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

Microbes & Human Health

Jim Steele used to be one of the skeptics. He’d be at a conference, listening to early research on the health benefits of probiotics. Steele scoffed at the small experiments. “We would literally try not to laugh in the audience, but we’d laugh pretty hard when we went out that night,” he admits.

But slowly the punch lines gave way to revelation. Steele, a professor in CALS’ Department of Food Science, conducts research on lactic acid bacteria, with a focus on Lactobacillus species. They’re important for human gut health, critical for the production of cheese and yogurts, and are the most common probiotic genus. He knew how incredibly useful they were, but still watched with a humbling disbelief as the data on the health potential of these microbes kept getting broader, deeper and more intriguing.

Our microbiota—what we call the totality of our bacterial companions—is ridiculously complex. Each human harbors a wildly diverse ecosystem of bacteria, both in the gut and elsewhere on the body. They have us completely outnumbered: where the typical body may contain a trillion human cells, your microbial complement is 10 trillion. They have 100 times more genes than you, a catalog of life potential called the microbiome. (The terms “microbiome” and “microbiota” are often used interchangeably in the popular press.)

While our initial, germaphobic impulse may be to freak out, most of these bacterial companions are friendly, even essential. On the most basic level they aid digestion. But they also train our immune system, regulate metabolism, and manufacture vital substances such as neurotransmitters. All of these things happen primarily in the gut. “In many ways the gut microbiota functions like an organ,” says Steele. “It’s extraordinarily important for human health,” with as much as 30 percent of the small molecules in the blood being of microbial origin.

Early research has suggested possible microbiota links to protecting against gastric cancers, asthma, numerous GI disorders, autoimmune disease, metabolic syndrome, depression and anxiety. And the pace of discovery seems to be accelerating; these headlines broke in just a few months last spring:
• Mouse studies suggested that the microbe Akkersmania muciniphila may be a critical factor in obesity;
• Kwashiorkor, a form of severe malnutrition that causes distended bellies in children, was linked to a stagnant microbiota;
• Risk of developing Type 2 diabetes was linked to an altered gut microbiota.

The catch: For all the alluring promise of microbes for human health—and it’s now clear they’re critically important—we have almost no idea how this complex system works.

The human gastrointestinal (GI) tract is a classic black box containing hundreds or thousands of species of bacteria (how many depends on how you define a species). There are viruses, fungi and protozoans. Add to that each person’s distinct DNA and their unique geographic, dietary and medical history—each of which can have short- and long-term effects on microbiota. This on-board ecosystem is as unique as your DNA.

Beyond these singularities, the action is microscopic and often molecular, and even depends on location in the GI tract. Most microbiota studies are done with fecal material. “Is that very informative of what’s going on in the ileum?” asks Steele, referring to the final section of the small intestine, which is thought to be the primary site where immunomodulation occurs. “From an ecosystem perspective, fecal material is many miles away from the ileum. Is it really reflective of the ileum community?”

Meat, With a Touch of Fruit

When Jeff Sindelar talks about the ingredients he’s working with, you’d think he was making juice. Not quite. He’s adding things like cranberry concentrate, cherry powder, lemon extract and celery powder to meat.

But Sindelar, a CALS professor of animal sciences and a UW–Extension meat specialist, is not adding them for flavor. He’s looking at ways to ensure that meat products labeled “organic” and “natural” are safe to eat.

Sales of organic and natural foods are booming, with double-digit percentage gains almost every year. As more and more food processors scramble to meet that demand, they’re encountering a special challenge. Because they must process these meats according to organic and natural label requirements, they are unable to use the vast majority of antimicrobial agents employed in standard meat processing.

“Most ingredients and technologies that serve as antimicrobials—ingredients that can improve safety by either suppressing, inhibiting or destroying any pathogenic bacteria—are not able to be used in products labeled ‘natural’ and ‘organic,’” Sindelar says.

The trick is to find alternative materials and processes that deliver safety—and also offer the look and flavor that consumers value.

Sindelar has identified some options. “A number of different natural-based organic acids offer a significant improvement to food safety,” says Sindelar, who is working in partnership with Kathy Glass, associate director of the CALS-based Food Research Institute. “We have tested a number of different ingredients such as cranberry concentrate, grape seed oil and tea tree extract.”

Some compounds from natural sources work as well as such standard preservatives as sodium nitrite, sodium lactate or sodium diacetate, to name a few. But it can take heavy doses of some natural ingredients to provide equivalent results—causing some undesirable side effects.

“Cranberry concentrate is a very effective natural antimicrobial,” says Sindelar. “But if you use the amount needed to significantly control the growth of bacteria, the meat turns cranberry red.”

Part of the researchers’ work involves “challenge testing”—adding pathogenic microbes to the meat to make sure that a given ingredient prevents the growth of bacteria throughout processing and storage. If substantial numbers of microbes grow, that ingredient is ruled out as being an effective natural antimicrobial.

Successful tests have already led to new products. Cherry powder combined with celery powder, for example, “is already being adopted by processors because of how effective these ingredients are in improving meat safety and quality,” notes Sindelar. And the search for other natural additives continues.

Both researchers are certain they’ll find success—particularly as they continue working in partnership with producers in the field.

“Collaborative research between the university and industry is essential to understand the synergistic effects of these ingredients—and to ensure the safety and quality of natural and organic meats,” says Glass.

Growing Our Future

As you read the feature stories in this edition of Grow, I invite you to consider how they reflect the mission, vision, guiding principles and priority themes for our college as we’ve identified them in our strategic planning.

The enormous potential of microbes for enhancing human health—reflecting our priority theme of health and wellness—is sure to be a predominant area of research in the next decade as new tools continue to improve our understanding of how microbes work with us as human hosts as well as in the environment.

Our cover story on pizza cheese exemplifies our work in food systems (a priority theme) and crosscuts into another theme, economic and community development. Food development is one of the things CALS does best, and I look forward to seeing what unimagined products will result from our new dairy research facility—which, thanks to the hard work of so many members of the CALS community, is included in the 2013-2015 state budget.

As for our third feature, knowing how to communicate science effectively is

As we map our future, the approaching year of 2014 offers and important occasion to reflect upon our past.

a science in its own right. We speak to the overarching importance of science communication in the eighth of our guiding principles—and we are fortunate to have excellent national leadership in this area on our life sciences communication faculty.

These stories reflect the cutting-edge activities we’ve been talking about this past year as we’ve discussed how CALS can best grow the future, as our new tagline states. The publication resulting from that work is posted at cals.wisc.edu/stratplan. We invite you to take a look!

As we map our future, the approaching year of 2014 offers an important occasion to reflect on our past. It’s CALS’ 125th anniversary, or “quasquicentennial.” This milestone will give us a chance to celebrate our college’s many achievements, which we plan to highlight throughout the year at such events as CALS Week and Honorary Recognition as well as in news stories and a social media campaign involving alumni and friends of CALS from Wisconsin and around the world.

What do you consider to be CALS’ shining moments, past or present? And—to connect this milestone to our strategic planning—what activities should we pursue to ensure that the next 25 years will be as vibrant as the last? What do you think will be our next big ideas or breakthroughs? We’re eager to hear your thoughts at CALS125@cals.wisc.edu.

Protecting our Pollinators

People and bees have a long shared history. Honeybees, natives of Europe, were carried to the United States by early settlers to provide honey and wax for candles. As agriculture spread, bees became increasingly important to farmers as pollinators, inadvertently fertilizing plants by moving pollen from male to female plant parts as they collected nectar and pollen for food. Today, more than two-thirds of the world’s crop plants—including many nuts, fruits and vegetables—depend on animal pollination, with bees carrying the bulk of that load.

It’s no surprise that beekeeping has become a big business in the farm-rich Midwest. Wisconsin is one of the top honey-producing states in the country, with more than 60,000 commercial hives. The 2012 state honey crop was valued at $8.87 million, a 31 percent increase over the previous year, likely due in part to the mild winter of 2011–2012.

But other numbers are more troubling. Nationwide, honeybee populations have dropped precipitously in the past decade even as demand for pollination-dependent crops has risen. The unexplained deaths have been attributed to colony collapse disorder (CCD), a mysterious condition in which bees abandon their hives and simply disappear, leaving behind queens, broods and untouched stores of honey and pollen. Annual overwintering losses now average around 30 percent of managed colonies, hitting 31.1 percent this past winter; a decade ago losses were around 15 percent. Native bee species are more challenging to document, but there is some evidence that they are declining as well.

Despite extensive research, CCD has not been linked to any specific trigger. Parasitic mites, fungal infections and other diseases, poor nutrition, pesticide exposure and even climate change all have been implicated, but attempts to elucidate the roles of individual factors have failed to yield conclusive or satisfying answers. Even less is known about native bees and the factors that influence their health.

Poised at the interface of ecology and economy, bees highlight the complexity of human interactions with natural systems. As reports of disappearing pollinators fill the news, researchers at CALS are investigating the many factors at play—biological, environmental, social—to figure out what is happening to our bees, the impacts of our choices as farmers and consumers, and where we can go from here.

Small Wonder

Wisconsin has a state dance (the polka), a state fossil (the trilobite), a state beverage (milk, of course) and 18 other official state symbols. But a group of CALS bacteriologists say that honor roll neglects a major player in the Badger state’s quality of life: Lactococcus lactis.

Not familiar with the name? You probably know the bacterium better by its handiwork—namely, turning milk into Cheddar cheese. Cultures of Lactococcus lactis are at work in virtually every dairy plant in the state, driving an industry that contributes some $18 billion to the state’s economy each year.

That kind of impact warrants recognition, argues Rick Gourse, chair of the bacteriology department. Gourse and colleagues are pushing a state bill to designate Lactococcus as the official state microbe, which would make Wisconsin the first state to bestow such distinction on a microorganism. Sponsored by Rep. Gary Hebl, the bill passed the State Assembly in the spring but was not considered by the Senate. Hebl is pledging to reintroduce the bill during this fall’s legislative session.

“I thought this idea seemed frivolous at first,” Gourse admits. “I soon realized that it presents a unique opportunity to raise awareness about the importance of microbiological research for understanding and preventing disease. It also highlights the positive role of microbes in key Wisconsin industries, including cheese, brewing and bioenergy.”

Supporters also hope a state microbe would help counter public fears about germs, which often only get attention as causes of disease or illness. But if the Assembly’s first hearings on the bill are any indication, there’s still a lot of room for education on that point.

“During a presentation (about the bill), someone said, ‘I want to wash my hands, thinking about all these germs,’” recalls Michelle Rondon, a bacteriology faculty associate involved in the effort. “That’s exactly the kind of thinking we are trying to change. The vast majority of microorganisms are either innocuous or beneficial, and Lactococcus lactis is an excellent reminder of that fact.”

—Nicole Miller MS’06

Ranjini Chaterjee

Chatterjee worked as principal investigator at Farasis Energy, focusing on engineering microbes to produce more environmentally friendly fuel from biomass feedstocks. She remains fascinated by the energy of microbes, especially their capacity to generate potentially useful chemicals and the tools and technologies that can be applied to harness them for industry. Currently she works with Genetic Chemistry, a Palo Alto-based company that develops chemical compounds from microbes for pharmaceutical and other industries. Chatterjee is engineering and evolving microbial pathways in yeast to produce antimicrobial chemicals that could be used in drug development and other applications.

MySpace: Doug Weibel

  • job: Assistant Professor of Biochemistry
  • lab: Fourth floor, Biochemistry Building Addition
  • current Research: The biochemistry of microbes

What’s the research question on your mind right now?
How do bacterial cells make the switch from individual behavior to collective, multicellular behavior?

Who works in your lab?
One postdoctoral fellow, four graduate students, five undergraduate students, one incoming undergraduate student and a high school student. This summer we also had a first grade teacher working in the lab and 10 undergrads working on the International Genetically Engineered Machine competition. It’s a busy place right now.

Describe a typical day in the lab.
Actually, I haven’t done an experiment in months, so I can’t say with 100 percent certainty. But everyone is working on a different project, so there are very few activities that are routine, with the exception of growing bacteria and washing glassware.

What’s the view from the window?
My office faces the 1956 wing of Biochemistry. The lab has a terrific view of Elmer, the old elm tree.

What’s playing on the radio?
Right now, “Rainbows,” by Radiohead. In the lab, the preference seems to be to work without music. I respect that decision—it promotes interaction and conversation.

What’s the most unique feature of your lab or office?
I had blackboards installed in my office. Several of my colleagues think this represents unusual behavior.

If you had to evacuate, what would you grab first?
Well, if my kids were in the office, which they often are on Saturdays, I would grab them first.

Clean desk or messy desk?
A clean desk. I can’t work efficiently in a messy environment.

Any personal items in the lab?
Nail polish. It comes in very handy for all sorts of things (microscopy, annealing, gluing, etc.).

Where do you get your best work done?
In my office very early in the morning.

Why did you go into research as a career?
Because science is a blast.

What’s the coolest thing you’ve learned by doing research?
That I can get paid for doing this job. It still amazes me…

What's in the Water?

SHARON LONG is an associate professor of soil science in CALS, but that title only hints at her multidimensional role for the university and the state. As director of environmental microbiology for the Wisconsin State Laboratory of Hygiene, Long runs a public-service unit that analyzes some 60,000 water samples each year, part of the state’s effort to keep its wells and drinking water safe from microbial contamination. As if that weren’t enough to keep her busy, she has appointments in UW-Madison’s Nelson Institute for Environmental Studies and the College of Engineering’s civil and environmental engineering department.

What’s with all of your titles?

Well, my work is very interdisciplinary. When you’re talking about tracking pathogen sources in water-and keeping them from reaching people-you need access to people with a bunch of different backgrounds. You need people who understand microbiology. You need people who understand public health. You need people who understand laboratory testing. And you need people who can solve problems. One of the things I really like about Wisconsin is that it’s so interdisciplinary by nature. I can have a foot in all of these camps and hire students from each of those areas.

My role is to bring in the tools that allow us to figure out what might be making a water sample unsafe and how the pathogens got there.

Your work with the State Laboratory of Hygiene is very applied. Is it common for a professor to have that role?

Yes, that’s been the tradition. The lab is technically part of the university, and they always try to have a strong connection to the research community here. My role is really to bring in the research perspective-to bring in the tools that allow us to figure out what might be making a water sample unsafe and how the pathogens got there.

Where do the samples come from?

All over the state. The lab is a client-based service, and so anyone can send a sample in to be analyzed. We get a lot of samples from private well owners who want to be sure that their well hasn’t been contaminated by animal waste or other things. And we also test for a number of municipalities, including Madison and Milwaukee.

Is this routine testing, or are you investigating problems?

It can be both. For instance, we did a lot of testing after the floods last summer. When people came back to their homes, many were worried about flood waters going over the tops of the wells, and a fair number of those tests did come back unsafe.

What happens then?

Well, in that case, we worked with the Department of Health and Family Services and the Department of Natural Resources to get information out to people in the affected areas. Generally, the first thing they do is super-chlorinate the well and pump it through. Then, if it comes back contaminated again, we try to find out what’s in there and where it may be coming from. We start looking to see if there’s a continuing source of contamination.

And that’s where your research comes in.

Right. The first level of testing generally just tells you about the presence or absence of coliform bacteria, which we use as a broad-level indicator because they live in almost every warm-blooded animal. So that test tells us that we may have some kind of contaminant getting into the water supply. Then the question becomes what kind of contamination we’re dealing with and in what quantity. There is a standard set of microorganisms we can look for, and that’s the path that pretty much any public-safety lab would follow.

But if the question becomes about more than just identifying the particular pathogen, we do have some tools that allow us to start to figure out where the pathogens came from. The field is called microbial source tracking, or MST. We have tests that can tell us whether the source of the pathogen was human or non-human, and there are even some tests that allow us to go deeper than that and ask what kind of animal was the source of the contamination. For example, we can do a test where we discriminate between grazing animals and all other animals, which could tell us if the contamination was coming from a nearby farm or some other source.

How can you tell?

Every species of animal has a unique intestinal environment and therefore a unique mix of microorganisms that live in that environment. The idea is to use some high-level microbiology to identify differences in the microorganisms that can tell us where they lived. So if we have contamination in a new residential development that is located next to an active swine farm, you want to look at those microorganisms and figure out whether they came from humans or pigs. If it’s humans, you would want to look at the septic system as a likely source of contamination, but if it’s pigs, you’d try to see if animal waste was contaminating the water supply.

It sounds like CSI.

It is. But really, it has only been within the past 10 years that science has progressed enough to do this. People have been studying source tracking since the 1970s, but we’re finally getting to the point where we can apply it with some level of certainty.

I understand you’ve used this technology recently in a contamination problem at a restaurant in Door County. Can you tell me more about that case?

Yes, that was really fascinating. This was a brand-new restaurant in one of the popular vacation areas up there, and not long after it opened, a number of people got sick. The concern was that since there was a lot of agriculture in the area that maybe there was contamination from animal waste. But when we applied our source tracking, we found human markers, meaning that it had to be a human source. It turned out that a pipe from the septic holding tank was not hooked up properly, and the sewage was going straight down into the aquifer and reaching their well.

Do you think pegging the source as human helped identify that problem?

Certainly, because it put the focus on the septic system. It was a brand-new system, and it was very well designed, so there wasn’t much reason to suspect it would be a problem. But the test caused the county to go back and reevaluate it. I hear the restaurant has since put in a state-of-the-art system for treating its well water. They’ve probably got the cleanest water in Door County now.

That’s good news. But seeing all these cases of contamination-does it ever make you think twice about drinking tap water?

Not at all-at least not in this country. One of the societies I belong to is the American Water Works Association, and at their annual conferences they actually pay extra to make sure that all of the water bottles are filled with tap water. We’ve got great water, and I never think twice about it.

Something to Sneeze At

SCIENCE MAY NOT HAVE A CURE FOR THE COMMON COLD, but now we have its playbook. In February, a team of researchers from several institutions-including UW-Madison’s Institute for Molecular Virology-revealed the genome sequences of all 99 known strains of the cold virus, the first time the viruses’ genetic mechanisms have been exposed in full. “We know a lot about the common cold virus,” says Ann Palmenberg PhD’75, a biochemistry professor who led the study, “but we didn’t know how their genomes encoded all that information. Now we do, and all kinds of new things are falling out.” For instance, scientists might find weak spots in the viruses’ genetics that new drugs can be designed to attack. But don’t shelve the Kleenex just yet: Palmenberg says cold viruses have a knack for swapping genetic sequences when they meet inside a cell. “That’s why we’ll never have a vaccine for the common cold,” she says. “Nature is very efficient at putting different kinds of paint on the viruses.”

Going to Extremes

ON THE ICY BOARDWALK ABOVE BLACK POOL, Tom Schoenfeld is working as fast as his numbing fingers will allow. He lowers a hose into the steaming pool, one of dozens of hot springs in the West Thumb portion of Yellowstone National Park, and then slides the other end into a keg-sized plastic jug. Shuffling along the slick wood planks, he begins piecing together the rest of the water filtration system that he developed for Lucigen Corporation, a Madison-area biotech company where he is vice president of enzyme discovery. The system, which concentrates the bacteria and viruses living within the spring, takes about 30 minutes to set up and an additional two hours to produce a couple of liters of teeming liquid. And though Schoenfeld arrived here at the break of dawn on this freezing September morning, he barely has enough time to get his work done before the tourists arrive. Tourists always delay things.

Researchers who study extremeophiles are partly motivated by curiosity, but also by the realization that extreme forms of life, like high-endurance athletes, have extraordinary abilities.

Despite its name, Black Pool is gemstone blue and perfectly clear. Its scalding waters produce a thick steam that rises from the pool and floats across the boardwalk, enveloping Schoenfeld in a fine mist. Water droplets soak his clothes and frost his eyelashes. As he reaches to switch on the generator that powers his equipment, he hesitates. There’s water all over it-and on the electrical cords leading to the pumps.

“Wear your gloves when you turn that on, man,” says David Mead, Lucigen’s president, who has accompanied Schoenfeld on seven visits to Yellowstone’s hot springs. As much as they can, the two look out for each other in the field and so far so good. Neither has been electrocuted, and they hope to keep it that way.

Electric shock, however, is only one of many perils they face collecting biological samples from Yellowstone’s springs. Once, a herd of unruly bison flushed the researchers from the edge of a backcountry pool, forcing them to wait several hours before they could return to collect Schoenfeld’s equipment. Another time, hiking through a dense forest, Mead tripped and narrowly missed impaling himself on the jagged branch of a downed tree. But above all else, they worry about the hot springs themselves. According to the book Death in Yellowstone, at least 19 people have died after falling or jumping unwittingly into the park’s pools, which are heated by an underground volcano. And as the book relates in sometimes gruesome detail, no matter how quickly a person scrambles out, falling into near-boiling water is a death sentence.

But for Schoenfeld and Mead, these risks are worth taking. That’s because they believe there are million-dollar microbes living in the park’s pools-bugs that, if found and studied, could unlock the doors to major medical breakthroughs and biotechnological advances. And if history is any guide, the bugs are almost certainly there, surviving and thriving in conditions that would kill almost any other form of life.

All Schoenfeld and Mead have to do is find one of them.

Welcome to the adventurous world of extreme microbiology. Like hundreds of other research scientists, Mead and Schoenfeld travel to Yellowstone to seek out extremeophiles-microorganisms that thrive in extremes of temperature and pressure and other inhospitable environments. These bacteria and viruses survive not only in hot springs but in metal-contaminated soils, pools of acid and lakes so salty that crystals bejewel the shoreline. The researchers who seek them out are partly motivated by curiosity, but also by the realization that extreme forms of life, like high-endurance athletes, have some extraordinary abilities. They harbor powerful proteins-known as enzymes-that enable them to make the most of their surroundings, efficiently turning otherwise inaccessible materials into the food and energy needed to sustain life.

“The bottom line,” explains UW-Madison microbial geologist Eric Roden, who teaches an undergraduate course on extremophiles, “is that extremophiles can do things that other organisms can not.”

Scientists first stumbled onto these rare organisms just a half century ago, when microbial ecologist Thomas Brock, then a professor at Indiana University, found a type of bacteria living in Yellowstone’s Mushroom Spring. Brock, now an emeritus professor of bacteriology at UW-Madison, had been searching for an ecosystem hot enough to support only a few forms of life. On a field trip to Yellowstone in 1964, he began examining the spring’s outflow channel. Starting at the cool end of the channel, where a lush, colorful mat of organisms covered the streambed, he worked his way up to hotter and hotter sections.

“When I got up close (to the spring), I started seeing this stuff,” says Brock, who joined the UW-Madison faculty in 1970. “It didn’t have any pigments. It didn’t have any chlorophyll or anything like that, but it looked like it was alive.”

And it was. Brock was able to grow and study this “stuff” in the lab, and in this way discovered the first extremophile, a heat-loving bacterium he named Thermus aquaticus, which is capable of growing at temperatures up to 80 degrees Celsius, not far below the boiling point of water. (Later, it was discovered that T. aquaticus lives in most residential hot water heaters, a harmless squatter.)

Five Things Everyone Should Know About … Probiotics

1.     Probiotics are microbes that can do good things inside your body. Certain bacteria and fungi can help our bodies fight disease and work more efficiently. In fact, we already have a lot of these helpful microbes—known as probiotics—inside our digestive tracts. But many people add more by consuming probiotic supplements designed to combat specific ailments.

2.     For such small creatures, probiotics have grown very big. While a few proponents have been arguing their benefits for decades, probiotics were virtually nonexistent in the mass market 20 years ago. That began to change with the introduction of products such as Dannon Activia, a probiotic-enhanced yogurt. Aided to some extent by Dannon’s aggressive marketing efforts, public awareness of probiotics has risen from 9 percent in 2001 to 31 percent last year. Now consumption is skyrocketing, and in 2007 alone, 750 new probiotics products were launched in the United States.

3.     These things just might work. In the past, academic researchers, including myself, were highly skeptical of the health claims made about probiotics products. The research was so poorly designed and executed that it made proponents look like snake oil salesmen. However, in recent years, the body of evidence has grown more and more compelling, and many well-constructed studies now have shown health benefits from specific bacterial strains at specific doses.

4.     The key is getting the right microbe—in the right amount. Different microbial strains do different things, and if you don’t have exactly the right one for your needs, you may be wasting money. For example, the bacterium Lactobacillus rhamnosus can mitigate diarrhea after a course of antibiotics, but only if a patient consumes 10 billion to 20 billion cells of the LGG strain per day over a period of 10 to 14 days.

5.     Buyer beware: Labels on probiotics products aren’t uniformly helpful. Many product labels are incomplete, omitting key information about strains and doses. Some labels even make misleading health claims. Before starting a regimen of probiotics, it’s a good idea to do some extra research. Look online or contact the manufacturer to gather all the data.

James Steele, a CALS professor of food science, studies the bacteria that influence Cheddar cheese flavor. A few years ago, he expanded his research program to include the mechanisms by which probiotics influence human health.