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The microbiome thread: From farm to food to h

Deep within our bodies, millions of microbes help digest our food and provide nutrients to keep us healthy.

It’s a symbiotic relationship that dates back millennia, when the first bacteria appeared on Earth 3.5 billion years ago. Ubiquitous in the soil and environment, these microbes tagged along as more complex plants and animals evolved and became an essential part of human function. In fact, the human microbiome contains more bacterial cells than actual human cells.

“Even though they’re not part of our genetics, they exist in and on us,” said Dr. Davendra Ramkumar, a Champaign gastroenterologist and Associate Professor at the Carle Illinois College of Medicine (COM).

Ramkumar and his wife, Dr. Japhia Ramkumar, internist and Associate Professor at the Carle Illinois COM, have key roles in a project seed-funded by the Illinois Regenerative Agriculture Initiative (IRAI) to explore the microbiome connection from farm to food to human health. “Regenerative Agriculture and the Human Health Nexus in the Age of Climate Change” is an initiative of Basil’s Harvest, an Illinois nonprofit promoting regenerative ag and human health. The project will shed light on how regenerative farming practices lead to healthier soils and plants, which produce healthier food, which in turn influences gut health and, ultimately, overall human health. The collaboration, which includes researchers at the University of Illinois Urbana-Champaign, the Illinois Water Resources Center, and the University of Wisconsin-Stevens Point, has received a second year of IRAI seed funding.

“There’s a movement emerging that envisions transforming our agriculture systems in order to transform our health. Regenerative agriculture is a cornerstone in this movement,” the proposal states.

How does it all connect? Bacteria in our gut microbiome survive by extracting nutrients from what we eat. In return, they provide us with vitamins, help produce hormones, and modulate our immune system. A healthy microbiome leads to a healthy human.

One of the best food sources for the human microbiome is insoluble plant fiber — i.e., a high-fiber diet — which produces short-chain fatty acids that provide a crucial source of fuel, among other benefits.

“The way you feed it well is with a diverse, plant-based, whole food diet,” Japhia Ramkuma said. It’s a message we’ve all heard before, but “now we know why.”

Conversely, research shows that poor diets — heavy in ultra-processed foods, unhealthy fats, salt, sugar, and animal protein — disrupt the microbiome. That upsets the symbiotic balance and can cause diseases such as obesity, metabolic disorders, or a growing number of chronic intestinal conditions. Studies show there’s a clear difference in the microbiomes of healthy people compared to those affected by disease. And manipulating the microbiome, through diet or other means, can treat or prevent disease, Dave Ramkumar said.

Their theory is that maintaining a healthy diet is the simplest way to maintain a healthy microbiome, rather than taking supplements such as prepackaged prebiotics and probiotics. And getting healthy food relies on healthy, regenerative agricultural practices that prioritize soil health: things like minimizing soil disturbance, planting diverse crops, and using no-till cover crops. Though this research is still new, some studies show that produce grown through regenerative ag has higher vitamin and mineral content, and that minimizing hormones and antibiotics in animals leads to a healthier fat profile in meat.

The partners have established a Coalition of Regenerative Agriculture, Food and Health (CRAFH), which will build a community of stakeholders to promote these connections, increase research, and expand market opportunities so farmers will adopt regenerative agricultural practices.

The project came together through a combination of “serendipity and really good ideas,” said Japhia Ramkumar. As an internist, she had long focused on the health effects of climate change, working with her husband to raise awareness and incorporate those concepts into the medical curriculum. Dave Ramkumar has studied inflammatory bowel disease and Crohn’s disease and has used fecal transplants to successfully treat intestinal infections and restore a patient’s microbiome.

“As physicians, we are concerned about what we see as this plague that’s afflicting society: metabolic disease, obesity, chronic diseases. We were looking for ways to spread this word,” Japhia Ramkumar said.

In 2018 the Ramkumars applied for a grant to connect the idea of access to properly grown food and a healthy microbiome, with an educational component for local schools and public health clinics that emphasized healthy eating and reducing food waste. They didn’t get the grant but created a three-year curriculum for local middle schools.

Through the grant process they made connections with the Regenerate Illinois coalition, which is how they first met Erin Meyer, Founder and President of Basil’s Harvest and a dietitian, chef, and food systems expert. A few years later, in May 2021, Meyer reached out to Japhia Ramkumar to discuss an IRAI grant proposal connecting regenerative agriculture to food, farm, and health care systems. Meyer saw those systems as silos, and the microbiome as the connecting thread.

“That is exactly what we were trying to do, back in 2018 in a different way,” Japhia Ramkumar said. “We were the doctors in 2018 who didn’t have the agriculture or the food systems end of it to make it happen. Then here’s this person looking for the doctors to help make it happen.”

Basil’s Harvest had already put together a “white paper” about the connection between regenerative agriculture, soil, the microbiome, and human health, and Meyer wanted to bring researchers and other stakeholders together to connect the dots. She was interested in adding a health-care component, so Dave Ramkumar’s experience as a gastroenterologist and knowledge of the gut microbiome made him a perfect fit. They wrote the grant in two weeks, bringing in other Co-PIs: Yu-Feng Lin, Director of the Illinois Water Resources Center; Carl Rosier, Soil Microbial Ecologist with Basil’s Harvest; and Pratik Banerjee, Associate Professor of Food Safety at the U of I.

The research team, led by Dave Ramkumar, started with a literature review, gathering data on the role of the microbiome in diseases, the connection between regenerative agriculture and food quality, and the effects of pesticides and herbicides on the human microbiome. They are compiling that into a paper they hope to publish this year, and it will also serve as a basis for developing educational materials.

Their initial target audience is health care professionals: physicians, medical students/residents, and dietit­ians and dietetics students. They have already created an educational module on the microbiome for a “Cook Well, Eat Well” culinary medicine program developed by a separate Basil’s Harvest initiative, for family medicine residents at the University of Illinois College of Medicine and OSF HealthCare in Peoria. The course, focused on “food as medicine,” combines hands-on cooking with presentations on regenerative agriculture, nutrients, and the microbiome.

That module served as the foundation for a two-week elective for medical and dietetics students that focuses on sustainable/regenerative agriculture and food systems and the connection to the microbiome, which CRAFH hopes to pilot this year at the Carle Illinois College of Medicine and the University of Wisconsin-Stevens Point.

“We want health care providers to not just look at food but think about, ‘How did you get this food, how is it produced, how is it grown?’ ” Japhia Ramkumar said.

CRAFH also developed a survey for dietitians, physicians, and students in those fields to find out what they know and still need to learn on these topics. The group hopes to launch it during the second year of the grant, and will also refine and develop surveys for other groups; recruit farmers, scientists, and physicians for CRAFH; and try to secure more permanent funding.

Eventually, the hope is to drive up demand for regeneratively produced food from doctors, patients, hospital systems, and the wider community, using these same educational efforts with other stakeholders — from farmers to food distributors to supermarkets to consumers.

Meyer said regenerative agriculture needs to be incorporated into all facets of agriculture: row crops like corn and soybeans as well as food crops. That will require looking at regional food systems and market demand, to ensure that “farmers are able to grow more food and be paid a fair price to get that to the market,” she said. That way, consumers can purchase whole foods grown locally to support human and environmental health.

Dave Ramkumar said row crops and commercial farming will continue to be essential to the economy, “but they can be run better. We just need more acreage for regenerative agriculture.”

The CRAFH project’s focus is on research and education, not the market side, but Basil’s Harvest has another initiative connecting farms directly to hospitals and other institutions to shorten the supply chain and provide healthy food. Through its “Regenerative Agriculture in the Heartland” farm-to-institution initiative, Basil’s Harvest connected OSF Hospital in Peoria to a local mill and farmers in East Central Illinois and Minnesota to supply organic oats for its kitchen.

Meyer, who is from the Peoria area, started Basil’s Harvest — named for her garden-loving dog Basil — with her husband and kids to sell home-grown organic items at the farmers market. They eventually partnered with local farmers to sell shares for weekly boxes of produce. Later, after a tornado destroyed the operation, she worked as director of a nonprofit that connected culinary professionals to diversified, sustainable farming operations for food. She resurrected Basil’s Harvest as a nonprofit to extend that idea to health care. Basil’s Harvest also has a research team collecting data on soil chemistry and biology from East Central Illinois farms to study the health of the soil microbiome.

Ultimately Meyer envisions transforming the system by changing the way we talk about growing, processing, delivering, and eating food. “Doctors learning how to prepare healthy, delicious meals that are simple and take this information to their patients — to me that’s a huge start,” she said.

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