Illinois scientists highlight impact of diet in world’s largest citizen-science microbiome project

Illinois scientists highlight impact of diet in world’s largest citizen-science microbiome project

 

Salad

URBANA, Ill. – Researchers at the University of Illinois, including Hannah Holscher, assistant professor of food science and human nutrition, and Kelly Swanson, professor of animal sciences, along with scientists at the University of California San Diego School of Medicine and collaborators around the world have published the first major results from the American Gut Project, a crowdsourced, global citizen science effort.

The American Gut Project was co-founded in November 2012 by Rob Knight, Jeff Leach, and Jack Gilbert. The project’s goal was to better understand human microbiomes — which types of bacteria live where, how many of each, and how they are influenced by diet, lifestyle, and disease.

To do this, citizen scientists contributed $99 and received a kit to collect a stool sample and instructions to mail it back. Along with the sample, each participant answered a voluntary survey that included questions about general health status, disease history, lifestyle, and diet. Scientists processed the samples using a genetic barcoding technique, then mailed participants a report detailing what’s living in their guts.

“We observed a much greater microbial diversity than previous smaller studies found, and that suggests that if we look at more populations, we’ll see more diversity, which is important for defining boundaries of the human microbiome,” said Daniel McDonald, scientific director of the American Gut Project at UC San Diego School of Medicine.

As of mid-2017, the project included microbial sequence data from 15,096 samples provided by 11,336 people, representing primarily the United States, United Kingdom, and Australia, along with 42 other countries or territories. The project and its affiliate, British Gut, have received more than $2.5 million in individual contributions to date through crowdfunding sites FundRazr and Indiegogo.

“It’s really amazing that more than 10,000 people — members of the public who want to get involved in science whether or not they work in a lab or have a PhD — have mailed their poop to our lab so that we can find out what makes a difference in somebody’s microbiome,” said Knight, who is also a professor in the UC San Diego School of Medicine and Jacobs School of Engineering, and director of the Center for Microbiome Innovation.

As nutritional scientists, Holscher and Swanson were involved in the diet data collection and interpretation. Some of the findings reported in the mSystems paper discuss how eating a diet rich in different plants, like fruits, vegetables, legumes, nuts, and whole grains is related to the composition of the gut microbiome.

Specifically, the researchers found that the number of plant types in a person’s diet was related to the diversity of his or her gut microbiome — the number of different types of bacteria living there. Participants who ate more than 30 different plant types per week had gut microbiomes that were more diverse than those who ate 10 or fewer types of plants per week. The gut samples of these two groups also differed in the types of molecules present.

Holscher explains that previous research has shown that plants differ in the type and amount of dietary fiber they contain, affecting how much can be broken down and by what specific microbes.

“Humans cannot break down dietary fibers for energy. Instead, microbes in our gut break down these fibers. However, each microbe has specific enzymes that allow them to use certain fibers for energy,” she says. “For example, one microbe may be able to break down the fiber found in apples while another has enzymes to break down the fiber in whole grains. The microbial community works together to degrade and metabolize each food source. The results of this study suggest that the recommendation to ‘eat the rainbow’ is also important for gut health.”

Most of the findings emerging from the American Gut Project so far are simply observations or associations, and in many cases researchers can’t yet extrapolate the ultimate effect on human health. For example, while the researchers observed that people who eat many plants have a more diverse gut microbiome than those who don’t, they don’t yet know if increasing a person’s microbial diversity from its current level would have a direct positive effect on his or her health.

“The American Gut Project is dynamic, with samples arriving from around the world daily,” Knight said. “The analysis presented in this paper represents a single snapshot, but we want eventually to go beyond making maps of the microbiome to making a microbiome GPS that tells you not just where you are on that map, but where you want to go and what to do in order to get there in terms of diet, lifestyle or medications.”

For the complete list of co-authors and institutions participating in the American Gut Project, view the full mSystems paper at:http://dx.doi.org/10.1128/mSystems.00031-18

The American Gut Project (AmericanGut.org) is funded by participants via crowdsourcing. Researchers who contributed effort or data analysis to the project are funded, in part, by the U.S. National Science Foundation (1144807), Sloan Foundation Microbiology of the Built Environment Program, Wyss Institute, Howard Hughes Medical Institute, U.S. Department of Energy (DE-AC02-06CH11357.NS), European Research Council (starting grant 336452-ENIGMO), WELBIO (WELBIO-CR-2012S-02R), Société Nationale Française de Gastro-Entérologie (Robert Tournut Award), Wellcome Trust, UK Medical Research Council, JPI Dinamic, National Institute for Health Research (NIHR) Clinical Research Facility at Guy’s & St Thomas’, NIHR Biomedical Research Centre at Guy’s and St Thomas’, UK NHS Foundation Trust, and King’s College London.

 

Sources: Hannah Holscher, 217-300-2512, hholsche@illinois.edu;
Kelly Swanson, 217-333-4189, ksswanso@illinois.edu

Media contacts: Lauren Quinn, 217-300-2435, ldquinn@illinois.edu;
Heather Buschman, 858-249-0456, hbuschman@ucsd.edu;

Date: May 15, 2018

Congratulations 2018 Graduates!

Congratulations to our 2018 Graduates!

  • Melisa Bailey, MS in Nutritional Sciences
  • Jennifer Kaczmarek, MS in Nutritional Sciences
  • Andrew Taylor, MS in Food Science and Human Nutrition
  • Erika Belloso, BS in Food Science and Human Nutrition
  • Elana Benishay, BS in Food Science and Human Nutrition
  • Jessica Bennett, BS with Distinction in Molecular and Cellular Biology
  • Ashley Griffin, BS in Food Science and Human Nutrition
  • Domenica Goyes, BS in Food Science and Human Nutrition
  • Anne Hou, BS in Food Science and Human Nutrition
  • Katie Lamps, BS in Food Science and Human Nutrition
  • Maya Nienaber, BS in Food Science and Human Nutrition
  • Hannah Peabody, BS in Food Science and Human Nutrition
  • Alice Pen, BS in Molecular and Cellular Biology
  • Amanda Rhee, BS in Food Science and Human Nutrition
  • Megan Reingold, BS in Food Science and Human Nutrition
  • Xinrui (Sylvia) Ren, BS in Food Science and Human Nutrition

 

 

 

 

Dr. Holscher awarded 2018-2019 NCSA Faculty Fellowship

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign has named Faculty Fellowship awardees for 2018-2019. These six Illinois faculty members will work with NCSA to investigate a wide array of subjects including cancer, agriculture, cinema, economics, civil infrastructure and more.

Each faculty member will work closely with experts at NCSA on a project that aligns with research focus areas and/or major projects (i.e., the Blue Waters projectXSEDE, the Midwest Big Data HubIndustry program).

OMIX DEVELOPMENT: A VISUAL ANALYTICS PLATFORM FOR MULTI-OMIC MICROBIOME DATA

Hannah HolscherFood Science and Human Nutrition
Microbial communities have a significant impact on human health. Growing research has demonstrated the influence of the host microbiota in cancer and the interaction with the human immune system, which impacts potential diagnosis and treatment. Also, gastrointestinal microbiome perturbations and diet are independently linked to public health issues including obesity, nonalcoholic fatty liver disease, and type 2 diabetes. Holscher’s project will study the impact of the human microbiome on health status using machine learning approaches developed by Dr. Zhu and the VI-Bio group. Her work will also inform the development of the NCSA VI-Bio group’s prototype OmiX, an informatics tool which will enable scientists to study microbiome-human interaction.

Learn about the other fellows and NCSA:

 http://www.ncsa.illinois.edu/news/story/ncsa_announces_2018_2019_illinois_faculty_fellows

 

Walnuts impact gut microbiome and improve health

Walnuts impact gut microbiome and improve health

PUBLISHED MAY 3, 2018

URBANA, Ill. – Diets rich in nuts, such as walnuts, have been shown to play a role in heart health and in reducing colorectal cancer. According to a new study from the University of Illinois, the way walnuts impact the gut microbiome—the collection of trillions of microbes or bacteria in the gastrointestinal tract—may be behind some of those health benefits.

Walnuts are just one in a line foods that contain dietary fiber and have interested scientists for their impact on the microbiome and health. Dietary fiber acts as a food source for gut microbiota, helping the bacteria to do their jobs—breaking down complex foods, providing us nutrients, or helping us feel full, for example.

Fruits, vegetables, whole grains, nuts, and legumes are important plant sources of dietary fiber. Eating a variety of these foods helps promote a diverse gut microbiota, which in turn helps to support health.

Findings from the study, published in The Journal of Nutrition, show that consuming walnuts not only impacted the gut microbiota and microbial derived secondary bile acids, but also reduced LDL-cholesterol levels in the adults participating in the study; good news for cardio, metabolic, and gastrointestinal health.

“We found that when you consume walnuts it increases microbes that produce butyrate, a beneficial metabolite for colonic health. So the interaction of walnuts with the microbiome is helping to produce some of those health effects,” says Hannah Holscher, assistant professor of food science and human nutrition at U of I, and lead author of the study. “It is about getting to the ‘black box’ that is all the microbes in our GI tract to see how they are interfacing with the food we eat and having downstream health effects.

“Some of those health effects are hypothesized to be related to the metabolites bacteria produce,” she adds.

For the controlled-feeding study, 18 healthy male and female adults consumed diets that either included 0 grams of walnuts or 42 grams—about a third cup or a palm-full of walnuts—for two, three-week periods. Fecal and blood samples were collected at the beginning and end of each period to assess secondary outcomes of the study, including effects of walnut consumption on fecal microbiota and bile acids and metabolic markers of health.

Walnut consumption resulted in higher relative abundance of three bacteria of interest: Faecalibacterium, Roseburia, and Clostridium.

“The microbes that increased in relative abundance in this walnut study are from one of the Clostridium clusters of microbes, and there’s increased interest in those because they have the ability to make butyrate,” Holscher says. “Unfortunately in this study we didn’t measure butyrate, so we can’t say that just because these microbes increased that butyrate did increase. We still need to answer that question.

“There is a lot of interest in Faecalibacterium because it has also been shown in animals to reduce inflammation. Animals with higher amounts also have better insulin sensitivity. There is also growing interest in Faecalibacterium as a potential probiotic bacteria, and so we are trying to follow up on foods that help support Faecalibacterium.”

The findings also show, with walnut consumption, a reduction in secondary bile acids compared to the control. “Secondary bile acids have been shown to be higher in individuals with higher rates of colorectal cancer,” Holscher explains. “Secondary bile acids can be damaging to cells within the GI tract, and microbes make those secondary bile acids. If we can reduce secondary bile acids in the gut, it may also help with human health.”

Previous research that prompted this microbial research showed that the amount of energy (calories) derived from walnuts after we eat them is less than previously thought.

“When you do calculations to determine how much energy we predicted we would get from eating walnuts, it didn’t line up with the energy that was absorbed,” Holscher says. “You’re really only absorbing around 80 percent of the energy from walnuts that labels say. That means that the microbes get access to that extra 20 percent of calories and the fats and fiber left in them, and so what happens then? Does it produce a positive health outcome, or a negative health outcome? Our study provides initial findings that suggest that the interactions of microbes with the undigested walnut components are producing positive outcomes.

“We need more research to look at additional microbial metabolites and how those are influencing health outcomes, instead of just characterizing the changes in the microbiome,” Holscher says.

The paper, “Walnut consumption alters the gastrointestinal microbiota, microbially derived secondary bile acids, and health markers in healthy adults: a randomized controlled trial,” is published in The Journal of Nutrition. Co-authors include: Hannah D. Holscher, Heather M. Guetterman, Kelly S. SwansonRuopeng An, Nirupa R. Matthan, Alice H. Lichtenstein, Janet A. NovotnyDavid J. Baer.

Holscher is an assistant professor in the Department of Food Science and Human Nutrition and Division on Nutritional Sciences; Guetterman was in the Department of Food Science and Human Nutrition; Ruopeng is in the Division of Nutritional Sciences; and Swanson is a professor in the Department of Animal Sciences and Division of Nutritional Sciences, all in the College of Agricultural, Consumer and Environmental Sciences at U of I. Baer and Novotny are at the USDA-ARS, Beltsville Human Nutrition Research Center. Matthan and Lichtenstein are at the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University.

Funding for the study was provided by USDA-ARS and California Walnut Commission.

Congratulations!

Congratulations to the following Nutrition and Human Microbiome Laboratory members for their recent awards:

  • Erika Belloso: Outstanding Senior in Dietetics, Department of Food Science and Human Nutrition, University of Illinois
  • Elena Benishay: Bronze Tablet Distinction, University of Illinois
  • Jessica Bennett: Graduation with Distinction, Department of Molecular & Cellular Biology, University of Illinois
  • Anne Hou:  Outstanding Student Researcher, Department of Food Science and Human Nutrition, University of Illinois
  • Sharon Thompson: Outstanding Poster Presentation, Nutrition Symposium, Division of Nutritional Sciences, University of Illinois

Fiber and Gut Health Podcast

Interested in learning more about fiber and gut health? Check out a recent podcast on the Radio Health Journal that I contributed to: https://radiohealthjournal.wordpress.com/2018/02/04/18-05-segment-2-fiber-and-the-gut/

Fiber is an important part of a daily diet, but many people do not know what fiber  does for the body. Dr. Hannah Holscher, Assistant Professor of Nutrition at the University of Illinois-Urbana-Champaign, explains that fiber is a non-digestible carbohydrate that is found in plants which human enzymes cannot break down, so the body relies on microbes.

Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us?

Exercise Alters Our Microbiome.  Is That One Reason It’s So Good for Us?

New York Times

By Gretchen Reynolds

Exercise may change the composition and activity of the trillions of microbes in our guts in ways that could improve our health and metabolisms over time, a new study finds.

Click on the picture above to check out the full story on our research that’s featured in a January 3, 2018 article in the New York Times.

Interested in reading our final published manuscript?  You can find that here:  https://insights.ovid.com/pubmed?pmid=29166320

Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, Holscher HD, Woods JA. Exercise-induced shifts in the gut microbiome and associated metabolites are dependent on obesity status. Medicine & Science in Sports & Exercise. 2017. DOI: 10.1249/MSS.0000000000001495

Fiber Is Good for You. Now Scientists May Know Why.

By Carl Zimmer, New York Times

Click on the picture to read the full story in the New York Times.

A diet of fiber-rich foods, such as fruits and vegetables, reduces the risk of developing diabetesheart disease and arthritis. Indeed, the evidence for fiber’s benefits extends beyond any particular ailment: People who eat more of it simply have lower odds of dying.

Hannah D. Holscher, a nutrition scientist at the University of Illinois who was not involved in the new studies, said that the results on mice need to be put to the test in humans. But it’s much harder to run such studies on people.

In her own lab, Dr. Holscher acts as a round-the-clock personal chef. She and her colleagues provide volunteers with all their meals for two weeks. She can then give some of her volunteers an extra source of fiber — such as walnuts — and look for changes in both their microbiome and their levels of inflammation.

Dr. Holscher and other researchers hope that they will learn enough about how fiber influences the microbiome to use it as a way to treat disorders. Lowering inflammation with fiber may also help in the treatment of immune disorders such as inflammatory bowel disease.

Fiber may also help reverse obesity. Last month in the American Journal of Clinical Nutrition, Dr. Holscher and her colleagues reviewed a number of trials in which fiber was used to treat obesity. They found that fiber supplements helped obese people to lose about five pounds, on average.

Click on the picture above to read the full story in the January 1, 2018 Science & Heath Sections of the New York Times.

Holscher receives prestigious Foundation for Food and Agriculture Research Award for early-career innovation in nutrition

Holscher receives prestigious Foundation for Food and Agriculture Research Award for early-career innovation in nutrition

URBANA, Ill. – Hannah Holscher, assistant professor of nutrition in the Department of Food Science and Human Nutrition at the University of Illinois is a recipient of the second annual New Innovator in Food and Agriculture Research award. The annual set of early-career grants to outstanding food and agriculture research faculty members is a program of the Foundation for Food and Agriculture Research (FFAR), a nonprofit established through bipartisan congressional support in the 2014 Farm Bill.

Holscher received a FFAR grant of nearly $600,000 to fund a project looking at diet, the human gastrointestinal microbiome, and metabolic health over the next three years. Research in Holscher’s laboratory at U of I, the Nutrition and Human Microbiome Laboratory, integrates the areas of nutrition, gastrointestinal physiology, and the microbiome. Her research focuses on the clinical application of nutritional sciences with an overarching goal of improving human health through dietary modulation of the gastrointestinal microbiome.

“The results of my research will provide information that will help consumers to make healthful food choices,” Holscher explains. “It will also inform dietary guidance given by registered dietitians, health care providers, and extension specialists. The findings will be applicable to food consumption, food and nutrition practice, and human health outcomes.”

“The Foundation for Food and Agriculture Research is pleased to support Dr. Holscher’s research as part of our work to catalyze innovation and foster a strong scientific workforce for the future,” says Sally Rockey, executive director of FFAR. “I look forward to seeing the impact of the New Innovator in Food and Agriculture Research award not only on Dr. Holscher’s career, but also on advancing agriculture.”

The New Innovator in Food and Agriculture Research program supports promising scientists who demonstrate not only a commitment to catalyzing innovation in food and agriculture, but also a dedication to mentoring students.

Holscher joins a group of other 2017 New Innovator in Food and Agriculture Research award recipients who were selected from across the United States in five categories: nutrition and healthy food choices; plant efficiency; optimizing agricultural water use; spurring food system innovation; and transforming soil health.

The second annual set of New Innovator awards brings the total FFAR investment in the program to more than $4.5 million. Learn more about the 2017 New Innovators and their research directions.