Tuesday, 04 October 2016 12:24

Metagenomics for Foodies

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Published in mBiosphere

Kefir is a viscous, sour-tasting, slightly alcoholic, milk-based beverage that's been consumed for centuries. It's made by adding a starter mix of bacteria and yeast – called the kefir “grain” – to pasteurized cow milk, though brewers have reported success with milk from goats, sheep, buffalo, and soy. As fermented dairy products go, it still lags behind yogurt and cheese in popularity, but in recent years kefir has enjoyed a surge in global sales.

That rise may be due, in part, to its reputed health benefits. For more than 100 years, scientists have suspected that the bacteria in fermented dairy products can improve intestinal health. More recently, articles and some studies have reported a wide spectrum of positive attributes -- that it helps lower cholesterol, prevent cancer, reduce inflammation, and treat ulcerative colitis. Paul Cotter, a microbiologist at the Teagasc Food Research Centre in Cork, Ireland, has been studying kefir for several years. He says those broad claims haven't been rigorously tested.

“When you claim something has compounds that can do everything, it becomes suspicious,” says Cotter. “Kefir's benefits haven't really been studied in a scientifically rigorous manner.” Most of the studies behind kefir's extraordinary health claims derived from experiments on cell lines or animal models.

At the same time, kefir hosts a rich and complex microbial community, and it's likely that the beverage does offer probiotic benefits. So how can scientists figure out what's going on with kefir? Cotter has an idea. He's recently turned to the tools of high-throughput sequencing to analyze the fermented beverage's microbial mix.

Scientists have been studying kefir and other fermented products at the Teagasc center since the 1990s. At first, they wanted to grow microbes from these foods, in hopes of isolating and producing new antimicrobial compounds that might, for example, be used in industry – as a preservative, for example. Cotter's lab at the center now specializes in food microbioime research.

In a new study published in the ASM open access journal mSystems, Cotter and his collaborators demonstrate how cutting-edge technology can be used to better understand kefir. They used shotgun metagenomic sequencing to study how the microbial populations change in kefir during a 24-hour fermentation process. They found that as fermentation goes on, the bacterial diversity diminishes, and species that dominate the population at the beginning are succeeded by others, hours later.

The study, led by Aaron Walsh, a graduate student in Cotter's lab, used metabolomics analyses to connect those individual bacteria species with metabolites associated with particular flavors. They connected an acidic taste to the presence of Acetobacter pasteurianus  bacteria, for example, and cheesy flavors to Lactobacillus kefiranofaciens.

Knowing which microbes influence which tastes points to a tantalizing implication: Can food scientists tweak the flavor and health benefits of kefir by changing the microbial ratios? In the new paper, the researchers carried out experiments where they changed the flavor compounds produced in kefir by supplementing with Lactobacillus kefiranofaciens and Leuconstoc mesenteroides. Another possibility, perhaps farther afield, is the idea that scientists could create synthetic kefir grains from the ground up, using only a customized selection of microbes.

The study has applications for health nuts. In addition to connecting microbes to flavors, the researchers identified genes that may be responsible for some of the intestinal benefits championed by kefir-drinkers.

Cotter, for his part, is a convert. He started drinking kefir as a result of his studies, and he recommends it to others. On the science front, though, he's excited because the combination of metagenomics with metabolomics suggests a vast new research area.

“We're pushing the boundaries in terms of applying new sequencing technologies to food,” he says.

Last modified on Tuesday, 08 November 2016 16:12
Stephen Ornes

Stephen Ornes is an award-winning science and medical writer in Nashville, Tennessee, whose articles have appeared in Scientific American, Discover, The Washington Post, Cancer Today, Science News for Students, and other outlets. His first book was a 2008 young adult biography of mathematician Sophie Germain, and he contributed two chapters to The Science Writers' Handbook. Visit him online at stephenornes.com, or on Twitter @stephenornes.

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