''People had some notion that there were pathogens that were carried by flies but had no idea of the extent to which this is true and the extent to which they are transferred," said Dr Donald Bryant, Professor of Biotechnology at Penn State University.
"We believe that this may show a mechanism for pathogen transmission that has been overlooked by public health officials.
"It will really make you think twice about eating that potato salad that's been sitting out at your next picnic.
"It might be better to have that picnic in the woods, far away from urban environments, not a central park."
DNA sequencing techniques were used to study the collection of microbes found in and on the bodies of the house fly (Musca domestica) and the blowfly (Chrysomya megacephala).
The house fly, which is ubiquitous around the world, was found to harbour 351 types of bacteria. The blowfly, which is found in warmer climates, carried 316. A large number of these bacteria were carried by both types of fly.
The team even investigated the microbes on individual fly body parts including legs and wings.
Flies probably pick up the bacteria from faeces and decaying organic matter which they use to nurture their young, the study indicated.
Scientists found 15 instances of the human pathogen Helicobacter pylori - which causes ulcers in the human gut - on Brazilian blowflies.
Dr Stephan Schuster, research director at Nanyang Technological University, Singapore, found that the legs transferred most of the microbial organisms from one surface to another, suggesting even a brief step onto food by the bugs could leave behind bacteria.
"The legs and wings show the highest microbial diversity in the fly body, suggesting that bacteria use the flies as airborne shuttles," said Schuster.
"It may be that bacteria survive their journey, growing and spreading on a new surface. In fact, the study shows that each step of hundreds that a fly has taken leaves behind a microbial colony track, if the new surface supports bacterial growth."
However, the researchers believe flies could have their uses - acting as early warning systems for disease or even living drones sent into tight spaces to search for microbes.
"In fact, the flies could be intentionally released as autonomous bionic drones into even the smallest spaces and crevices and, upon being recaptured, inform about any biotic material they have encountered," added Schuster.
The research was published in the journal Scientific Reports.