Researchers from Harvard University and the University of California, San Francisco have found that going on a diet may be easier for your gut microbes to adjust to than it is for you. Their latest study, published in Nature in December 2013 , demonstrates that gut microbes can shift their populations and metabolic functions within a single day in response to changes in the human diet.
Between 10 and 100 trillion microbes comprise the gut microbiome, an internal ecosystem that includes multiple species of bacteria, fungi, and archaea. These organisms subsist on dietary fibers and materials that are otherwise indigestible to humans, and in return for the food, shelter, and general hospitality that we provide, our intestinal microbes produce amino acids, the building blocks of proteins, and vitamins essential for our survival. This is a classic example of mutualism among species.
Beyond vitamin and amino acid synthesis, the many other roles of the human gut microbiome are only just being discovered. What has become increasingly apparent, though, is that just as the genetic makeup of our corporeal selves can either predispose or protect us from disease, so too can our microbial makeup. Particular combinations of microbes have been experimentally linked to the exacerbation of or protection from inflammatory bowel diseases, cancer, obesity, and even neurodevelopmental disorders such as autism.
The recent study from Peter Turnbaugh’s lab at Harvard University suggests that dietary change may be an effective means of re-shaping deleterious microbial populations and functions – even within a single day. “What’s been lacking is that we haven’t had many short-term dietary interventions in humans,” said Turnbaugh, a Bauer Fellow at Harvard. “We wanted to test if it’s even possible in humans for diet to have a rapid and clear impact on our gut microbial communities.”
They recruited six men and five women between the ages of 21 and 33 for the study, low numbers that nevertheless managed to show significant results. “A main criterion was that people were willing to comply with the study regimen,” said Lawrence David, first author on the paper and now a professor at Duke University. “We were really fortunate to recruit people who were so cooperative in terms of how they sampled [their feces] and how they recorded all their diets.”
It’s easy to see why it would be difficult to find cooperative volunteers. The subjects were placed on two extreme diets: animal- or plant-based. Participants on the animal-based diet were restricted to meats, cheeses, and eggs, effectively doubling their fat and protein intake and eliminating carbohydrates and fiber. Those on the plant-based diet decreased their fat and protein intake, increased their carbohydrates, and almost tripled their fiber.
Within a single day of the animal-based diet entering the large intestine, there was a drastic alteration in the composition of the volunteers’ gut microbiome: microbes that were well equipped for the changing environment thrived. David and colleagues turned to the literature to investigate the characteristics common to these flourishing microbes, and they didn’t have to look far; on the animal based diet, the most abundant bacteria were from a genus known as Bilophila, “Which if you break down the Latin means ‘bile loving,’” said David. Bile, produced by the liver, breaks down ingested fats.
But these population shifts weren’t the only changes occurring. Microbes were changing what they ate, and how they ate it. Microbes exposed to the carnivorous diet started turning on genes that helped them break down proteins and synthesize scarce vitamins, while the protein-poor herbivorous diet caused microbes to turn on genes that helped them break down carbohydrates and that may aid in synthesizing amino acids (Figure 1).
Figure 1. Changes to the gut microbiome on different diets
The authors speculate that this newly discovered ability of our microbes to rapidly shift functions evolved to accommodate a diet that in early humans fluctuated according to our opportunistic and omnivorous eating habits.
These findings have exciting implications for intervention in diseases such as liver cancer and inflammatory bowel disease, which have been linked to diet in mouse studies. Participants on the animal-based diet showed elevated levels of a bile-metabolite called deoxycholic acid (DCA), a microbial product linked to liver cancer in mice. Similarly, experiments in mice revealed that a diet containing saturated fats from dairy increased the population size of the bacterium Bilophila wadsworthia, which in mice was found to cause inflammatory bowel disease. It too was elevated in human patients on the dairy-containing, animal-based diet.
Although Turnbaugh was reluctant to state any general recommendations based on this study, he did admit which diet he, personally, would prefer: “Before we saw the data, I would have definitely chosen the animal-based diet. But that diet induced multiple changes to the microbiota that gave us cause for concern, so it may be time to reconsider my decisions at the dining table.”
Rachel Becker is a graduate student in the immunology program at Harvard University studying neural-immune interactions in autism and schizophrenia. Her other academic love is the gastrointestinal tract.
 Link to nature article: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12820.html?_escaped_fragment_=