U.S. Department of Health and Human Services

Long-term Diet Determines Which Bacteria Reside in the Gut

In their quest for greater understanding of how microbes inhabiting the body affect human health and wellness, scientists have found an association between individuals’ long-term diets and the microbes that predominate inside their intestines. The current study analyzed the community of bacteria (microbiota) that populate the intestine and the effect of diet on different types of bacteria. For the first study, designated as “COMBO,” a group of 98 healthy volunteers were asked to complete 2 questionnaires—1 asking for information on their diets over a long period of time (Food Frequency Questionnaire), and another asking the volunteers what they had eaten recently (Recall Questionnaire). The volunteers also provided stool samples, which contained bacteria from the intestines. The scientists then assessed the nutrients consumed by each of the volunteers by analyzing the dietary information from the questionnaires, and they identified the bacterial species within the gut microbiota by sequencing the bacterial DNA from the stool samples. Analyses of the DNA showed the gut microbiota of the volunteers contained two primary clusters of bacterial types found in the intestine, known as enterotypes—the Bacteroides enterotype and the Prevotella enterotype—with one of the two identified as dominant for each volunteer. By comparing dietary nutrients and bacterial species, the scientists determined that long-term dietary composition was associated with enterotypes. The Bacteroides enterotype was highly associated with a diet high in animal protein and saturated fat, whereas the Prevotella enterotype was associated with a high-carbohydrate diet. Ten of the volunteers also participated in a study called “CAFE,” in which they ate a controlled diet while living in a hospital environment. All of the CAFE participants had been identified in the COMBO study as having dominant Bacteroides enterotypes, associated with diets high in animal protein and saturated fat. Half of the volunteers were given the high-fat/low-fiber (Bacteroides) diet, and half were given a low-fat/high-fiber (Prevotella) diet. Changes in microbiota composition were seen within 24 hours of starting a new type of diet, as detected by changes in the collective microbial genomes. Although significant, none of these changes in microbiota composition resulted in lasting changes in the volunteer’s enterotype during the 10 days of the CAFE study. These studies indicate that, while dietary components over the short-term affect gut bacterial populations, long-term dietary composition determines the dominant enterotype of bacteria in the human intestine. This research has demonstrated an association between long-term diet and gut bacterial enterotypes. If future research finds that gut enterotypes, like dietary patterns, are associated with particular diseases, these results could have important implications for treating diseases through long-term dietary interventions to produce a healthy gut enterotype.

Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105-108, 2011.