The human microbiome is one of the most mysterious subjects in modern medicine, but two studies published today in Science are helping to change that. By drawing on the gut bacteria of nearly 4,000 subjects across Belgium and the Netherlands, scientists found new evidence that a person's diet and lifestyle has a profound effect on the bacteria in their intestinal system, and that bacteria can have a significant impact on their health.

To conduct their research, scientists examined our best window into what’s happening in a given person’s intestines: their poop. Poop samples were collected through a process of home-sampling and freezing. Researchers then analyzed that poop to generate a comprehensive look at how intestinal microbes interact with human behavior and general health.

"We still are not sure what the definition of a healthy microbiome is."

The results confirm the long-standing impression that a more diverse microbiome is at least correlated with improved general health. For instance, the studies found a small but significant link between less diverse biomes and a higher body mass index — the measure of whether a person is over or underweight. That link has been suggested by previous research, but remains controversial. Researchers also found a positive correlation between a more diverse biome and a diet high in fruits and vegetables.

At the same time, researchers saw extreme variation in bacteria from person to person, and it remains very difficult to say what makes a given person’s microbiome better or worse. "We still are not sure what the definition of a healthy microbiome is," says Stanford researcher Elisabeth Bik, who runs the Microbiome Digest blog and was not involved in the studies. "The authors of both studies found a large range of microbiome compositions among these individuals, and we need to look at large groups of individuals before we can see patterns in microbiome composition that are associated with health."

While direct health effects are still unclear, the studies point to a number of concrete steps a person can take to cultivate a more diverse microbiome. Specific dairy bacteria were found more often in samples from subjects with dairy-rich diets, strongly indicating that a person’s diet has a direct effect on their gut bacteria. Subjects who drank more coffee or tea generally had more diverse microbiomes, while subjects who drank more soda had less bacterial diversity. Drinking red wine was also associated with the presence of a specific anti-inflammatory bacteria, which may ward off illnesses like irritable bowel syndrome.

"We have not captured all microbial diversity that lives in our guts."

Other results were harder to decipher. One study found a microbiome correlation with red blood cell count and hemoglobin concentration, suggesting that certain species of gut bacteria could be connected to how the body processes oxygen. But until that connection has been confirmed by further research, it’s difficult to say what it might mean.

If we can solve those mysteries, some researchers think it could help us manage the growing threat posed by antibiotic-resistant bacteria. In an editorial in the same issue of Science, Sloan-Kettering physician-scientist Eric Pamer argues that treatments based on intestinal bacteria could be a crucial tool for patients dealing with a bacterial infection. Using conventional antibiotics wipes out many of the naturally occurring bacteria in a patient’s body, which can leave that patient more vulnerable to harmful bacteria in the aftermath of an aggressive treatment. Pamer argues that introducing beneficial or "commensal" bacteria during that period could help patients resist subsequent bacterial infections. "From a clinical standpoint," he writes, "the development of commensal bacteria as preventive and therapeutic agents is a high priority." Antibiotic-resistant infections already cause 23,000 deaths and cost the US $21 billion each year.

Still, the biggest lesson of the new studies is that scientists still don’t know all that much about the various bacteria that live in our intestines. The studies found that only 14 species of bacteria were shared across 95 percent of the population, out of a total of 664 species represented in the sample overall. Even with this research, the total human stool microbiome has yet to be sequenced, a major opportunity for scientists going forward. "It was somewhat surprising," says Bik. "Even when stool samples from 4000 people are analyzed, we have not captured all microbial diversity that lives in our guts."