The cover shows an X-ray photograph of an Apple. From

I suspect that the Venn diagram of Food Matters readers and readers of the journal Cell doesn't contain a lot in the overlap portion, but this week, that should probably change. Cell is one of the big three in biology science publishing (the other two being Nature and Science), and usually contains predominantly wonky, jargon-laden cutting-edge research on cell biology (broadly defined) - last year around this time, they published my own graduate work. But this week's issue is a special edition all about food, and it's filled with plenty of work that would be of interest to readers of this blog, and many of them are quite readable.

Unfortunately, basically all of it is behind a paywall so if you don't have institutional access, you're out of luck. But, I'm going to try to summarize a few of these papers over the next week as best I can - you'll just have to take my word for it.

Up first - a paper written by my current supervisor Rachel Dutton, and her former post-doc Ben Wolfe, who now has his own lab at Tufts University.

Fermented Foods as Experimentally Tractable Microbial Ecosystems

The title is pretty expressive, I think - the point of this review is that fermented foods can be great models for studying microbial ecosystems. We know microbial ecosystems are intimately connected to our environment, our agriculture and our health, but for most of its history, the field of microbiology has been limited to studying individual microbial species in isolation.

This is not how microbes typically live. We wouldn't study a goldfish in a bowl and expect to understand the entire ocean ecosystem. But studying any ecosystem as a whole is a challenging task, and this is no less true when there are billions of your subjects in a single gram of material. So how can we expect to unravel the myriad complexities of the human microbiome, especially considering that the vast majority of species in the gut can't be cultured in the lab?

Microbes grow on all kinds of foods, from salami to cheese to tea (kobucha). Figure from Wolfe et. al.

This is where fermented foods come in. Traditionally fermented foods contain complex, multispecies microbial communities, but are far easier to manipulate in the lab. To compare, let's consider a situation where we want to compare the growth of two microbes, either separately or together, to see how interaction affects each other. To do this experiment in an animal gut (to model the gut microbiome) is a challenge - normal animals have trillions of microbes in their guts already. So you have to make "germ free" animals - basically delivering mice by c-section and then hand-rearing them in a sterile box with filtered air and no contact with the outside world. This has been done, but these mice are crazy expensive, and interpretation of the results can be clouded by the biology of the host (these mice are not healthy).

But to do the same thing with cheese is easy (relatively): just freeze-dry some milk curd, mix it up with some agar and sterilize it in an autoclave. Then add microbes to your heart's content.


Microbes growing on "in vitro cheese." From a different Wolfe et. al. paper in Cell.

The microbes from these fermented foods are also easier to culture in the lab. We know how to make an environment suitable for their growth - we've been doing it for thousands of years. Making a gut-like environment is far less practical.

If our real goal is to understand the gut, or the soil, or the oceans, these systems obviously aren't perfect. But the way I see it, studying genetics in the fruit fly has profoundly altered our understanding of human genetics. Model systems have a rich history in biology. And while All models are wrong, some are useful. Fermented foods are definitely useful for interrogating microbial ecosystems, and happen to be pretty damn tasty too.