Understanding Metabolites in Fermented Foods

and Why They are Important to Our Health - Part 1 of 2

Last month, Kirsten came home from the Stanford Ferment Food Conference re-energized from the presentations and the conversations in hallways with scientists, chefs, educators like herself, and enthusiasts. Of course, I wanted to know more about everything she mentioned, and so for the next few Ferment Nerds articles, we will take a deeper dive into the research that was presented over those two days to really understand how this applies to us.

What are metabolites?

I want to start with metabolites, which, if you remember from Kirsten’s article, is something she was pretty excited about. I don’t know why but I seem to want to make the concept of a metabolite more complicated than it really is. At its simplest form you can think of a metabolite as a puzzle piece or Lego block, or more dear to my heart, an ingredient in your favorite recipe. Metabolites are molecules that come into existence as a result of the fermentation of dietary fibers and resistant starches by microbes. That’s it.

Slide explaining metabolites in the microbiome from Dr. Elisa Caffrey’s presentation as part of Lessons from Microbial Communication session at Stanford 2025

And these things they create are really good things we need, and while we have discussed them in previous posts as being created in our guts, in this post and paper, we are looking outside our body.

Slide from Dr. Elisa Caffrey’s presentation as part of Lessons from Microbial Communication session at Stanford 2025 in which she is looking at the benefits of metabolites from lactic acid fermentation and benefits to the microbiome.

Back to the conference. The session was about lessons of microbial communication, and one of the presenters was Dr. Mikaela Kasperek of the University of Illinois Urbana-Champaign. I chose a paper she and her colleagues published in 2024, Microbial aromatic amino acid metabolism is modifiable in fermented food matrices to promote bioactivity, in the journal Food Chemistry, which concerned how microbes use and break down amino acids in fermented foods, and if those processes could be enhanced through different Lactic Acid Bacteria (LAB) to be passed on to we humans. We will look at the first part in this post and save the LAB enhancements for part 2.

It’s important as it wasn’t that long ago that we were discussing the relatively new concept of postbiotics, which you can refresh your memory with here. This 2024 paper, gives us new insights not only into what specifically are these postbiotics and that they exist in commercial ferments we enjoy eating today. And that the level of some metabolites in these foods, and thus in our bodies when we eat them, can be increased by choosing certain LABs in the food production.

In Kirsten’s post, she mentioned three main motivators for eating fermented foods: preservation, flavor and health benefits. This paper gives us more knowledge about that third motivator because, until recent research like this, it has not been completely clear, what has been giving us those benefits. Recently, scientists have identified LABs in our guts that metabolize certain amino acids to produce metabolites that act like keys in the locks of our immune receptors in our cells, helping our bodies either calm those levels down or turn them up to fight invading germs. What this study did was look upstream, if you will, to see what the level of these beneficial metabolites are in the fermented foods we enjoy.

Dr. Mikaela Kasperek’s presentation on her paper Microbial aromatic amino acid metabolism is modifiable in fermented food matrices to promote bioactivity as part of the Lessons in Microbial Communication Session at Stanford 2025.

They looked at a dozen types of commercially available fermented foods, and many of these are likely in your fridge or on your counter. At least I hope they are. We will use the three categories the study used because that’s going to be important in understanding how this affects us later. First, there were dairy ferments: kefir, yogurt, and cottage cheese. Next, vegetable ferments, a particular favorite obviously around our home: sauerkraut, kimchi, pickles, fermented beets, and carrots. Finally, there was a miscellaneous category, where meat-based ferments of salami and fish sauce met kombucha and miso. What the research found was good news to us all. While the concentrations of these metabolites varied, they were present in all samples. This would have been a big enough ‘ah-ha’ for me, but the study went on to ferment their own versions of these in their lab, picking specific LABs known to be super producers of these specific aryl-metabolites that, for the bacteria, help them protect themselves but also are good for us. We will save our discussion of that for part two. For this post, let’s look closer at the metabolites studied and why they’re important to us.

Three aryl-lactates were studied, each coming from the breakdown of three specific aromatic amino acids (ArAA), which are building blocks of proteins that have a ring-shaped part called an aromatic ring. That made me think of the Olympics, of course, which will come into play in a moment. These three molecules are:

1) Phenyllatic acid (PLA), which comes from the breaking down of the amino acid phenylalanine (Phe), which we need to make the next amino and to produce brain microbial communications.

2) 4-hydroxyphenyllatic acid (4HPLA), which comes from breaking down the amino acid tyrosine (Tyr), which is made from PLA above and helps us make hormones like dopamine, again a big brain communicator. 4HPLA is important to our bodies in fighting off infections.

3) Finally, Idole-3-lactic acid (ILA), which comes from the breaking down of the amino acid tryptophan (Trp), of Thanksgiving turkey fame for its ability to produce serotonin, which chills us out before putting us to sleep. ILA seems to help control other microbes in our guts and thus convey health benefits. More to learn there in the future.

Dr. Mikaela Kasperek’s presentation on her paper Microbial aromatic amino acid metabolism is modifiable in fermented food matrices to promote bioactivity showing the three aromatic amino acids from the Microbial Communication Session at Stanford 2025.

So three small chemicals that are derived from three amino acids, all conveying healthy benefits to us, and now we know already loaded in the fermented foods we eat. But how much? Does any fermented food give us everything or do we need a number of them? You probably can guess the answer.

In total, across all of the aryl-lactates, dairy ferments of kefir and greek yogurt had the most, though serving sizes for dairy it was pointed out are larger than your typical fermented vegetable serving size. It should be noted, dear reader, that in our household this is not the case, thanks to Kirsten and her prodigious quantities of fermented vegetables experiments. In those fermented vegetables the total varied by brand. In the miscellaneous category—ferments from meat to tea, and beans—salami stood out above the others, but all had some. When looking at each of those metabolites specifically, there were favorites:

- PLA: team fermented vegetables took the gold, followed by a brand of kefir for silver and salami for the bronze. Remember PLA is important because it can stop bad bacteria and fungi in their tracks, keeping that fermented food safe for us. That’s the preservation motivator.

- 4HPLA, same brand of kefir as above for the gold medal, other kefir and yogurts for the silver and fermented carrots, representing the veggies, takes the bronze. 4HPLA is another bad fungi and bacteria fighter in our gut.

- ILA, salami, medaling in the previous races, finally pulls ahead to win gold on this race, followed by fermented carrots and yogurt. (Only fitting, given the tie to turkey, don’t you think?)

Okay, that’s a lot to process, at least for me, so we are going to stop there with part one and summarize what we have learned from this.

First, that one of our favorite microbes, Lactic Acid Bacteria (LAB), produce small chemicals for themselves and specifically they produce aryl-lactates from aromatic amino acids, aromatic rings, Olympics.

Second, that these metabolites exist in all the commercial fermented foods sampled, which means when we eat them we get their benefits and our own microbes don’t even have to make them for them/us.

Finally, the levels of these beneficial metabolites differ by type of ferment and by brand within that type. That likely is due to the LABs responsible for the fermentation, and that will be looked at in more detail in part two. Until then, make sure you are fully stocked with some tasty ferments and, more importantly, that you are eating them every day!

Next level bowls. Rice and Pickles bowls being assembled at Cultured Pickle Shop.

Be sure to read Part 2.