Investigating the fiber of our being: How our gut bacteria metabolize complex carbohydrates from fruits, vegetables

Research at the University of Michigan Medical School, the University of York's Structural Biology Laboratory, and institutions in Canada and Sweden, has begun to uncover how our gut bacteria metabolize the complex dietary carbohydrates found in fruits and vegetables.

Trillions of bacteria live in human intestines -- there are about ten times more bacterial cells in the average person's body than human ones. Known as "microbiota," these bacteria have a vital role to play in human health: they are central to our metabolism and well-being.

The research team has uncovered how one group of gut bacteria, known as Bacteroidetes, digest complex sugars known as xyloglucans. These make up to 25 per cent of the dry weight of dietary fruit and vegetables including lettuce, onion, eggplant and tomatoes.

In a recent issue of Nature, the researchers reported on a particular gene sequence that allows Bacteroidetes to carry out this function. They show that about 92 per cent of the population harbors bacteria with a variant of the gene sequence, according to a survey of public genome data from 250 adult humans.

Understanding how these bacteria digest complex carbohydrates informs studies on a wide range of nutritional issues. These include probiotics (the consumption of 'beneficial' micro-organisms as a food supplement) and prebiotics (the consumption of foods or supplements intended to stimulate the production of healthy bacteria in the gut).

"Its been appreciated for a long time that our symbiotic gut bacteria provide us with greatly expanded abilities to digest dietary fiber. However, the precise details of how this happens remain largely unexplored," says co-corresponding author Eric Martens, Ph.D., an assistant professor in the Department of Microbiology & Immunology at the U-M Medical School. Martens is participating in the Host Microbiome Initiative, part of the U-M Medical School's Strategic Research Initiative.

Large-scale genome sequencing efforts, like the Human Microbiome Project, have focused on the community of microorganisms that live in the human gut. But these approaches can only uncover functions that have already been experimentally described, and much of what is sequenced is still unknown.

"In this study, we took an empirical approach to decipher how one model gut bacterium digests one type of fiber that is abundant in the foods we eat. We were subsequently able to fit our findings into a much larger picture because of the existing data that the Human Microbiome Project has already gathered. It is really an example of synergy between separate approaches that ultimately help us see the big picture. "

Martens worked with researchers from the University of British Columbia, Canada, the Royal Institute of Technology, Sweden, and the York University Structural Biology Laboratory to carry out detailed structural and mechanistic studies into the precise functioning of specific enzymes. This work has shed further light on which organisms can and cannot digest certain fruits and vegetables, and how and why the "good bacteria" do what they do.

Professor Gideon Davies, who led the research at York University, says, "Despite our omnivorous diet, humans aren't well equipped to eat complex plant matter; for this we rely on our gut bacteria. This work is helping us to understand the science of that process.

"The possible implications for commerce and industry extend beyond the realm of human nutrition, however. The study of how enzymes break down plant matter is also of direct relevance to the development of processes for environmentally-friendly energy solutions such as biofuels."

Editor's Note: See the University of York news release at http://www.york.ac.uk/news-and-events/news/2014/research/dietary-fibre/