected from a farm.

The researchers also identified a number of known human pathogens, including those associated with nosocomial infections and generic infections like bacteremia and septicemia. For example, they found a bacterial species associated with urinary tract infections, but perhaps most concerning was the presence of Helicobacter pylori, which can cause stomach ulcers. The researchers also identified specific virulence factors associated with H. pylori. The team hypothesized that the flies picked up the bacteria from untreated open sewage sites or latrines.

Finally, the researchers wanted to test whether the flies could pick up bacteria from one site and transfer it to another. To do this, they coated agar plates with Escherichia coli and had flies walk on the plates. They then transferred those flies to plates not coated with E. coli. After, they found colonies of E. coli growing where the flies had stepped, illustrating that flies can transport viable bacteria from one site to another.

What's still unknown, Schuster added, and warrants further study, is whether the flies can pick up infectious agents from one location and actually deposit those bacteria a human, where they cause an infection.

Schuster said that he is particularly interested in looking at historical epidemics, like the Black Death in the Middle Ages, to see whether flies played any role in spreading those diseases. That could be done by studying rates of transmission and comparing them to fly lifecycles and travel patterns. In addition, he said that he would like to use the method to study ongoing epidemics.

Schuster added said that the study demonstrated that metagenomic sequencing could be a much more powerful tool than techniques for studying microbiomes that rely on gene amplification, although he acknowledged that the technique is much more costly and time consuming than 16S rRNA sequencing. But, he said, the unbiased sequencing approach enabled the team to identify not just the species present, but also their pathogenicity, virulence factors, and plasmids, which could be useful for public health and vector monitoring.