Among the trillions of bacteria that populate us, most reside in the gastrointestinal system, where their species number in the thousands. But the variation in the number of species between individuals is so great that scientists were beginning to despair of ever detecting a significant pattern to the diversity. Then a study published in May 2011 found that gut flora cluster into three basic patterns of species—a finding that surprised researchers within MetaHIT, the European project cataloguing and analyzing bacteria in the human intestinal tract. It’s one more example of evidence turned up in the past year of these bacteria’s close intertwining with our physiology, a line of research Proto explored in its infancy (“Our Native Flora,”Summer 2010). Resident microbes help extract energy from food, stimulate the immune system and provide a buffer against invading pathogens, among other important tasks. Only recently have scientists managed to link imbalances in our microbial makeup to cancer, inflammatory bowel disease and obesity.

Each of the three “enterotypes”—named Bacteroides,Prevotella and Ruminococcus after their most abundant species—produced different vitamins and processed energy differently. Already scientists are attempting to correlate the enterotypes to diet and other factors. Gary Wu, a gastroenterologist at the Perelman School of Medicine at the University of Pennsylvania, and his team sampled the gut flora of people who had provided long-term dietary information, finding that the Bacteroides enterotype was correlated with animal protein and saturated fat intake, whereas Prevotella was associated with carbohydrate-rich diets. Researchers are now working with human gut bacterial species and so-called germ-free mice—mice with no flora of their own—to see what happens to these bacterial communities as the mice consume diets with varying amounts of protein, starch, sugar and fat.

Yet since Proto reported on the microbiome, researchers have begun to move beyond the connections between gut flora and metabolism to look at how our microbes might interact with our brains. The early evidence suggests that they exert a powerful influence on a mouse’s emotional state and its brain development. Rochellys Diaz Heijtz and her colleagues at the Karolinska Institute in Stockholm discovered that germ-free mice grow up more active and exploratory than those with an intact microbiome, who are more cautious and anxious. It remains to be seen whether the same effect occurs in humans—and just what else the microbes that outnumber our own cells 10 to 1 are doing to us.