Our health is tied to trillions of organisms that live in and on us. But the extent of their impact has only recently come into focus. And scientists are just starting to figure out “who” is there—and why. Microbes in the digestive tract are particularly difficult to culture in the lab, so our major populations of mini-residents have remained mysterious. But with new rapid—and affordable—genetic sequencing machines, researchers are now able to survey and identify the spectrum of microbes in individuals and across different populations. Instead of having to grow organisms in the lab, scientists now can scan a fecal sample for genetic markers to see what organisms are there.
The American Gut Project, a citizen-science, crowd-funded effort to study our microbes on a massive scale, released on September 17 their first major group of results based on more than 800 people and more than 1,000 different samples. From the genetic screening of these samples, researchers can identify organisms down to the species level, showing, for instance, that many of us carry small quantities of would-be harmful organisms such as certain E. coli strains alongside larger populations of more beneficial bacteria.
The two most common bacterial phyla in our guts, according to the research, are usually Firmicutes and Bacteroidetes, which each contain a wide variety of species, including Clostridium (which can cause the dangerous infection C. difficile) in the Firmicutes group. The researchers liken assessing these major inhabitants to characterizing a forest by its trees, such as pine versus oak, to get a sense of the overall ecosystem. The proportions of different groups can vary widely—with some people hosting a gut that is 90 percent Firmicutes species while others host just 1 percent from that group.
What makes our guts so different? One obvious answer would be the food we eat. One of the project's leaders, Jeff Leach, eats a "paleo" diet (avoiding grains, processed foods and dairy); his gut was more than 75 percent Firmicutes; Michael Pollan, the author and plant-centric omnivore had a gut flora that was more than 50 percent Firmicutes; Shannon Ford, Mrs. United States 2011 who has celiac disease and eats a gluten-free diet, had less than 50 percent Firmicutes in her gut. These points on the chart are far from hard-and-fast patterns—and in fact are somewhat perplexing—so researchers looked for other variables that might be determining the composition of our guts.
Across the study population, though it was still slight, age seemed to make the biggest difference—more so than diet, exercise and sex—with babies having the most diverse microbial populations in their intestines. But on average, none of these factors correlated with dramatic, telltale patterns in microbe populations such as we might have hoped.
And some of the initial results seem confounding in terms of health impact. For example, those on a paleo diet had lower proportions of Proteobacteria, a phylum that is linked to inflammation. But they also had more Firmicutes, which have been tied to higher rates of obesity. So, it’s not clear that this diet puts the eater on the path of microbial health. And it’s wise to recall that the members of these two bacterial groups can be wildly different. Proteobacteria, for example, includes E. coli and Salmonella as well as less harmful species. (For perspective, our phylum, Chordata, includes every animal with a spinal cord—from us to frogs.) So making these links more solid will require more detailed analysis of these complex populations.
We already knew that certain interventions, such as broad-spectrum antibiotics, can alter the makeup of our gut's microbiota rapidly and dramatically. The new research offers a stark demonstration of this in gut microbiome samples provided by Michael Pollan. After a course of antibiotics, his populations shifted drastically, diminishing his Firmicutes population to close to 25 percent. Even three weeks after finishing his antibiotics, his flora had not regained its previous balance.
This project is just getting started. As of late August, researchers at the American Gut Project based at the University of Colorado, Boulder had received more than 2,000 samples for sequencing. And more samples mean richer and potentially more helpful data. "As additional participants with unusual diet and exercise characteristics join the study (e.g. more vegans or more people who never exercise), we will be able to say more about how these unusual lifestyles affect your gut microbes, and perhaps provide recommendations about what lifestyle factors are associated with healthier gut bacteria," the researchers noted in the report (pdf).
These early American Gut Project results have yet to be published in a peer-reviewed journal, but they represent a step toward a better understanding of the totality of our health. Perhaps once we know what often goes on in the gut, in sickness and in health, researchers will be able to discover new, better-targeted treatments and make more helpful lifestyle recommendations.