If you've taken antibiotics to cure a respiratory infection and ended up with gastrointestinal problems, you’ve met your microbiome. The antibiotics that you took to kill the pathogenic bugs that made you sick, also wiped out the bacteria that live in your healthy digestive track. Without them your intestines are a wreck.

Just knowing that microbes are present, though doesn’t give scientists a clear picture of what the bugs are doing and why they are there. Frederic Bushman, PhD, professor of Microbiology, and others are using the latest DNA sequencing techniques to characterize some of those helpful bacteria.

In one recent study, his team found that the type of food we eat influences what kind of bacteria thrive in our gut. He found that vegetarians were more likely to have bacteria that fall into the broad grouping called Prevotella, while people who ate diets rich in meat and animal fat tended to have bacteria in a group called Bacteroides. What’s more, they found that short-lived changes in an individual’s diet could alter the species of bacteria they carried in their gut, but not the broad group. Bushman thinks these sorts of patterns might be part of the way diet affects human health.

But if helpful bacteria are a link between diet and health that is not the only way the bugs influence human well being. David Artis, PhD, associate professor of Microbiology, and colleagues found that when they treated mice with antibiotics, the animals became more susceptible to viral infections. In other words, when the team killed off commensal bacteria, the animal’s immune system lacked some of its punch to fight off foreign invaders.

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