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Beer, Bread, Cheese — and Penicillin

How Fermentation built civilization

Dr. Terry Simpson's avatar
Dr. Terry Simpson
Aug 23, 2026
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When we talk about the microbiome, people think about the colon and trillions of microorganisms. Have you ever considered that humans have other interactions with microbiomes that occur with our cooking? On this week’s episode of FORK U, we continue with our series “Food That Made Civilization.” The topic is Fermentation.

How Fermentation Built Civilization

We were selecting a microbiome without knowing it. Bacteria, yeast and molds. Feed the ones that worked, keep the conditions they liked, and do it again.

Your grandmother may have kept the bowl that made better bread. She saved some of yesterday’s dough to start tomorrow’s. Others learned that milk mixed with a bit of salt and kept in a goat’s stomach became yogurt or cheese instead of something that had to be thrown away.

In Asia, they salted cabbage, put it into a jar, and buried it, and it allowed them to survive the winter. And perhaps in what is modern day Iran, they learned that when they crushed grapes, stored them in special containers, they made wine. And in Mesopotamia (now Iraq), ancient Sumerians left written recipes of barley brewing dating back over 5,000 years that was probably beer.

There were no microscopes, or bacterial cultures. We didn’t know that yeast metabolized sugar into alcohol and carbon dioxide, or that lactic-acid bacteria changed the chemistry of cabbage and milk.

But what they didn’t see was a colony of bacteria, yeast, and mold, creating environments in which organisms thrived, and transformed foods into something more edible and even stable for preservation.

Those microorganisms gave us bread, beer, wine, cheese, kimchi, vinegar and eventually penicillin.


What Did Ancient Beer Taste Like?

We are fascinated by what people before us ate and drank.

From the Midas Tomb in ancient Phrygia, now Turkey, they discovered that people had made a fermented drink from barley, grapes and honey. It was probably beer, wine and mead in the same cup.

Based on a chemical analysis of these vessels, Dogfish Head Brewery used modern yeast to make a beer called Midas Touch. But I wished we could have cultured the yeast and bacteria from one of those vessels?

As much effort as Dogfish used to reproduce the ingredients on the basis of chemical analysis, the beer is not the same. The barley, grapes, and even the water are different. Some of those grape varieties may not even exist anymore. The temperature and storage conditions we are guessing at best. And the microbes undoubtedly changed over the three thousand years while waiting to resume their shift.

Dogfish Head analyzed ingredients from pottery in China. That 9000 year old pottery once held a fermented beverage made from rice, honey and fruit. This was being drunk years before the Great Wall was built. Which makes me think, the Great Wall was the velvet rope, seeing if your name was on the list for the rice wine party.

But consider it like this: even pizza lovers from New York will tell you that without the NY water, or coal fired oven, you cannot make a true NY pizza.

The yeast we use now are descendants of those used by our ancestors. But the microbiome changes, they reproduce, mutate, mix with other organisms from the flour, the grain, the fruit, the hands and the environment. Yeast today are more different from their ancestors than we are from ours.

But we are never drinking the exact same beer. We are drinking what became of that ancient experiment. Just like you never step in the same river twice.

Then We Finally Saw Them

Then came Antonie van Leeuwenhoek, who developed the first microscope. He was not a physician. He was not a professor of microbiology. There was no microbiology. He was a fabric salesman with an obsession for making good lenses. When he put those lenses together, he saw a world no one knew existed. He pointed it at everything, water, tooth scrapings and eventually beer. He saw tiny living things moving around in a world humans had never seen. Leeuwenhoek called them animalcules, little animals. He even looked under his microscope and wine and beer.

France Has a Wine Problem

By the middle of the nineteenth century, France had been through revolution, empire, monarchy, another revolution, republic, and empire again. The country had plenty of political problems. But there was one problem that could unite almost any Frenchman. They didn’t know why sometimes their wine would spoil. Yes, there is the occasional bottle that is “corked” and that is an inconvenience. But losing the entire batch is a disaster.

Louis Pasteura chemist was commissioned to help solve this problem. Leeuwenhoek could see them. Pasteur wanted to know what the hell they were doing. They were doing the chemistry. The yeast was associated with alcoholic fermentation. Other organisms were associated with lactic fermentation. Different microorganisms produced different outcomes. And suddenly all those odd instructions from your grandmother made sense. Use this bowl. Save some of that dough. Keep a little from the good batch. Don’t use that barrel again.

Pasteur found that gently heating wine could prevent some of these microbial problems without boiling or ruining the wine. Which gives us one of my favorite historical details: pasteurization was developed for wine before it was used for milk. The raw-milk crowd should put that on the T-shirt.

My Great-Great-Uncle Changed Surgery

James Young Simpson — my grandfather’s uncle — helped transform surgery with chloroform anesthesia.

Anesthesia meant surgeons could finally operate without four people holding the patient down. Unfortunately, patients could survive the operation and still die several days later from infection.

That is where Joseph Lister enters the story.

Lister read Pasteur’s work on fermentation and putrefaction, and wondered if microorganisms could spoil wine, perhaps they could also spoil wounds.

Fermenting grapes can be wonderful. Fermenting wounds, not so much

Lister began using carbolic acid to treat wounds, instruments and surgical infection rates fell. That became the start of modern, safe surgical technique.

Pasteur was worried about spoiled wine. Lister was worried about dead patients.

In your kitchen, you practice microbiology.

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