Fermented Foods Part 4: Incorporating Food Fermentations Into Microbiology Courses

Fermented foods are fun to make at home, as previously discussed in Part 1 and Part 2 of the Fermented Foods Series. So, wouldn’t it also be fun to learn about them in a college course? One school is making this happen. Through the process of preparing fermented foods, students taking a microbiology course for the first time can learn basic concepts about microbes as well as how to conduct research.

As a recap, in the previous post, Part 3 of the Fermented Foods Series, I discussed the potential health benefits of fermented foods and how to assess the reliability of the health claims. So, if you missed it, go back and check that one out.

Here in Part 4, I’m sharing an interview with Dr. Michael Taveirne from the Department of Biological Sciences at North Carolina State University about how he and his colleagues redesigned their general microbiology course so that it incorporated food fermentation—the pickle project—to teach students basic concepts about microbiology, research, and the application of the scientific method. 

In this interview, we discuss the purpose and structure of the course, how this type of course allows students to gain experience doing research, why fermented foods work well for this type of course, the difficulties of the course structure and research in general but how those difficulties are actually beneficial, the results they’ve gathered so far, and the future directions of this course.

Question: Tell me a little bit about this microbiology class you teach that incorporates food fermentation?

Answer: The class that involves this “pickle project” at NC State is our general microbiology lab course. This is completely a team effort with my colleague, Dr. Alice Lee, our research technician Sandy Gove, graduate student Jennifer Greenstein, and a former undergraduate student Brian Ford. This collaboration started in Fall 2016. We piloted it for two years in our honor’s and major’s lab sections, and in Fall 2019 we have moved the research module into our large-enrollment general microbiology lab, which has 14 sections and ~350 students.

Our general micro labs were great at teaching typical techniques in microbiology, like isolation streaking, Gram staining, microscopy, and metabolic tests, but there was a lack of critical and creative thought around the scientific method.

In the previous iteration of the course, we didn’t have a research project. The one thing students did was identify an unknown bacterium, which has its pros. But again, the unknown is really not a true unknown as the instructors know what it is. So, the students go through a series of tests, and there’s some critical thought, but it’s not like a regular research project. Everything worked.

Overall, it was great because this class enrolls about 700-800 students each year. So, it’s really nice when things work on a logistical aspect. But it was not teaching students that science does not work as expected every single time, and sometimes you don’t get the results that you expect. Additionally, this didn’t allow students an opportunity to modify experiments based on their results or to come up with new questions for those unique results.

So, we decided to try to incorporate more of a CURE (Course-based Undergraduate Research Experiences)-based approach built on a guided inquiry model where students have some choice.

We decided on food fermentations because 1) they’re an excellent tool to study microbiology, and 2) they’re relatable to students. You see these products in everyday life; however, you might not necessarily know the microbiology behind it.

We collaborated with some of our colleagues at NC State Food, Bioprocessing, and Nutrition Sciences Department, who eventually got us in contact with The Mount Olive Pickle Company. Our initial question was with regard to salt concentrations in pickling brine solutions. Most commercial cucumber fermentations use a 6-12% salt brine in their fermentations, but there was not much microbiology research on why these were good ranges. 6% is pretty high for production costs and also has environmental impacts.

So, we wanted to ask how differing salt concentrations can affect the fermentation process, both at the microbiology level, but also at the business level. What if we lowered the salt concentration? Would that still produce an effective fermentation product, but also, at the same time, produce a viable commercial product?

It was actually an intriguing aspect to our class where we were bringing in both the microbiology side, where students had to assess all of these different microbiological aspects around fermentation. But they also had to look at the real-world aspects and more of the business side to say, yes, maybe we can lower this concentration to 1 or 2%. And it works on the microbiology side, but maybe that doesn’t produce a good product. Maybe the pickle is mushy, colored differently, has altered flavors, or it has this phenomenon called bloating, where you get secondary fermentation and CO₂ production resulting in big air pockets within the pickle.

So, it was a unique way for students to not just look at the science side but also the business side.

Question: Do you think that the students feel like they have more ownership over the project than they would in a traditional lab course?

Answer: Absolutely! Students not only have an independent research project but also have some choice on variables associated with their specific project. We offer the students a choice with regard to the salt concentration—allowing them to pick a salt concentration for their fermentation jar (between 2-12%). Students work as groups of four on one fermentation jar at a certain salt percent over a six-week period. Over the course of the project, they develop a research question, a hypothesis, and predictions on results they might observe. They then conduct their experiment collecting, observing, and interpreting results, and finally communicating those results in a scientific research poster.

The one thing that students really don’t grasp at the beginning of the project, but see the benefit towards the end, is that we don’t know the answer to their specific research question. They’re always asking us, is this what we should get? And we say, “We don’t know, but that’s the reason we’re doing these experiments, to find the answer.” So, they eventually get to that point where they realize that they are the only person who really knows the answer to their question.

And they really have this kind of ownership and sense of “wow, this is really a cool research project!”

Question: Why do you think that food fermentation is a particularly good topic for teaching microbiology?

Answer: I think it’s a great topic because it’s an ancient process that humans have been using for thousands of years for food preservation, and it’s something students see in their everyday life but maybe don’t realize the extent to which these processes and products rely on microbes.  It’s also relevant to the metabolism section in our cognate lecture course, a topic that may not be the most interesting to many students. But when we bring in these examples of real-world applications of modifying and forcing certain microbes to go through these metabolic processes to generate your yogurt, pickles, beer and wine, and cheese, students see it’s not just a biochemical pathway they have to memorize, it’s a unique process that leads to all of these end products that ultimately generate many food products. 

When they see it as a more real-life situation, it makes it more relevant.

Question: Can you tell me a little more about what the students do in the class?

For many students, this is their first experience in a microbiology lab. The course is split into three modules. The first module teaches students basic microbiology techniques, like aseptic technique, media preparation, serial dilutions, and Gram staining. The second module is the research project, and the final module is data visualization and presentation. Throughout the semester, they build up a core set of knowledge and then utilize that knowledge within their research project. The final assessment for this class is to present their project as a scientific poster.

Question: What would you say is difficult about running this type of lab?

Answer: The whole thing about research is that you don’t know what you’re going to get, and that is difficult at first to communicate to students. When a student comes into our labs, they’ve already taken some lab courses where everything may have worked as expected. However, as this lab is built off an actual research project, things may not work as expected. So, we try to educate students to say experiments always work.

But experiments don’t always give you what you are expecting. When the students don’t get a result that they expect, they think they did something wrong. We tell them, that’s actually a result. We just don’t know the answer. And maybe our hypothesis is incorrect. It’s a perfectly valid result if you did the experiment correctly. We try to communicate the true process of research and critical and creative thought. I always tell students, it’s research for a reason.

You’re doing it over and over again, and you’re going to get results that don’t line up with your hypothesis. But that’s good because that then opens the door for you to ask new questions. And that’s really what drives science forward.

Question: Do you feel like the difficulty turns into something positive in the end?

Answer: Yes, I think we’re getting students excited about research. We’re helping them understand what a research project is and to really grasp the goals of the scientific method. If they’re interested and like it, they now have an experience that can help them in finding opportunities in independent research labs, internships outside of the university, or summer programs, utilizing this course as a foundational platform.

Question: What sort of results have you seen so far from these experiments testing different salt concentrations?

Answer: We’ve collected data across four semesters and see this beautiful theoretical microbial population dynamic changes over time, where you have a decrease in Enterobacteriaceae or spoilage microorganisms, and an increase in lactic acid bacteria. We actually see that across all different salt concentrations, even with a 2% salt concentration, our lowest concentration. It does work well, but we’re still questioning if it will translate to a large scale and if it results in a viable commercial product.

We currently don’t have the approval to do any taste testing of the samples, so we can’t really say how the actual end product tastes. The only thing that we use to assess the quality of the final product in the lab is “a pickle dissection,” where we actually cut open the pickle and look for this process of bloating, the presence of air pockets. That’s currently our only end-product assessment.

Question: I’m really interested now that you mentioned it. Can you tell me a little bit more about the beginning of the fermentation where you have the spoilage microorganisms? Where are those coming from (skin, food)? And can you tell me about what makes the fermentation safe in general despite the presence of these spoilage microorganisms?

Answer: Cucumbers are naturally colonized with both lactic acid bacteria (L.A.B.s), as well as spoilage microorganisms. Most of these microorganisms can come from the environment where the cucumber is grown, including the soil. We do a light wash of the cucumbers at the beginning to remove any dirt or soil, but we don’t scrub them because the bacteria naturally present on the cucumber serves as the inoculum for the fermentation. We currently are only doing natural inoculums, but are working on using starter cultures in future semesters. We then pack our jars with the cucumbers, add our brine solution, close the cap, and let the bacteria do their work. 

The salt at these high concentrations is inhibitory for most bacteria, including pathogens and spoilage microbes. But the lactic acid bacteria are salt-tolerant, so those bacteria start to metabolize (ferment) the available glucose into lactic acid (cucumbers are predominantly made up of glucose). 

Lactic acid is really what gives you the flavor of your pickle—that acidic, vinegary aspect. We also start to see a decrease in the pH. A low (acidic) pH is a secondary environmental condition that prevents the growth of pathogens and spoilage microorganisms but still allows the growth of beneficial microbes.

If we plot the concentration of these two different groups of bacteria (spoilage microorganisms and lactic acid bacteria), we roughly see at the beginning that we have equal populations of both lactic acid bacteria and spoilage microorganisms. By day seven, we start to see an increase in the beneficial lactic acid bacteria and a decrease in the spoilage bacteria. And usually, by day 14-21, the concentration of spoilage microbes fall below our limit of detection. It’s not that they’re not present. It’s that we can’t detect them with our plating methods. By this time, the lactic acid bacteria are extremely high (~1×10^9 CFU/mL) and plateau. The EHS office is very happy we’re not cultivating any pathogens. 

Question: What ideas do you have for the future for the class?

Answer: You can only learn so much about salt concentration after about four or five semesters. So we are currently looking at different research questions, including different types of salts. One thing that the pickle industry is looking at is the use of calcium chloride, which is a little bit less toxic to the environment than sodium chloride. But it does have some issues with the fermentation process, so there is active ongoing research in that area. Another thing we are interested in assessing is the use of starter cultures. We’re interested in having students purchase some commercial starter culture kits and see if that affects the fermentation process. Students get to determine how these starter cultures are working at the microbial level and also assess if they are really needed and worth your money.

Question: Do you have any last thoughts you’d like to share?

Answer: We submitted a bioRxiv preprint on this course redesign project incorporating inquiry-guided research into a large-enrollment lab course, and are currently looking to publish it. So, we’re trying to tidy that up so anybody can download and incorporate it into their lab. It’s a great lab to include in a general microbiology course, and it would be good if you had some microbiology experience to run this specific project. The project has been difficult even for us. Our group of microbiologists is not trained in food fermentations, so we have relied on our colleagues in the Food, Bioprocessing, and Nutrition Sciences Department for advice on many experiments. We want to ensure that we’re providing all of the materials in the correct manner so they can be successfully done in other undergraduate microbiology labs. We are also willing to help in any way we can.

Key Takeaways:

• Incorporating fermented foods into general microbiology courses is an exciting and fun way to learn basic concepts about microbiology and research.
• Providing students with the opportunity to conduct their own research project gives them a sense of ownership.
• Research projects centered around fermented foods work especially well for these types of courses because they are a completely microbiological process that is relatable since these foods are a part of our everyday lives.

What’s up next…

In the next and final part of the fermented foods series, I will share two interesting takes on fermented foods. One (Part 5a) is from a company that is using a different marketing strategy than most fermented foods companies, and another one (Part 5b) is from a lab that uses kombucha for an unexpected purpose. Stay tuned!