The Mighty Microbiome

The term "microbiome" has become widely used in recent years as people devotedly devour kimchi, kefir, and kombucha in an attempt to improve their digestion, depression, and blood pressure. Indeed, we now know that the trillions of microbes--viruses, bacteria, and fungi--that live on our skin and in our guts, lungs, and reproductive organs, among other places, play critical roles in our well-being.

Scientists have found, for example, that the types of microbial species present in a person's gut influence his or her ability to respond to certain medications, such as chemotherapy drugs. They've learned that this gut bacteria also plays a role in our ability to manage our weight, and it can affect our mood, perhaps even how well we sleep. Microbiomes picked up by infants during birth are thought to guard them against the development of type 1 diabetes and asthma. Likewise, bacteria-filled breast milk may also protect babies in this way. On the skin, microorganisms ward off pathogens and may even help to prevent skin cancer.

In the environment, scientists have documented collections of microbes performing all manner of functions in waterways, soils, and even air. They've learned that highly complex phytobiomes--systems comprising plants, their environments, and the billions of organisms that live on and around them--govern much of a plant's growth and health. Researchers have also discovered large amounts of pharmaceuticals--including antibiotics that end up breeding drug-resistant bacteria--in our natural water systems. Microbiomes occur in our built environment as well, from food production facilities to operating rooms to our own homes.

Using high-throughput sequencing, scientists have teased apart microbiomes to identify individual species of microbes, and in doing so have generated indescribably large datasets. They've analyzed these data with a variety of newly created computational tools, including artificial intelligence and machine learning, and they've used this information to document relationships between microbes and various aspects of our lives. But their exploration and understanding of how these collections of microorganisms actually function in our bodies and our environment has only just begun.

Driven by an appreciation for the importance of microbiomes in our lives and the recognition that so much remains to be discovered, leaders in the College of Agricultural Sciences helped to create the Microbiome Center--housed within the Huck Institutes of the Life Sciences--in 2017. Their goal was to foster interdisciplinary research collaborations among faculty members in the college and across the University who study microorganisms so they could tackle some of the most important outstanding questions in the field of microbiome research; for example, "How can we use microbes to promote crop growth?" and "What changes can we make in our diets to improve our health?"

An executive committee representing eight colleges, three campuses, and two institutes was tasked with overseeing the center, and this group named Carolee Bull, professor and head of the Department of Plant Pathology and Environmental Microbiology, as its interim director.

"True innovation is made at the boundaries of what we know and at the intersections of disciplines," said Bull. "The Microbiome Center brings together a broad community of scholars to look at problems through different lenses and discover novel solutions."

According to Bull, in two short years, Penn State's investment in microbiome research has surpassed that of most academic institutions, especially for a center not solely dedicated to human health. In fact, it now includes more than 80 faculty members, over half of whom belong to departments within the College of Agricultural Sciences. And the college has plans to hire more.

"Penn State is fast becoming a leader in this new and growing field," said Terrence Bell, assistant professor of phytobiomes.

The University is also investing in educating the next generation of microbiome researchers. For example, in a recent college-funded initiative, faculty members in the college created mBiome, a program designed to provide graduate students with an interdisciplinary understanding of microbiomes so they can examine the possibilities of their use to enhance crop yield and quality, reduce the environmental burden of agriculture, improve food quality and safety, and promote human health. The program accepted its first cohort of eight graduate students in fall 2018 and has since expanded to include twelve affiliated graduate students.

"As investigators begin to understand the complexity of the microbiome, they are uncovering the important, and often obscure, role microbes play in the overall biology of plants and animals and their relationships with the environment," said Gary Thompson, associate dean for research and graduate education. "The college recognized this critical component of food and agriculture and chose early on to significantly invest in this emerging field, especially in student and faculty talent. Today, the Microbiome Center is a highly productive and collaborative venue that enables these interdisciplinary faculty members and students to serve as leaders in the field of microbiome research."

A Winning Wine

Investigators

Josephine Wee, assistant professor of food science

Jasna Kovac, assistant professor of food science

Helene Hopfer, Rasmussen Career Development Professor of Food Science

Question

Can we produce a better wine?

Impact

Yeast is essential to winemaking, and although Saccharomyces cerevisae is the most common species used to ferment grapes into wine, other yeasts are also important. Scientists are examining the microbial species present within vineyards across Pennsylvania to see how certain combinations influence the flavor and aroma of the end product. They have isolated more than 200 yeast strains and are experimenting with adding them to wines in specific sequences and in certain amounts and combinations to create unique characteristics that may enhance their appeal and help increase winemakers' profits.

Complex Cocktails

Investigators

Terrence Bell, assistant professor of phytobiomes

Kevin Hockett, assistant professor of microbial ecology

Question

Can we create soil inoculants that promote crop health without harming the environment?

Impact

Certain soil microorganisms are known for their contributions to crop viability; for example, they can suppress plant pathogens and influence nutrient availability. Scientists are creating better methods for studying soil microbes and investigating their ecology--how they interact with each other and their environments--with a goal of identifying combinations of bacterial species that can be added to agricultural soils to promote crop health. They believe that inoculants comprising diverse species or a single species that exhibits diverse traits may better support plant health across a wide range of environments than less diverse inoculants.

Down the Drain

Investigator

David Geiser, professor of mycology and director of the Fusarium Research Center

Question

Where are we acquiring dangerous fungal infections?

Impact

Researchers sampled nearly 500 sink drains from buildings--businesses, homes, university dormitories, and public facilities--throughout the United States. They analyzed fungal DNA from the drains and compared them to those recovered from human infections. They found several species of Fusarium, including four new ones. Some species of Fusarium can cause dangerous, sometimes fatal, infections in humans, most often entering the body through a wound. Understanding where these Fusarium live could help people avoid infections.

Leaf Spot Disease

Investigator

Carolee Bull, professor and head of the Department of Plant Pathology and Environmental Microbiology and director of the Microbiome Center

Question

Can we prevent crop-damaging leaf spot diseases?

Impact

Leaf spot diseases caused by the bacterial pathogen Pseudomonas syringae damage crops--such as watermelon, pumpkin, and zucchini--by infecting their seeds and ultimately interfering with their ability to photosynthesize. In 2003, the bacterium destroyed around 8,000 acres of watermelon and squash in Florida alone. Researchers are studying the biology and epidemiology of P. syringae in these crops. In particular, they are using diagnostic metagenomic and other approaches to examine the microbiomes associated with the seeds of these crop plants. Their goal is to develop resistant plant lines for seed and crop production.

A New Mushroom Disease

Investigator

Carolee Bull, professor and head of the Department of Plant Pathology and Environmental Microbiology and director of the Microbiome Center

Question

What causes blotched mushroom caps?

Impact

Bacterial blotch is one of the most common and most devastating diseases in cultivated mushrooms, resulting in significant crop losses for farmers. It is of great concern to the Pennsylvania mushroom industry, which leads the country in mushroom production. With a goal of developing biologically based management tactics to aid the mushroom industry, scientists are investigating the causes of blotch in Pennsylvania mushroom production houses and documenting methods growers can use to prevent the disease.

Environmental Chemicals

Investigator

Andrew Patterson, professor of molecular toxicology

Question

How do environmental chemicals influence our gut microbiome?

Impact

Environmental chemicals, including those obtained via the diet, are known to modulate the gut microbiome community as well as its metabolic function. Recent studies report that environmental chemicals can directly impact the gut microbiome, can be modified by the gut microbiome, or can have their metabolic fate altered. Research supports that similar to antibiotics, environmental chemical exposure may alter the composition and function of the gut microbiome, which can influence host health. Studies are underway to evaluate how low-level, chronic exposure to these chemicals may alter the interaction between the host and the gut microbiome.

Avoiding Food Poisoning

Investigators

Jasna Kovac, assistant professor of food science

Luke LaBorde, professor of food science

Question

Can we prevent dangerous foodborne disease outbreaks by improving understanding of microbiomes in food processing environments?

Impact

Foods contaminated with bacteria--such as Listeria monocytogenes and Escherichia coli--can severely sicken and even kill. Researchers are examining the conditions under which these microbes thrive in food processing and packing facilities with the goal of establishing effective control strategies. In a recent study, they found that harmless microorganisms that coexist with Listeria may facilitate its persistence, possibly by enclosing it in slimy biofilms that resist sanitization.

Resistant Starch for Your Health

Investigator

Darrell Cockburn

Question

How does resistant starch contribute to our gut health?

Impact

The bacterium Eubacterium rectale in our intestines is known for producing butyrate, a short-chain fatty acid that protects against diabetes, among other health benefits. Consuming resistant starch, such as uncooked potato starch, increases the abundance of E. rectale in the intestine and, therefore, the abundance of health-promoting butyrate. In a recent study, researchers identified the mechanism by which E. rectale binds to starches, which ultimately could help in the development of dietary strategies aimed at reducing disease.

The Roots of Wine Grapes

Investigators

Michela Centinari, assistant professor of viticulture

David Eissenstat, interim head and professor of ecosystem science and management

Terrence Bell, assistant professor of phytobiomes

Question

How do different management practices influence the root-associated microbiomes of wine grapes?

Impact

Scientists are examining how grapevine root traits--such as root type and branching order--together with the soil microbiomes surrounding the roots contribute to healthier plants. Ultimately, their goal is to harness the power of root microbiomes to maximize fruit production, improve soil health, and limit the use of chemicals.

Cultivating Mushrooms

Investigator

John Pecchia, associate research professor of mushroom science

Question

Can we build a better substrate for growing mushrooms?

Impact

Substrate preparation is a critical step in the cultivation of mushrooms, which, valued at more than half a million, are important to the economy of Pennsylvania. Researchers are investigating the dynamics of microbial populations during composting and cropping to understand how they affect mushroom yield and disease development. Recently, they found that different temperature regimes during pasteurization impact concentrations of bacterial by-products such as ammonia, too much of which can inhibit mushroom growth.

By Sara LaJeunesse
Portraits by Mike Houtz