I can't write an intro better than this:

Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered.

Jonathan Eisen's group at UC Davis sought to redress this lack of knowledge, and recently published some results in PeerJ, a relatively new open access online journal. The methodology is pretty straightforward: prepare 3 different types of meals, and compare the microbes present. It's a wonder no one has thought to do this until now.

The microbiome - the collection of microscopic organisms that live in us and on us - is an increasingly exciting field of research, and has been implicated in many aspects of human health, from obesity and diabetes to autoimmunity and cancer. As a result, many researchers and companies are hoping to develop new therapeutics that target or manipulate the microbiome in the interest of treating disease. From developing patented microbe pills to treat intestinal infections like C. difficile, to eating foods meant to encourage certain microbes to grow, this space is filled with potential ideas, and no shortage of charlatans interested in exploiting sciencey-sounding words to sell their products (no links to them, sorry).

The bad news is, we still don't know a ton about what a "healthy" microbiome looks like, let alone how to move from a disease-promoting microbiome to a health-promoting one. But all that is beside the point for this paper - they just wanted to know: what exactly is in the food we eat, and how variable is it?

The authors prepared or purchased 3 meals each for 3 different diets. The "American" diet was basically Starbucks and McDonalds (depressingly accurate), while the "USDA" diet contained well-balanced meals with fruits and vegetables in the recommended servings. The "Vegan" diet is similar to the USDA diet, but they removed any animal products (you can click here to see the makeup of each of the meals). Interestingly, rather than preparing the meals in the lab, they used someone's actual kitchen. On the one hand, this makes a ton of sense, since a lot of microbes are going to come from the environment, and a lab is hardly typical. On the other hand, this environment can't be well controlled, and considering the results, I wonder if they weren't actually testing the microbial composition of this kitchen rather than that of the foods.

In any case, once the meals were chosen and prepared, that's where the real work began. They checked for the presence of microbes, both by spreading them on petri dishes and looking for the growth of microbial colonies, and by using DNA sequencing to identify precisely what's present. In most cases, the meals were analyzed as a whole, so it's tough to say precisely where they came from. But in the so-called American diet, the only thing present is a Starbucks venti mocha frappuccino, so we know all the bugs came from there... almost 50,000 individual viable microbial cells, representing over 1,000 different species.

But that's just my prurient interest, the bulk of the results come from comparing the diversity present in each of the separate diets and somewhat surprisingly (to me at least), there wasn't a substantial difference.

Graph of microbial diversity in 3 different diets
Each of these graphs is a different way of calculating the measured microbial diversity - they don't seem to detect much variation. Click to enlarge.

The types of microbes present was also largely similar, though there were a lot more (in terms of numbers) in the USDA and vegan diets.

So what does this mean? We don't know!

Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health.

These are the interesting questions, at least to me. But our knowledge is so rudimentary that we still need to spend time characterizing what's there before we can hope to perform controlled experiments. I for one would like to see a wider variety of diets prepared in a wider variety of kitchens - I'm a bit worried that the environment shaped these results more than the foods themselves. This is a fine first step, and necessary to establish a baseline, but we have a long way to go.

Until then, I need another cup of coffee.