History of Fermentation – How do we know what ancient people drank?

Nothing ever changes. People drink beer, eat cheese, leave feces behind. While we are all reading from the same play book, I often wonder what ancient people’s relationship with alcohol or other fermented foods were. Logically, it would stand that fermented food would be extremely popular in the ancient times as methods for preserving edible calories were limited; fermentation would be an obvious way to keep food longer. In fact, one of the reasons Homo sapiens survived better than other hominids may be due, in part, to the activity of our alcohol dehydrogenase. Primates who could hold their liquor, but that’s a discussion for another time.

So, if you wanted to know what an ancient person ate or drank, what methods are available to you? There has been some work in this area over the past few decades. You can look for agricultural evidence, you can do some spectroscopy methods on vessels that held wine or beer, you can comb through ancient history depending on how well versed you are in dead languages.

Another method is to analyze human feces. Human feces is full of genetic markers from the gut microbiome as well as remnants of the food the human consumed. If you could find some feces from a few thousand years ago, preserved, it is theoretically possible to do some DNA sequencing or protein analysis on those samples and at least survey what species of plants and bacteria were present in the sample.

In a recent paper, a group of scientists in Europe did exactly that. Side note, I wish my title as a scientist included “Institute of Mummy Studies” but I’m a boring microbiologist.

The authors of the study obtained samples originally isolated over a period of time that were radiodated to different time periods. There were samples from the Bronze Age (~3300 years ago), Iron Age (~2500 years ago), and the Baroque period (~300 years ago). The stated goal of the researchers was to understand the diet and the impact on the gut microbiome. The paper spends a lot of time on the providence of the sample. How feces can survive thousands of years, how it was isolated, how it was stored. I guess this is what mummyologists need to control for in their work. If you don’t care about how poop can survive in a cave forever, you can skip to the conclusions section.

Photos of ancient poop from the paper cited above.

The figure is from the linked paper above, all the credit to the authors for this descriptive photo. We are going to focus on the data from the two middle samples from approximately 650 BCE. To put this sample in context, around 650 BCE the Assyrians were destroying Babylon. Christianity did not exist. The ancient city of Carthage won their independent from Tyre. I hoped that turned out well for them.

Protein analysis of the middle samples from the Iron Age revealed distinct markers from both Penicillium roqueforti and Saccharomyces cerevisiae. Any fan of this blog for sure knows the second one, that’s the “beer yeast” or rather the standard ale yeast. What about that Penicillium? Well, that’s the organism used to make the antibiotic Penicillin but also, it is the mold associated with blue cheese. It is the reason why blue cheese has those veins of blue throughout. And if you were just taking the drug, the organism wouldn’t be in your feces, this person was eating cheese and drinking beer.

They sound cool, we could hang out.

So you have a 2500 year old poop and there’s some markers for fungus in it. How do you know it is not a contaminant?  Following up on the protein samples, the authors were able to reconstruct >92% of both genomes through a technique known as “shot gun sequencing”. The researchers checked the ancient DNA damage pattern of the mapped reads. Both fungi displayed typical ancient DNA damage patterns, meaning both strains are “pre-domestication” from a modern point-of-view. These are likely deposited at the same time as the sample. While Babylon fell in the background.

Further analysis of the P. roqueforti strain was needed to determine if it was used to make blue cheese or was a spoilage organism at the time of the sample. There are four different phylogenetic branches for this Pencillium species: a Roquefort cheese clade, a non-Roquefort cheese clade containing blue cheeses others than Roquefort, a silage/food spoilage clade, and a wood/food spoilage clade. The ancient P. roqueforti strain showed highest similarity to the non-Roquefort cheese strains, consistent with the blue cheese branch, however it lacked some tell-tale signs of the domestication of that mold seen in the modern clade of those yeasts. The absence of this is further evidence that this is an ancient sample of the mold DNA. The final analysis revealed ∼70% cheese-producing ancestry (60% of the non-Roquefort and 10% of Roquefort cheese) and ∼30% food-spoiler ancestry. That was probably some funky cheese.

Moving onto the beer, the phylogeny (molecular relatedness) of yeasts has had a ton of work done on it in the past 20 years. The literature can be really intimidating. I’ll tackle it eventually. For the purposes of our discussion, we can talk about a few big groups: Beer 1, Beer 2, wine, and the rest (bread for example). These are all closely related but are different clades. The ancient S. cerevisiae strain clustered to the wine and beer 2 strains, resembling primarily the wine ancestral population (47%), followed by 29.2% beer ancestries.

There’s a temptation to try and over analyze data like this, make conclusions not from what is present but from what is absent. For example, can we use this information to speculate what kind of beverage this person was drinking or how it was made? Was it spontaneous? The researchers looked for other yeasts associated with beer spoilage or spontenous fermentation and did not find them. Does this absence of evidence imply that they were pitching cultures 2500 years ago? Who knows? This data cannot tell you that. This data tells you that ancient peoples enjoyed a beer and a cheese snack.

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