Fast food vs. the African diet: The bacteria battle waged in your gut

Not to mention the toll, he said, the fast food regimen took on the young man's body: "My son was at first excited to get 10 days of fast food, but after day three, the novelty had worn off," Spector recalled. Spector is now working on testing the fast food diet in a group of volunteers to see whether their microbiomes are similarly affected.

While Spector works to learn more about the connection between fast food and the microbiome, a number of studies are already giving us an idea which foods are good and bad for the gut.

Morgan Spurlock showed us how eating nothing but McDonald's for 30 days wreaked havoc on his body, including his liver, mood and sex drive, in the Oscar-nominated documentary "Super Size Me."

Spector's study is the first one so far to hone in on the microbiome and how it is affected by a fast food regimen. However, several studies have explored the effects of diets high in fat and low in fiber, which are probably similar to the diets of frequent McDonald's-goers.

A small 2014 study swapped out the low-fat, high-fiber diet of 20 rural Africans in South Africa for meats and fried foods; on the flip side, researchers switched the high-fat low-fiber diet of 20 African-Americans in Pittsburgh for a typical African diet, including cornmeal porridge and root vegetables.

The researchers reported that after only two weeks of diet "Westernization," the microbiomes of Africans were producing about half the levels of a molecule called butyrate, which has been linked to lower inflammation, as before their diet intervention. In contrast, the microbiomes of Americans started churning out about twice as much butyrate after they went on the healthier African diet. The Africans also acquired more bacteroidetes, the same group of obesity-associated bacteria that took over Spector's son's microbiome.

"The exciting part of this is that it suggests it is never too late to make a change and reduce fat in your diet, and that you don't have to have lived on a healthy diet all your life," said Dr. Stephen O'Keefe, lead author of the 2014 study and professor of medicine in the University of Pittsburgh Division of Gastroenterology, Hepatology and Nutrition.

Part of the reason that the African diet in O'Keefe's study promotes a healthy gut microbiome may be because of its relatively high levels of a type of fiber called inulin, found in certain plant foods. These foods, which include garlic, leeks, wheat and barley, are "general fertilizers for the microbiome," Spector said.

Inulin helps encourage the gut microbiome to produce butyrate, an acid that feeds cells in the colon and keeps inflammation in check, said Rob Knight, professor in the pediatrics and computer science and engineering departments at UC San Diego. Studies have also suggested that diets high in inulin lead to increases in health-promoting bifidobacteria, which break down carbohydrates to short-chain fatty acids, which may in turn decrease the risk of cancer, digestive and heart disease.

The bacteria in fermented foods such as yogurt appear to be a good influence on the bacteria residing in your gut. A 2011 study by Knight and his colleagues found that eating two servings a day of yogurt did not change the composition of the microbiome in 14 adults. However, the researchers looked more carefully at the activity of the microbiome in mice and found that bacteria in the yogurt appeared to communicate with the gut bacteria and tell them to up their ability to metabolize starches and sugars, and also to produce higher levels of the inflammation-fighting molecule butyrate. The study was funded in part by Danone Research, part of the Danone food company, which makes Dannon yogurts.

The study only looked at one type of yogurt, so it is not clear whether certain types, such as those that are high in protein and low in sugar and fat, might be better than others. "It's fascinating how different yogurts are nutritionally," Knight said.

Pickles and kimchi are also fermented foods that promote a healthy gut microbiome, Knight added.

Artificial sweeteners such as aspartame and saccharin help keep your calorie intake in check, but they don't seem to trick the gut microbiome. "We always thought artificial sweeteners were the perfect free lunch, but we're ignoring the other biology going on," Spector said.

A small 2014 study asked a group of almost 172 Israelis to describe their diet over the past year. The researchers found a link between the consumption of artificial sweeteners and greater abundance of groups of bacteria associated with type 2 diabetes, as well as higher levels of some members of the bacteroidetes group.

A growing number of studies suggest that coffee wakes up your microbiome, too. A 2009 study of 16 volunteers found that drinking three cups of joe over three weeks was associated with an increase in the levels and activity of health-promoting bifidobacteria.

Although some foods are generally considered good or bad for the gut microbiome, there is a lot of variation between people. For example, eating red meat could be particularly bad for individuals harboring high levels of bacteria that produce a metabolite that has been linked to atherosclerosis.

In the next couple of years, tests could be available that would predict whether a person's microbiome is incompatible with red meat, Knight said.

"Suppose you had that bacteria (linked to atherosclerosis) but didn't want to give up red meat, you could eat other foods that encourage the growth of bacteria that get rid of (that) bacteria," he said. Some tests are available that tell you whether your gut microbiome resembles that of someone who drinks too much or who is vegetarian.

Knight encourages people to join his project called American Gut. After making a donation of $99, people can send a stool sample to his lab in California, which analyzes and catalogs the microbiome to help understand how different microbiomes are associated with health.