And as they study the richly interwoven communities of the microbiome, they’re creating one of their own on the Purdue campus, bridging departments and areas of expertise and sharing ideas with the potential to reshape multiple fields. Microbiome research is typically found in medical centers and biology departments, not in a college of agriculture. This unique setting gives Purdue’s microbial experts a holistic perspective, as they reveal how the global microbiome serves as the hidden interface between more visible forms of life on earth.

Feeding your inner ecosystem

Public acceptance of the microbiome can be tracked by the rise of the probiotic. It wasn’t long ago that most people lumped all bacteria and their microbe peers into the blanket category of “germs,” using antibiotics and antibacterial products to eradicate them without prejudice. Today, as we begin to understand that many microbial species work with us, not against us, probiotic goods have proliferated in the form of pills, yogurt, kimchi and other grocery aisle staples, typically billed as promoting a healthier digestive system.

One big problem, says Stephen Lindemann, assistant professor of food science, is that science still doesn’t quite know what a “healthy” human gut microbiome looks like, never mind how a probiotic helps realize it. Researchers have focused on cataloging and characterizing the microbiomes of various environments, essentially taking a sample of genes and using the information to take attendance of the species present in the population. Scientists can then compare these populations in different groups — say, people with celiac disease and people without — but have learned little about which particular populations cause or prevent illness, and how.

“Without that kind of mechanistic understanding we can’t really tune the microbiome to do what we want it to do,” Lindemann says. “We’re stuck in a world where we can only say this output is correlated with health or unhealth, or with respect to a specific condition. There’s nothing actionable there.”

So in Lindemann’s lab, they’re digging into how the human gut microbiome handles a common but important set of nutrients: dietary fibers. Our own gastrointestinal system can’t fully digest many of these complex carbohydrates, so we rely on our microbial tenants to convert them into usable components. Lindemann’s group tests how different fiber sources affect the composition and activity of the microbiome. They found that even physical grain features such as bran particle size can produce radically different effects.

“The problem — and opportunity — is that we have found that, with respect to the structure of dietary fiber, everything matters,” he says.

By examining these responses, he hopes to find new ways to use diet to influence the microbiome, nudging these ecosystems toward healthier outcomes with the right mix of cereal grains for maximum benefit. Farther in the future, he envisions “designer carbohydrates,” with plants bred and cultivated for their microbiome-enhancing properties and custom fiber diets for individuals based on their specific microbial needs and responses.

“It’s really important we think about microbiomes as ecosystems, because they are full of interactions,” Lindemann says. “Our goal is to try to come up with the principles that guide the ecology of the gut, so that we can then use those principles to engineer or manage it.”

Harnessing the animal microbiome

That vision for human health can easily be extended to animals, where the diets and digestive microbiome may differ, but many of the goals are the same. Tim Johnson, assistant professor of animal sciences, has looked at the proliferation of antibiotic-resistant microbes in livestock that are fed antibiotics to promote growth and prevent illness. Animal producers are looking for ways to raise their livestock without antibiotics, turning to diet and the microbiome as a potential solution.

“In the past, the approach was to suppress bacterial growth in the gut. But that’s going to suppress both pathogenic and beneficial bacteria — microbes in the gut that stimulate the immune system and prevent disease,” Johnson says. “So now the idea is, instead of relying on antibiotics, let’s actually try to promote the gut microbiome and make use of all the beneficial bacteria that are there to promote health.”

In collaboration with animal nutritionists and livestock producers, Johnson’s lab researches new feed additives that can produce these desired effects in swine and poultry. Starting with the basic corn or soybean-based diet of these animals, they’re adding in different complex carbohydrates and closely observing how the microbiome responds: how its population of microbial species shifts, and how its generation of different beneficial nutrients, such as fatty acids, changes. After those relationships are established, the right mix of additives could be a viable, and more sustainable, alternative to feed antibiotics.

“The end goal is to reduce our need to treat animals with antibiotics and hopefully to reduce levels of antibiotic resistance as well,” Johnson says.

Beyond the gut

Many animal microbiomes do things that their human counterparts can’t. Ruminants, including cattle, giraffes and sheep, have strategies to break down grass, leaves and other plants that we find indigestible. To do so, fungal members of their gut microbiome produce powerful enzymes for extracting nutrition from plant matter.