In June last year, after five years of work by about 200 scientists from 80 universities, the US-based Human Microbiome Project released its initial analyses...The results paint an extraordinary, though preliminary, portrait of the richness of our microbial life. The researchers found more than 10,000 species of microbes living in and on their subjects, with each person carrying about 8 million different bacterial genes (compared with 22,000 or so human genes).

''The more closely we look, the more bacterial diversity we find,'' said one of the scientists, Susan Huse, from the Marine Biological Laboratory, when the microbiome ''map'' was released. ''We can't even name all these kinds of bacteria we are discovering in human and environmental habitats. It's like trying to name all the stars.''

Just as we unconsciously help the microbes in their quest for survival, so do many of them return the favor, whether by producing beneficial compounds, helping us to digest our foods, or boosting our immune system. By colonizing our skin, gut and other surfaces, they help reduce the opportunities for more dangerous bugs to take hold. The research found that most healthy people carry pathogens, or microbes capable of causing disease, prompting speculation that there may be hitherto unrecognized benefits from such relationships.

Phillip Tarr, director of pediatric gastroenterology and nutrition at Washington University School of Medicine in St Louis, said that research into the human microbiome offers ''a whole new way of looking at human biology and human disease. These organisms, these bacteria, are not passengers. They're metabolically active. As a community, we have to reckon with them much like we have to reckon with the ecosystem in a forest or a body of water.''

As Amy McGuire, an associate professor of medicine and medical ethics at Baylor College of Medicine, told a media briefing about the study, the implications of this emerging field of science are profound. ''There are also very interesting questions about whether the fact that we have more microbial DNA in and on our bodies than human DNA changes how we think about what it means to be human,'' she said.

While these are early days, this burgeoning field of research seems to signal a profound shift in our relationship with the microbial world. ''This is only the beginning,'' writes Joy Yang, a researcher at the National Human Genome Research Institute. ''We have learned that the bacteria living in and on us are not invaders but are beneficial colonizers. The hope is that, as research progresses, we will learn how to care for our microscopic colonizers so that they, in turn, can care for our health.''

Yet we've been doing the opposite for many years by waging a long-running war with our microbiome. This has often been unintentional, through shifts in our food supply and way of life, or even in the way we give birth. (It's been suggested, for example, that the global growth in caesarean deliveries may have reduced the transmission of health-giving microbes from mother to baby.) But much of the warfare has been deliberate, conducted via an arsenal of antibiotics, antibacterial wipes and other efforts to avoid germs.

From the earliest days of antibiotics, the bugs fought back. According to Lyn Gilbert, an infectious diseases physician and clinical microbiologist at Westmead Hospital in Sydney, it was only a short time after penicillin became available for treatment of civilians in Sydney in 1946 that a resistant strain of Staphylococcus aureus was found in about half of the surgical wound infections at the Royal Prince Alfred Hospital.

While much concern about antibiotics overuse has focused on how it promotes the emergence of treatment-resistant organisms, perhaps the collateral damage has been much more profound.

''The Menace of Antibiotics'' was the title of a presentation at a major conference in San Francisco last October by Martin Blaser, a physician, epidemiologist and professor of microbiology at NYU School of Medicine. Blaser's talk covered many of the concerns he has raised in journal articles in recent years, suggesting that antibiotics have affected the microbiome in ways that have had adverse long-term health consequences.

Blaser suggests, for example, that the widespread eradication of Helicobacter pylori (a bacterium associated with stomach inflammation and duodenal ulcers) may be implicated in the rise of conditions such as obesity, type 2 diabetes and asthma. He also argues that the eradication of relatively benign bacteria leaves us exposed to the risk of being colonized by more harmful bugs.