Synthetic Cheese and the Microbiome

Counter Culture Labs is a company that stemmed from an MIT iGEM team that made synthetic cheese. Their goal is to make vegan cheese that tastes just like the real thing with the single important difference being it is not derived from a cow, but rather a lab bench. Synthetic food is starting to trend. Already, we have seen synthetic beef, which could come in handy in saving non-renewable resources that we currently use for common food products.

A valid point was raised in the synthetic cheese article about the effect on the human microbiome. Even if something is chemically the same as the food in seeks to mimic, will it interact with our microbiome the same way? If those interactions are different, how do we measure them or go about determining whether they are good or bad changes? How far away are we from inoculating our synthetic cheese with say, a “model cheese microbiome” that would still input the same food-associated biota to our bodies? Does it matter?

Synthetic biology is an interesting field, but as with all new technology (especially biotech), there are many unaccounted for interactions that researchers may or may not be create from scratch or even quantify. Hopefully, the researchers creating this synthetic cheese take the microbiome into account now and realize how important these biological interactions can be.

5 thoughts on “Synthetic Cheese and the Microbiome

  1. Hi Alex – thanks for your interest in our project! Just a quick correction: Counter Culture Labs is not a company that was set up to make vegan cheese. We’re a non-profit community DIYbio lab in Oakland that has been around for about 2 years now, and Real Vegan Cheese was our 2014 iGEM project, in collaboration with BioCurious.

    This is just one of many projects going on at CCL though. In fact, we’re planning a soil sampling outing across Oakland for the weekend after next, in honor of Earth Day and the UN International Year of Soils (see We’re hoping to get some 16S sequencing done through uBiome, some standard soil assays (including lead content, which is a big issue in Oakland) through UMass, and secondary metabolite profiling through DrugsFromDirt.

    As for how differently the gut microbiome will respond to our synthetic cheese… likely less than the difference in its response to Kraft slices versus a cave-aged Stilton!


    1. Thank you for the correction! I think I misread/misinterpreted the original article I found. I’m still really interested in how synthetic cheese might differ microbiologically from “traditional” cheese. Cheese is such a diverse and cool biome for microbes, it’s just fascinating!

      1. We’re actually planning to start some experiments with some of the traditional cheese making cultures like Lactococcus lactis and Streptococcus thermophilus, to see how they will grow on carbon sources other than lactose, and what flavor and aroma profiles they produce under those conditions.

        S. thermophilus is unusual in that it actually grows *better* on lactose (a glucose-galactose disaccharide) than on straight glucose, even though it cannot digest the galactose half of lactose.

        Part of the flavor profile also comes from microbial degradation of some of the cheese proteins. That part we’re not too concerned with, because our proteins should be identical to those found in regular cheese, and should break down into similar degradation products. This is also the part that we may need to prove to the FDA, via some standard digestibility assays.

        The final component that’s important is the fat that will be in our cheese. Obviously, we don’t want to use butterfat, but we want to replace it with something that has a similar mouth feel. Palm oil might work, but that carries it’s own heavy environmental cost. Purified coconut oil is our leading candidate so far. Of course, using a different fat will select for a different cheese microbiome during the aging process as well.

        So, ironically, the part that I’m *least* concerned with, in terms of its effect on the cheese microbiome (and thus flavor) is our recombinantly expressed cheese proteins. Most likely, it will be those other components that fall more under “recipe development” rather than “synthetic biology” that are bound to have the biggest impact on the cheese microbiome.

      2. Note that it’s also a valid question to ask what the effect is of some of these aged nut cheeses that are now on the market. Human civilization has discovered through a process of trial and error that the traditional cheese making process tends to select for beneficial lactic acid bacteria that are yummy for our tummy. Presumably, ancient molecular gastronomistsalso discovered a few foods that are NOT advisable to ferment or age, through the same process of trial and error .

        Do we really know that if we take a nut paste, add some salt and other ingredients to make it taste more like cheese, inoculate it with a cheese culture, and then age it for a few months, that we won’t accidentally be selecting for any harmful bacteria? Not really, I think.

        Is that going to stop me from trying out someone’s new attempt at making an aged nut cheese? Not really.

        1. Interesting, so the cheese proteins are the same so it shouldn’t make a difference for the rest of the cheese-making process. And they probably get digested by the body and its gut microbiome in the same way. Thank you for all the info! I didn’t even realize nut cheeses existed since I only ever seek out dairy-derived cheese.

Leave a Reply

Alex Alexiev

Alex Alexiev is a recent UC Davis graduate with a BS in microbiology working in Jonathan Eisen’s lab on aquariums as part of the microbiology of the built environment.