Be a Sauerkraut!

By Embriette Hyde, PhD, Project Manager, American Gut Project

A movement has been taking the United States by storm-the fermented foods movement-and I’m really excited about this and how American Gut is getting involved!

It all started this past January with the San Diego Fermentation Festival. The Festival was scheduled for Sunday, January 31st. On January 20th, Austin Durant of the San Diego Fermenter’s Club and one of the amazing Festival organizers proposed an idea to us-why don’t we see if food vendors slated to attend the Festival were willing to sample themselves and their foods? We agreed this would indeed be intriguing, as not much is known in terms of exactly how fermented foods consumption affects the microbiome (though we do know that fermented foods have a really positive impact on health). So, Austin reached out to vendors telling them about this amazing opportunity, and those that were interested in participating contacted me directly. By the following Monday, I had 8 interested individuals. We went on full-speed mode and had all samples in the lab by Wednesday, January 27-four days before the festival. Our amazing wet lab team worked hard to extract DNA, run the PCR, and get the DNA to the sequencing center, who also put in a heroic effort. In parallel, our collaborators in Pieter Dorrestein’s lab here at UCSD prepped the samples for metabolomics analysis. By 4pm on Friday, January 29, we had our first look at what the microbial sequencing and mass spec data looked like-and it was exciting!

First of all, this was the quickest we had turned around a multi-omics data analysis effort (48 hours is literally unheard of)-and that in and of itself was pretty exciting (you can read the published open access manuscript here). On top of that, we were able to extract some interesting observations from the data:

  1. The microbial communities of fermented foods can be quite complex (others not so much)-see Figure 1 below. We certainly don’t understand them fully. One of our participants was a local brewer, and in speaking with her she told me that we had produced a profile for her beer that looked like a spoilage community, but obviously wasn’t since she had drank the beer and it tasted fine. This is intriguing, as it suggests that there may be a “timeline” along the fermentation process. It may be that spoilage communities aren’t immediately damaging to the product-and knowing whether that is true could have a big impact on food fermentation.
  2. As expected, the microbial communities detected in human fecal, skin, and mouth samples differed from food prep surfaces and from food samples. Interestingly, however, the microbial communities in two food samples looked like stool samples in terms of their composition. However, when looking at the metabolites, these two samples looked just like the other food samples (see Figure 2 below). This really highlights the fermenter communities-even if they vary in composition-perform the same, expected functions.
  3. When looking at a subset of the American Gut cohort, we saw that microbiome diversity increased with fermented foods consumption (see Figure 3 below). This is also interesting, given that in the vast majority of cases, increased diversity is associated with health, while decreased diversity is associated with disease.


Figure 1. Mean relative abundances of genera present in skin, mouth, and stool samples of one individual, plus the fermented foods consumed by that individual.

Figure 1. Mean relative abundances of genera present in skin, mouth, and stool samples of one individual, plus the fermented foods consumed by that individual.


Figure 2. A procrustes plot compares clustering patterns observed using 16S rRNA marker gene sequencing and metabolomics analysis. Spheres belonging to the same sample are connected; the gray end of the connector indicates 16S sequencing, while the black end indicates metabolomics.


Figure 3. Microbime diversity increases with fermented foods consumption in a subset of American Gut participants.


Based on these results, we’ve ramped up our effort to recruit more fermented food enthusiasts (and their food) into the American Gut cohort. This study was a good first look, but was a relatively small sample size. We also realized that drilling down and asking more specific questions-the types of fermented foods consumed and not just the quantity-may yield important patterns and associations that we couldn’t identify by broadly categorizing all foods into the “fermented foods” group. So, we created a specific fermented foods survey for participants to take if they want, and the survey was recently approved by the IRB-so it’ll be available to participants soon!

We’ve also been traveling and plan to travel to local (and not so local) events to promote the project and get support for our fermented foods cohorts. The first big event we attended after the San Diego Fermentation Festival was the Santa Barbara Earth Day Festival, where we spread awareness of American Gut and tried to recruit hobby and business fermenters into our cohort.


Educating people about the gut microbiome and signing people up for American Gut at a blustery San Diego Fermentation Festival!


Emily Pierce ready to discuss American Gut with future participants! Sampling kombucha. Signing up a new participant.

Bringing American Gut to the Santa Barbara Earth Day Festival-and even sampling some kombucha!


We’ll also make appearances at the Santa Barbara and Portland Fermentation Festivals this September. I’m looking forward to chatting with people, spreading the word about American Gut, and getting more samples into our cohort so we can begin to really tease apart the relationship between the microbiome, fermented foods consumption, and health!


This post is the first in a three-week series that will include the following guest posts:

Monday, August 1: Sandor Katz was one of the first to get on board with our ramped-up efforts to reach more fermented food enthusiasts, and was kind enough to get one of his recent classes on board with sampling themselves and their foods. You can read Sandor’s guest post about his class’s sampling effort next week!

Monday, August 8: We are honored to collaborate with cheese microbiologist Dr. Rachel Dutton, who is leading fermented foods research here at UCSD. Learn all about the microbiology of cheese and the work students are doing in Rachel’s lab on August 8!

Keep your eyes peeled for our upcoming fermentation posts, and let’s raise a kombucha to fermented foods and the microorganisms that make them so delicious and healthy!