The role environment plays in microbial diversity

First thing’s first: I know I spent most of 2015 not blogging but I’m hoping that I’ll have more time in the upcoming year to put together at least a couple of interesting posts. 2015 was an interesting beer year for me, including a 6 week long mad brewing spree to get all of my beers ready for my August wedding, tasting new beers from around the world, and making a wild cider from a VT friend’s backyard apples (and subsequently using the culture to make wild beer). I promise that I’ll post more in 2016 than in 2015 – it’s my Brew Year’s Resolution.

Speaking of Brew Year’s Resolutions, I’ve spent a lot of time recently listening to Drew Beechum and Denny Conn’s new podcast Experimental Brewing. It’s an excellent biweekly podcast with great production value and interesting beer-related topics. I’d definitely recommend checking it out. In a recent episode, they had an interview with Nick Impellitteri (biobrewer over at reddit, beeradvocate, etc), the founder and “Chief Yeast Wrangler” over at the Yeast Bay.

I won’t go into too much detail about the interview – after all, you could just go listen to the episode – but there was one point Nick mentioned that found particularly interesting. He mentioned at one point (and I’m paraphrasing) – that it’s not worth worrying about the ratios of various microbes within a sour blend. As soon as you modify the environment of the blend by adding it to wort, everything is thrown off and the ratios of microorganisms will shift. I agree that it’s not worth worrying about it but a question remains – is it possible to predict which microbes will succeed in the final blend, and will pitching the same blend of microbes without concern for the ratios (say, with a starter vs without) result in appreciably different beers?

Coincidentally, I had the opportunity last month to attend a seminar given by Dr. Benjamin Wolfe, a scientist at Tufts University. I’d classify his work as a definite dream job. Not only is his lab doing high quality, high impact research, but he’s doing it with some of my fermented favorite foods: cheese, salami and kombucha. His lab uses these foods as a platform to study the interaction of microbes and microbial diversity.

One of the projects he discussed was data that was published in Cell in 2014. The article is Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity,1 and it’s work that (I believe) was done during his postdoc in Dr. Rachel Dutton’s lab at Harvard. He also discussed some other really interesting work but it’s beyond the scope of this blog so I’ll be focusing on a couple of aspects of this paper. The major thrust of the paper was to identify the community of organisms that are found on the surface of aged cheeses, to establish the factors that drive what species thrive in a given cheese community (queso clique? fromage family?), and to determine whether these communities form reproducibly. You can watch a video summary of the project here put together by CellPress:

Using a fungal identification method (ITS) and bacterial identification method (16S sequencing), Wolfe and colleagues obtained and characterized the genera of fungus and bacteria present on the rinds of 137 cheeses from the US and Europe.2 What they found was an incredible diversity in types of organisms present – they identified 24 different genera on these cheese rind samples, with an average of 6.5 bacteria genera and 3.2 fungal genera per sample. There are likely many times more species on a given rind. They then used a bioinformatic method (principal component analysis) to determine what traits may result in a given set of organisms occurring on any one rind. Surprisingly, there was no correlation between geographical origin of a cheese and the makeup of a community. In other words, where the rind came from had a nonsignificant effect on microbes. (I would be interested to know if this could be recapitulated in breweries engaging in spontaneous fermentation from different regions of the world!)

So what does influence the composition of a microbial community? In short, it appears be the local environment –  i.e. the cheese itself. The three factors highlighted by the paper were pH, salt concentration, and moisture content. Interestingly, they also observed that certain bacteria are more strongly associated with certain fungi, suggesting some sort of cooperative growth, or an affinity for similar environments. They also saw that bacteria were highly responsive to the fungi present while the opposite was not the case. Finally, and perhaps most relevant to my original question, they found that seeding cheese with a known collection of microorganisms resulted in a reproducible ratio between the organisms. In other words, when given an identical environment, microbes will grow in a predictable pattern resulting in a similar ratio of organisms at the end of the experiment.

All of this said, this brings me back to Nick Impelliteri’s statement about the ratios of microbes in a sour blend, and why you shouldn’t worry about it much. I wonder if these findings in cheese might apply to a beer. If they do, it would suggest that with a given collection of organisms and a given recipe (a consistent environment), a beer should be able to reliably fermented the same way every time. Of course, real life is always more complicated and there are a variety of reasons why minor variation might occur, but it does imply that a microbial community tends to stabilize over time to conform to the environment and the other species present.

I’d love to know if the same principals of microecology apply to beer as they do to cheese. If they do, it would have pretty significant implications for the reproducibility of sour beers. For example, what environmental characteristics are relevant in defining the ecological diversity of microorganisms in beer (pH, IBUs, carbohydrate sources, alcohol content, osmotic pressure)? Knowing these whether these concepts apply to beer would also lend insight into the cooperative and conflicting roles that microorganisms play in making a successful sour beer (or not)!


the paper can be found behind a paywall here: .  A 2015 commentary regarding the use of fermented foods (including beer!) as models of ecosystems by Wolfe and Dutton can be found here:

2Note that this strategy identified genera – i.e. Staphylococcus, Pseudomonas, Vibrio, etc, and not individual species.

Other notes:

Finally, I should note that Dr. Ben Wolfe runs a site called, a great resource for learning more about the role microbes play in food – definitely check this out!

Apologies after the fact for such a text-heavy post, but the rules on reproducing journal figures are a bit unclear to me…


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