More than half of the study subjects had samples collected a month to a year following the initial collection and some had three samples taken. In general, microbial populations present in the first sample were there in the last one as well and did not show any big blooms in the study subjects.
Getting a sense of which microbes are living in our intestines turns out to be a much more complicated task than simply looking at slides under a microscope. Many of the microbes that live inside our bodies don't do well in an oxygen-filled lab environment, so they have proved difficult to culture. This project sidestepped that problem by using genetic sequencing to catalogue species by their genetic profiles instead.
The question, however, of how to measure, track and count these organisms that we know so little about also presents some research dilemmas. One method researchers used to identify different species involves tracking the bacterial 16s gene, which humans lack. This gene appears to be different enough in each bacterial species to allow for rapid scanning and sorting of the organisms. The effectiveness of this detection method remains unclear. "In some ways, we're simply counting different features that are easiest for us to measure, but we don't know that those are the most important things," says David Relman, of the Stanford School of Medicine, who was not involved in the new studies but wrote an essay about them in the same issue of Nature.
Nevertheless, Relman notes, the findings are important early first steps, which will help inform and streamline later research. "I think it would be hubris to say this project answers something or provides the end of the story," he says. Coming work will need to zero in on individual variables, such as diet, environment and health status, to look more closely for trends in microbiome communities.
Tarr suggested that better understanding what a healthy microbiome looks like, for example, could help us prevent virulent infections, such as Clostridium difficile. C. diff is often acquired in a hospital. Our best preventative weapon so far has been better hygiene, and our treatments are only mediocre. But, he noted, if we could find out the characteristics of a microbiome that puts people more at risk for acquiring a difficult C. diff infection, we could theoretically screen incoming patients for their microbiome's genetic profile at admission, heading off potentially fatal infections.
These "who's who" lists of our microbiome "are potentially useful and biologically important as a frame of reference, but they do not tell you what the microbes are actually doing at any one time," notes Jeremy Nicholson, head of the Department of Surgery and Cancer at Imperial College London, who was not involved in the most recent studies. He and his colleagues published a study in Science last week examining some of the metabolic interactions of the microbes in the human gut and their host. "To understand them functionally as part of the big human health picture," he notes, we will need a more detailed picture of how human diet and lifestyles—including stress and medications—are impacting the microbial communities, along with how their changes are then changing us. "Understanding these interactions is where the new therapies are to be found."
Another study, published online today in Nature, reveals how a diet high in saturated fat can, in fact, change the microbial communities in the gut. This shifting population can spur an immune response that can lead to inflammatory bowel disease in those who are genetically prone.