Microbiome Monday: Microbes and Metabolism

News posts

It's Microbiome Monday again! Before the Museum’s upcoming exhibition The Secret World Inside You opens November 7, we’re offering weekly primers on the microbiome and the research surrounding it from Curators Rob DeSalle and Susan Perkins, as well as from other scientists who are working in this exciting field.

Today's post from Dr. Perkins explores how microbes help animals of all kinds—from wood-eating termites to human gourmands—digest food and get the most nutrition out of our meals.

A Microbial Feast

In New York, an order of chow mein may always be just a phone call away, but for most animals, getting a meal is harder work. To find food more easily, some forms of life exploit food sources that are otherwise unavailable to most other organisms, like wood, plant sap, and blood. While man may not be able to live by bread alone, a leech can get by on nothing but blood for its whole life. Making these limited diets work is a team effort, though, in which microbial partners provide missing nutrients.

Tsetse Fly

Blood-feeding animals like the tsetse fly depend on microbes in their gut to produce all the nutrients they need.

Courtesy of Wikimedia Commons

Wood-eating insects like termites and woodroaches host bacteria, archaea, and protists in their guts that help to convert the tough cellulose fibers of food back into simple sugars. Aphids suck up sugar-rich plant sap, but rely on symbiontic bacteria called Buchnera to provide them with protein. And blood is easy to digest and full of both sugars and protein, but notoriously lacking in B vitamins, so animals like tsetse flies and leeches thus have their own symbiotic bacteria to round out their nutritional needs. In most cases, these partnerships are so important that the microbes are inherited vertically—just like the DNA passing from parent to offspring—to ensure that the new generation has the symbionts it needs to eat well in place.

Unlike these specialized species, humans are notorious omnivores, much like our cousins, chimpanzees and bonobos. That’s why primate microbiomes may seem more flexible and fungible. A recent study compared the gut microbiomes of humans from various parts of the world to those in chimps, bonobos, and gorillas.

Their microbiomes help primates like these bonobos digest their omnivorous diets.

Primates like humans and these bonobos eat omnivorous diets that their microbiomes help them digest.

Courtesy of Wikimedia Commons

Overall, the human gut microbiomes showed significantly less diversity than those of wild primates, and underscored some differences in our diets. For instance, the genus Fibrobacter, active in fermenting plant material, is all but gone in people, whereas Bacteroides, which is associated with diets rich in animal fats and proteins, is much more abundant—by a factor of five—in humans than apes.

Within humans, though, we still are varied eaters. Vegan, gluten-free, pescatarian, Paleo—these are just a few of the dietary restrictions people commonly adhere to. Scientists are now looking at the relationship between these diets and our gut microbiomes, because the bacteria play such fundamental roles in our digestion as well as contributing to our immunity, weight, and propensity to chronic diseases.


Microbes in the human gut turn the compound carnitine, found in red meat, into a chemical associated with increased risk of heart disease.

Courtesy of Wikimedia Commons

For meat-lovers, an important set of studies recently brought a dose of bad news. Researchers at the Cleveland Clinic have demonstrated that our gut bacteria convert carnitine, a compound found in high proportions in foods like red meat, and choline, which is abundant in eggs, to the by-product trimethylamine N-oxide (TMAO), which can be an indicator of heart disease risk.

Interestingly, vegetarians who were given a steak or other red meat did not show subsequent high levels of TMAO, suggesting that their microbiota contain fewer of the microbes that make TMAO. While diet is just one factor that contributes to heart disease or other ailments, this study suggests that a "flexitarian" diet—mostly  vegetarian with occasional meat— might be the healthiest of all.