Overuse of antibiotics is not only creating resistant strains of bacteria but also changing the complex ecology of the human body. Our Croakey co-ordinator writes at Inside Story.
We will probably never know their names, but the contribution of 242 American men and women who were willing to share the intimate details of their microbial profile with the world is having a profound impact on our understanding of health and illness, and is even raising questions about what it means to be human. Research into the microbiome — the viruses, bacteria and other microbes living with us — also puts a whole new slant on some long-standing public health problems, like the overuse of antibiotics. But more on that later.
In June last year, after five years of work by around 200 scientists from 80 universities, the US-based Human Microbiome Project released the initial analyses of blood, stool and saliva samples, as well as swabs taken from various locations on the volunteers’ bodies. The results paint an extraordinary, though preliminary, portrait of the richness of our microbial life. The researchers found over 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). They described their findings as “the largest and most comprehensive reference set of human microbiome data associated with healthy adult individuals”.
“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.”
The research, published in a series of articles in Nature and Public Library of Science journals, found that the composition of our microbial load varied enormously, both between individuals and between sites within the same person. It also found that their functions are surprisingly similar — many different types of microbial communities can do similar work. Or as one scientist put it, “apparently, there are many different ways to be healthy when it comes to our microbes”.
We unconsciously help the microbes in their quest for survival, and many of them return the favour, whether by producing beneficial compounds, helping us to digest our foods, or boosting our immune systems. By colonising our skin, gut and other surfaces, they help reduce the opportunities for more dangerous bugs to take hold. The research found most healthy people carry pathogens, or microbes capable of causing disease, prompting some speculation that there may be hitherto unrecognised benefits from such relationships.
At a National Institutes of Health briefing accompanying the release of the findings, Phillip Tarr, director of paediatric gastroenterology and nutrition at Washington University School of Medicine in St Louis, said research into the human microbiome offered “a whole new way of looking at human biology and human disease”. According to Tarr, “we’ve now been introduced to this biomass in each and every one of us. 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.”
With most of us carrying 10 times more microbial than human cells (although they make up only a small proportion of our body mass), some researchers are talking about “human ecosystems” or “super organisms”. As Amy McGuire, an associate professor of medicine and medical ethics at Baylor College of Medicine in Houston, told the briefing, the ethical, legal and social implications of the emerging field of microbiome 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.
The upsurge of scientific interest in the human microbiome came when scientists working on the Human Genome Project realised that so much of the genetic material they were discovering wasn’t of human origin. They investigated further, helped by technological advances that enabled DNA sequencing at a fraction of the previous cost.
Another lesson from the genome project was the wisdom of establishing a reference database of a “normal” human microbiome. Hence the release of the volunteers’ data last year, with the goal of enabling further investigations. As one of the Nature paper says, “Collectively the data represent a treasure trove that can be mined to identify new organisms, gene functions, and metabolic and regulatory networks, as well as correlations between microbial community structure and health and disease”.
These are early days in this burgeoning field of research, but it 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 colonisers. The hope is that, as research progresses, we will learn how to care for our microscopic colonisers so that they, in turn, can care for our health.”