A detailed genetic analysis of human faeces has revealed that we harbour 1,200 different viruses in our gut.
Little is known about most viruses
The researchers, from San Diego State University found that more than half were previously unknown to science.
Most are phages - viruses that infect and kill bacteria - which are perfectly harmless to humans.
Writing in the Journal of Bacteriology, the researchers say their findings could lead to new treatments for gut disorders.
The gut contains up to 500 types of bacteria which play a crucial role in helping to digest food, and regulating our bowels' health.
The researchers say that phages could be used to tweak the balance of these bacteria.
They say: "Understanding the population structure and dynamics of the normal human intestinal microbiota [micro organisms] has important implications for human health, nutrition, and the development of probiotics for the treatment and prevention of gastrointestinal disorders."
Only the viruses and bacteria that cause disease have been studied in detail.
Most of the world's bugs cannot be grown in the laboratory - and therefore cannot be identified.
But the San Diego team was able to garner information about them by extracting their genes from samples of human faeces.
The researchers compared the genetic material they discovered with DNA sequences from known bacteria and viruses.
They found matches to families of phages, to previously described bacteria, to tiny organisms called protozoa and to DNA fragments called mobile elements that are shared by bacteria and viruses.
Dr Bob Rastall, an expert in food technology at the University of Reading, told BBC News Online the study was significant as we currently knew little about the viruses present in the gut, despite the fact that they probably played an important role.
Firstly, they prey on bacteria, and so control the numbers of bacteria in the gut.
And secondly, they can change the genetic structure of bacteria, potentially altering the effect they have in the gut.
Dr Rastall said much work was taking place to develop foods that could either introduce new organisms into the gut, or promote the growth of certain types that were already there.
He said: "The significance of the phage work is that at the moment we are working partially sighted in that we do not take into account the impact of phages.
"They could be a reason, for example, why some probiotic bacteria do not persist in the gut after introduction."
Professor Glenn Gibson, a colleague of Dr Rastall's at the University of Reading, also welcomed the study.
He said: "Certainly the authors have used up to date technologies to address a difficult issue.
"As is the case with gut bacteria there is a lot of diversity to unravel with the viruses.
"I don't doubt that some of the phages may result in novel therapies against recognised pathogens. Often the best way to kill a microbe is to use another one."