111: The Cheese Microbiome with Rachel Dutton

Jul 3, 2019

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Cheese rinds contain microbial communities that are relatively simple to study in the lab while offering insight into other, more complex microbial ecosystems. Rachel Dutton discusses her work studying these cheese microbiomes, one of the few microbial ecosystem types where almost all of the microorganisms are culturable.

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Julie’s Biggest Takeaways

The cheese microbiome makes a great study system because

The communities are relatively simple (as few as 3 different microbial species)
The microbial members are almost all culturable (in stark contrast to most microbial communities)

The microbes colonize the cheese rind as a biofilm, which consists of the microbes and their secreted extracellular products. Like all biofilm communities, architecture and spatial structure are important for microbial interactions on cheese rinds, as are oxygen gradations, food access, and proximity to microbial neighbors.

Rachel and her lab performed DNA sequencing on over 150 cheese samples from 10 countries to identify the microbes present on these rinds. By comparing these sequences to those they could grow in the lab (Rachel’s lab makes “in vitro” cheese medium consisting of desiccated, autoclaved cheese), they realized almost all of the organisms identified by molecular means were present in their cultures.

Does the cheese environment influence the microbial communities or do the microbial communities influence the cheese environment? Both! The pH, temperature, added salt and temperature act as knobs or dials that allow cheese makers to fine tune the final cheese product.

Rachel was inspired to work on cheese after taking the Microbial Ecology course at Woods Hole, where the students spent a lot of time looking at the beautiful but complex interactions within microbial mats. Upon cutting open some Tomme de Savoie from a French colleague, she noted similarities between the microbial mat and the layered cheese rind

Featured Quotes

“The biofilm that colonizes the surface of the cheese has a lot to do with how the cheese ends up looking and smelling and tasting, and we actually eat this biofilm when we eat the cheese.”

“We’re able to see that of all of the things that we identified by reasonable sequence abundance, we could also find them in culture. This told us that we were able to get a lot of these microbes in culture, which is not really possible in microbial ecosystems, but is one of the really strong advantages of working in the fermented food community.”

“We’re looking at these interactions because they’re happening on cheese and we can study them in the lab but they are things that are happening broadly across ecosystems, which I think is very exciting.”

“We’ve done some work on the succession of species over time. You have these very very reproducible successions over time, even though a lot of these cheeses are not inoculated with specific species; these are species that are coming in from the environment but they’re very reproducible communities. There are some beautiful dynamics that happen and we’re starting to look at the interactions between species that may be driving some of these dynamics.”

“We have this big need for model systems. One of the things I hope is that we’ll have more people developing simple model systems for microbial ecology so we can compare results and see what the general principles are.”

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