Death of a sourdough

Ethan Freedman: Last year, I failed someone. His name was Mel.

(Piano starts)

Ethan Freedman: To be fair, Mel wasn’t really a “someone.” He was my sourdough starter: a collection of water, flour and billions of microbes to lead me through the yeast shortages and isolation of 2020’s coronavirus pandemic.

And for a while, he did, supplying me with tasty, crispy bread.

But — like for many other amateur bakers, I’m guessing — that dream came to an end one day, after I had neglected to feed Mel for a couple weeks as he sat on the countertop. If you don’t know, to feed a sourdough starter, you remove a little of the old starter and add in fresh flour and water — sort of like changing the water in a fish tank. The microbes can then eat the carbohydrates in the flour. If you leave it at room temperature like I did, you’d want to do this maybe once a day or so, but in a fridge, a starter can last longer since the lower temperatures make the microbes in the starter less active. 

When I opened the jar that had been sitting at room temperature on the countertop, unfed for a couple of weeks, I was met with mold and the odorous smack of rotten cheese.

So I turned to post-mortem Googling to assess what happened to Mel and found a lot of bakers describing how neglected starters could succumb to what they called “bad bacteria.”

But what are these “bad” bacteria? The microbes in a starter come from the flour, my hands and maybe even its surroundings — which didn’t change. So why were there suddenly new, “bad” bacteria once I stopped feeding it? 

To find out, first, I needed to understand what a normal starter looks like.

(Piano fades out)

Erin McKenney: So you have three main players: there are yeast — and, you know, people tend to associate yeast with bread — but in a sourdough starter, you additionally have lactic acid bacteria and acetic acid bacteria.

Ethan Freedman: That’s Erin McKenney, a microbiologist at North Carolina State University. She studies microbial ecology — which is like regular ecology, but with microorganisms — including the microbes in fermented foods like sourdough. And for the record, she’s also named her sourdough starter.

Erin McKenney: David Doughie.

Ethan Freedman: David Doughie, that’s right.* McKenney says that each microbial player does something for the bread. As the yeast feeds off the flour, it helps the bread rise by producing carbon dioxide. And the acids produced by those lactic and acetic acid bacteria give the bread that tangy sourdough flavor. So what happens on a microbial level when you stop feeding a sourdough starter?

*Note: Scienceline has been informed that the starter’s name is actually “Bavid Doughie,” not “David Doughie.”

Erin McKenney: I don’t know that anyone has ever studied this in a controlled lab experiment. So, thanks for pointing out an area of future research.

Ethan Freedman: You’re welcome! Although this may not have been explicitly studied, she has some ideas, clued in by what Mel had smelled like as he died.

Erin McKenney: Different communities of microbes produce different aromatic profiles. I can tell you that there is evidence that what you held did in fact indicate an abrupt shift in the microbial community in your sourdough starter.

Ethan Freedman: OK, so maybe these are the “bad” bacteria. But wait wait wait wait. Where did those microbes come from? If the microbes in my starter came from me and the flour and such, and that didn’t change, why are there suddenly new, different microbes?

Well, it turns out that those microbes have always been there, but they never gained a foothold because of the lactic and acetic acid bacteria.

Erin McKenney: Both types of bacteria are producing acids that decrease the pH in the sourdough starter. They’re kind of serving as a keystone species. They’re transforming their environments from the moment that they colonize them. By producing acid, they’re dropping the pH below the tolerance threshold of many other microbes, including mold.

Ethan Freedman: OK, so just to recap that: the lactic and acetic acid bacteria are eating the flour and water in the starter and producing acid. That acid then piles up in the starter, making the flour and water mixture more acidic. And that new acidic environment is a perfectly fine habitat for those bacteria, but not for other microbes — including microbes we don’t want. And research has shown that a healthy starter microbiome may have a variety of anti-microbial properties. 

You actually can see how this environment comes about when you make a starter from scratch. Tim Chin is a chef and writer based outside Boston who’s worked with sourdough for years.

Tim Chin: The very first few days, it often smells like funky cheese — a little bit putrid. And that is a sign that there are bacteria and other microbes that are unwanted in your culture. And then over time, as you keep feeding the culture, the beneficial microbes stabilize the culture and lower the acidity, so that it basically kills off or is inhospitable for these bad bacteria.

Ethan Freedman: But when you stop feeding a starter, those microbes might just keep producing acid. And without the process of taking some starter out and feeding new flour and water, your starter could just be getting more and more acidic.

Michael Gaenzle: I would expect that the lactics produce so much acid that they kill themselves eventually.

(Piano jumps in, fades)

Ethan Freedman: That’s Michael Gaenzle, a microbiologist at the University of Alberta in Canada. He says that the microbial ecosystem of a sourdough starter changes all the time, and we keep it stable by feeding it. But Mel’s rotten, cheesy smell and mold meant that my starter’s ecosystem was all out of whack. By not feeding it, I may have created the conditions for new microbes to colonize — probably microbes you wouldn’t want to eat.

(Piano rises softly)

Ethan Freedman: Microbes change our food for the better and for the worse all the time, but whether such transformations are beneficial or not depends a lot on the conditions we keep those microbes in. In the right conditions, microbes can help turn milk into cheese. But in the wrong conditions, that cheese can get moldy and inedible.

As for my decrepit sourdough starter, McKenney has a theory about where that smell came from. The normal sourdough smell comes from microbes digesting sugars and starches in flour, but digesting things like proteins and fats smells rotten and rancid, she says.

Erin McKenney: If you have a bunch of dead microbes, those dead microbial bodies contain a lot of protein and fat. So maybe the microbes producing those awful smells in your jar were, you know, dining on the corpses of, of dead microbes.

(Piano crescendos, and then fades to end)

Ethan Freedman: Gross. But Gaenzle tells me that Mel may not have been past the point of no return.

Michael Gaenzle: Your sourdough has a billion of active bacterial cells per gram. And even if you kill 100 million of these, you’re still left with a few that will catch on and take over as you start propagating and feeding again.

Ethan Freedman: Essentially, if you start feeding that neglected starter again, you could maybe restore it to that healthy balance. But Gaenzle did add that it might just be easier to start over. And with a starter that smelled rotten and moldy, you’d really want to make sure you restore it to normal before cooking with it. 

(Piano softly comes back in)

Ethan Freedman: So Mel, my friend, I’m sorry. I’m sorry to all your little yeasts and lactic acid bacteria and acetic acid bacteria. And I’m sorry that I could have saved you but sent you to live out your metabolic lifespan at the dump.

If you’re now worried you’ll make the same mistakes as I did, let me share this piece of advice McKenney gave me on how to stay confident as a sourdough baker.

Erin McKenney: Trust microbes. Bacteria have been around for twice as long as anything with more complex cells. Almost 4 billion years. They know what they’re doing.

Ethan Freedman: They know what they’re doing — meaning our job is to make sure they have the right conditions to do it. But if you happen to screw up and let your starter go like I did, don’t worry. Unlike microbes, we don’t always know what we’re doing. After all, we’re only human. 

For Scienceline, I’m Ethan Freedman.