Gut Reactions

GARRET SUEN, an assistant professor in the Department of Bacteriology and an Alfred Toepfer Faculty Fellow, focuses on microbiomes and how microbes convert biomass into nutrients. “Microbiome” has become a more common word in the public consciousness in recent years. While the definition of microbiome remains somewhat up for debate, Suen defines it as the totality of the microbes that make up a community living within a particular environment— whether that’s an ocean, the tip of a pinky finger or—in Suen’s case—a cow rumen.

Through his studies of the microbiome of the cow rumen, Suen is working to understand the evolution and ecology of microbial communities and how those communities change in response to the host, the animal’s diet and other influences. He wants to use the microbes and their activities to improve the health of the animals, benefit farmers and even produce biofuels. Suen’s research has also led him to the microbiomes of other herbivores, including sloths and pandas.

Why are you looking at the microbiome of the cow rumen?

I’m very interested in helping Wisconsin farmers improve milk production in their cows. I’m trying to understand the interaction between the host cow and the microbes it has inside its rumen, and I want to know how we might go about altering that interaction so that we can improve milk production efficiency. There are a lot of farms in Wisconsin with small herds—100 or 200 head. Especially for these farmers, milk production efficiency is really important.

What role do microbes play in milk production?

Well, cows are strict herbivores. They only eat plant biomass, and without microbes they would not be able to digest that biomass. The microbes break down the plant polysaccharides found in the plant cell wall—things like cellulose—and they convert that into simple sugars like glucose, which is then fermented into fatty acids that the animal uses as its source of energy. It is those fatty acids that are also the building blocks of milk fat. So if we can better understand that process and which microbes do it best, we can improve milk production and make the animals more efficient in how they use the biomass they consume.

Why is understanding the relationship between microbes and milk production important?

Beyond the benefits to cows and farmers, making milk production more efficient will help feed the expanding population. It’s a better option than increasing the number of farms and land usage. Also, if we can use microbes to change milk composition, we could help cows produce milk with different fats or sugars. Studies have shown that human breast milk is healthier for babies in terms of promoting immune development, and we know that the types of sugars found in human milk are different from those in cow’s milk. So can we learn from that? Could we find ways to use microbes to make cow’s milk more like human breast milk? Changing milk composition could also affect the quality of downstream products such as yogurts and cheese.

How does your work with cow microbiomes relate to biofuel production?

Let’s take corn as an example of a crop we can use to make biofuels. The corn kernel is just one small part of the plant. The rest of the plant, called stover, is usually either silaged or burned. But there’s a lot of carbon in the stover that’s being wasted. So we want to know if we could take that carbon, break it down into simple sugars and have microbes ferment them into new fuels like ethanol. Cows are highly optimized to do that first part because we domesticated cows. We pushed cows to be as efficient as possible to produce as much milk as possible, and optimized the microbes at the same time.

So we’re very interested in taking some of the individual microbes from the cow rumen, bringing them into the lab and seeing what types of products they can produce. One of the microbes we study actually produces ethanol directly from cellulose. We view the rumen as a place where we might be able to identify novel enzymes that could be part of a larger industrial production facility producing next generation biofuels. We’re learning from nature, as I like to call it.

Another animal you study is the panda. Why are you interested in the gut microbiomes of panda bears?

In captivity, giant pandas get very painful episodes, called mucoidal episodes, during which they produce abnormal poop known as mucoids. Normally panda poop looks like chewed bamboo. Their system is inefficient at extracting energy from the food that they’re consuming, so bamboo moves very quickly through the gastrointestinal tract. But once or twice a year, they stop eating completely and produce these mucoids, poop that looks like their gut lining—the gooey, mucosal layer of the gastrointestinal tract.

But why would pandas shed their gastrointestinal tract lining? To answer that question, we worked with Ashli Brown Johnson, an associate professor at Mississippi State University, to look at the microbiota in the mucoids and compare them to regular poop of two giant pandas at the Memphis Zoo. We found that they’re very different from each other. So we came up with the hypothesis that maybe what’s happening is that pandas are eating these rough pieces of bamboo, which are actually causing physical abrasions to the gastrointestinal tract. The pandas then have an inflammatory response to the abrasions that results in the sloughing off of the internal gastrointestinal tract layer, producing mucoids.

Why is helping these pandas important?

The key thing is that these mucoidal episodes usually coincide with the gestation period of a panda. If the pandas are trying to get pregnant but not eating, how hard will it be to get pregnant? How hard will it be to carry a fetus to term—especially when you should be eating more to support the developing fetus? We don’t know why these episodes coincide with gestation, but anything to help pandas breed is important. Successful breeding of pandas is difficult and a big problem.

Are you studying other animals with interesting gut microbiomes?

We’re working with Hannah Carrey in the School of Veterinary Medicine to study what happens to microbes in ground squirrels during hibernation. When animals prepare to hibernate, they pack on weight, and while hibernating, they drop their internal core body temperature to around the temperature inside your refrigerator. We’d like to know what’s happening in that system. Understanding the activity of the microbiomes before and during hibernation can give us insight into host metabolism and diseases such as diabetes and obesity.

We also recently published a paper on sloths, which are on the complete opposite end of the spectrum from pandas. Pandas are eating all the time and are inefficient at getting energy from their food. Sloths eat much less than what you would predict for their body size. Physiologically it makes sense because they have much fewer energetic needs, but the three-toed sloth poops only once a week. That made me wonder what is going on from a digestive perspective! What we’ve found in sloths is completely different from anything we’ve seen in terms of microbial composition, so we want to figure out what’s so different about them. Animals that eat too much or too little for their body size are very interesting in terms of their gut microbiomes.

Garret Suen using an anaerobic chamber to study ruminal bacteria.
Photo by Matt Wisniewski/UW–Madison WEI