Fermented Foods

A Global and Bacterial Investigation

Let's start with a poll! Select the foods which you think are fermented.

What is fermentation?

Through the lens of culture and society...


Fermentation began as and will remain a social endeavor. Initially arising as a means of preservation, there were social incentives to share recipes or bacterial starters to provide food for those around you. Because of the inherent property of ferments to grow and blossom, they can easily be split and divided with those around you.

Through the lens of chemistry and biology...


Fermentation is perhaps the world's oldest science. We generally define this to be the process by which microbes (bacteria and yeast) break down sugars into simpler substances. During this, they make byproducts like carbon dioxide (making it bubbly), alcohol (making it boozy) or lactic acid (making it sour). Early ferments relied on wild microbes -- whatever bacteria and yeast were on a sourdough maker's hand were the ones that inoculate the culture. With the advent of DNA sequencing over the past 30 years, we are able to identify and isolate strains, leading to the rise of precision industrial fermentation.

Through the lens of health and wellness...


According to yogurt lore, Genghis Khan fed his army yogurt to instill bravery. While this is unlikely to ever be proven, fermented foods contain two key components that are can contribute to a healthy gut microbiome: probiotics (live microbes) and prebiotics (nutrition for our gut microbes). Consuming fermented foods can both drive an increase in gut microbiota diversity and decrease systemic inflammatory markers the diversity of the microbiome.

Where can I find fermented foods?


We have good news! Fermented foods are all around us and around the world. In the following pages, we explore where we can find fermented foods globally and how they relate to one another both categorically and microbially. We hope that you will find the great variety of fermented foods and the great diversity of their bacteria as fascinating as we do.

How are Fermented Foods Distributed Around the World?
Welcome to a map of the world's fermented foods! Try dragging and hovering around the map.

When you are ready, try filtering for the category of fermented food in the upper left. For example, right now, you'll see that India has the greatest amount of all products; but when it comes to cheese, France (perhaps unsurprisingly) takes the lead. The countries in grey are ones for which we do not yet have data.

The bar graph demonstrates the top eight countries with the most fermented foods in the selected category.

To also explore the breakdown of foods within a country, try clicking on the country or its accompanying bar to populate a dendrogram that you can navigate to on the top!

This is mostly to help you get a sense of how wide the spread of foods are and to do a little exploration as to what kinds there are. We'll look into further breakdowns of each category and product next.
Fermented Food
Country of Origin
Category of Food
Description of Food
Source
Can you find these foods from the original poll?
Sauerkraut
Kimchi
Pane di Laterza (Sourdough)
Ayran (Yogurt)

What are these fermented foods made of?

Let's find out!

In the visualization below, explore the fascinating links between fermented products and the materials they're made from. Notice how some materials are the starting point for dozens of foods. Did you know, for instance, that France's Faiselle cheese is crafted from three different milks (cow, goat, and sheep)? Or that cow's milk is by far the leading source of various fermented products? Dive into the chart below to uncover more fun facts!

Force Directed Map

Sequencing method
Sample Information
Image of chosen fermented food
  • Sample
  • Country Made
  • Production Location
Taxonomy Information
  • Phylum:
  • Class:
  • Order:
  • Family:
  • Genus:

We know...

we are sad it's over too!

What can you take away from this?

What... you can ferment that?!


By exploring different countries and their host of fermented foods, you hopefully gained an appreciation for the vast world of fermented foods, and learned about some new types of fermented foods you hadn't heard of before! You saw that France, India, and Italy are hotspots for fermenting cheese, whereas China and South Korea are experts in fermenting roots and legumes.

Fermented Foods Around the World... where and what and how?


From Kimchi to Bastanga, we hope that you saw both how different cultures ferment foods of the same category around the world and how cultures ferment foods of widely different categories. There was a wide range within the category of beverages, you could find drinks from soju to champagne and from beer to ice wine. But at the individual description level, there were broad similarities: for example, India's fermented meats mostly fell into two time periods of fermentation: 7-15 days or 1-2 months.

What are these foods made of?


By exploring the relationships between fermented foods and their materials, we hope you've enjoyed discovering the intricate amount of ingredients that make up your favorite ferments.

Some bacteria are shared among most ferments, while yeast show more variability.


We saw that bacteria from the genus Lactobacillus are shared among kraut + kimchi, fruit + vegetable, freshwater fish, and meat ferments, whereas most dairy product contain Lactococcus. Other key bacteria include Streptococcus in yogurt, Pediococcus in meat and Vibrio in saltwater fish. For yeast, we see Aspergillus plays a big role in legume ferments and can spot Debaromyces in ferments of many different categories. Remember that while some of these microbes may sound scary (maybe you have heard of Vibrio cholerae in the context of cholera), there's much variability and context-dependence within types of bacteria. Just like some strains of E. coli can cause diarrhea while others are part of a healthy microbiome.

How is each category split by region?

We further explore the diversity of fermented foods by starting with a general overview of where the foods are located in regions across the world by category. You can click on any arc to zoom in on that category or hover to get more information.

We can see here, for example, that there are quite a lot of cheese and beverages (think, alcohol), as we might expect. But there's also quite a lot of cereal, meat, and fish, among other categories!

We'll next add some more information to the sunburst.

How is each category split by country?

Now, we've added another layer which breaks down the regions into individual countries. We notice that some of the heavy hitters are France in Cheese, but Italy too! Italy also has a lot of products in the meat category (we can think of their ham). Fish, on the other hand, figures prominently in Southeast Asia, and is spread pretty evenly between Thailand, the Philippines, and Laos. You can still click and hover!

Scroll further to get into the nitty gritty of each product.
Each country now has the individual fermented food products. Click on the title of any food product to see more information. A provided source link will take you to that page. Otherwise, refer to the provided citation.

We encourage you to try to find fermented foods you know and explore around. Clicking on the items from the poll will highlight them in the list. Hint kimchi and sauerkraut are both vegetables!

Div describing network

Network

You can interact with me! Discover how materials and products connect by hovering over the circles for product details. Hover over the icons to see material info and their food connections!

Zooming in on 80 Samples

Let's take a closer look at 80 fermented foods. You can hover on the points on the map to populate the Sample Information card.

Are there any fermented foods you haven't seen before? Can you find Hakarl, the Icelandic fermented shark? What about Fermented durian and Fermented jellyfish?

It sure would be cool to know what microbes there are within these seemingly very divergent fermented foods...

How can we see what's inside these fermented foods?

From the samples shown on the left, we first isolate bacteria and yeast cells, pop them open to get DNA, read the DNA sequences of all microbes within the sample. Using databases of pre-mapped DNA to microbe, we can know how much of each microbe is present in the sample. We plot these on a relative abundance plot, which tells us proportions of bacterial or yeast content.

Last stop: Bacteria and Yeast Central

You have unlocked the taxonomy tab! Here, a bar graph of the most abundant bacteria or yeast in the selected sample is shown. When you hover a given microbe, it will highlight in the other bars and populate Taxonomy Information card so you can see which microbes are shared among samples! Try filtering with the category dropdown to focus on specific ferments you are interested in!

Can you find a similar dominant bacteria shared between kraut + kimchi, fruit + vegetable, freshwater fish, and meat ferments? What about between yogurt + dairy and cheese? Which yeast are commmon in legume ferments?

Conclusions

Ferment Onwards and Upwards...

Image 1
Liana Merk

Harvard Biophysics PhD G2

Image 2
Hope Ha

Harvard College ’24, Applied Math in Government

Image 3
Rebeca Fontoura

Harvard College ’25, Computer Science + Music

Sources

The bulk of the fermented food data and ontology was collected by Lena Flörl and Rodrigo Hernández-Velázquez under Professor Nicholas Bokulich at the Laboratory of Food Systems Biotechnology ETH Zürich, Switzerland. We are grateful for their sharing of the data. Ongoing data collection is in the works, and a larger dashboard in preparation by the lab. The country-specific sequencing data was collected by Liana as part of an eight-month-long solo traveling research project.

Some figures were created with Biorender.com.

Thank you!

We made this for our CS171 final project. It would not have been possible without Profs. Hanspeter Pfister and Johanna Beyer as well as our wonderful TF mentor, Sophie Webster. We thank our classmates and friends who filled out the poll contributing to data about fermented food guesses!