Fermentation revival in the classroom: investigating ancient human practices as CUREs for modern diseases

ABSTRACT

A course-based undergraduate research experience (CURE) was designed to integrate key microbiological principles and techniques into an authentic research experience in a classroom setting and was implemented in an undergraduate microbiology laboratory course. Students conducted a 6-week study in order to determine the identity and quantity of unique probiotic species from various types of kefir. This course module followed an inquiry-based pedagogical approach in which students use the scientific process to investigate an unknown question with no predetermined outcome. During each lab, relevant microbiological topics and laboratory concepts were presented. Students then performed various laboratory techniques, reinforcing the lecture material with hands-on experience. In addition, students participated in reflection through group presentation of their results, bioinformatic analysis and literature review. Based on data collected from pre- and post-study survey responses, both student knowledge and attitudes towards the topics covered improved due to participation in this CURE. Importantly, this CURE can be implemented at many levels of education, requiring only minimal resources and common laboratory equipment.

In an innovative course-based undergraduate research experience (CURE), students use the scientific process to investigate the microbial composition of kefir, an unknown question with no predetermined outcomes.

INTRODUCTION

Undergraduate microbiology courses cover a vast array of topics in a short period of time, generally in lecture or laboratory format. Often, concepts covered in the classroom do not translate to the laboratory experience, and vice versa. This creates a disconnect in the information and hands-on experiences that students receive. Incorporating course-based undergraduate research experiences (CUREs) into the curriculum helps alleviate this disconnect and creates a more encompassing, holistic learning experience for the students (Bangera and Brownell 2014; Linn et al. 2015; Ballen et al. 2017). For this reason, the course module ‘Fermentation Revival in the Classroom’ was developed as an innovative teaching approach for an undergraduate microbiology laboratory course in order to integrate core microbiological principles, laboratory concepts and hands-on techniques and to provide a resource for other microbiology instructors.

An important topic covered in all introductory microbiology courses is fermentation (Briggs et al. 2017). While laboratory experiments involving fermentation are common (Young and Kiefer 2014; Gober and Joullie 2015; Agustinah, Warjoto and Canti 2019; Pakpour and Hussain 2020), the approach described here integrates the concept of fermentation with multiple topics, such as the human microbiome and probiotics, as well as laboratory concepts and techniques, such as bacterial enumeration, Gram staining, polymerase chain reaction (PCR) and bioinformatics. In this study, the student demographic consisted largely of pre-health professional students. Educating these future healthcare professionals about these concepts and techniques is crucial to stimulating forward thinking in medicine. Through this unique, hands-on learning experience, these prospective healthcare professionals become immersed in the aforementioned translational topics, fostering tangible connections between nutrition, the human microbiome and patient health.

Although additional research is required, some studies suggest that introducing probiotics, including beneficial bacteria and yeast, into the gastrointestinal environment aids in maintaining the appropriate balance of beneficial microbes in the gut (Markowiak and Slizewska 2017). Kefir is a popular fermented milk beverage that naturally contains probiotics. It is available commercially, but kefir can also be easily prepared at home by the consumer. This provides an ideal opportunity for demonstration of the fermentation process, with ease of implementation in a classroom setting. The probiotic content of homemade kefir may differ from that of commercial kefir, potentially in quantity as well as diversity of species, and is generally unknown to the average consumer. In this study, the contents of the kefir being tested are unknown, even to the instructors. As there are no predetermined outcomes in this research experience, students learn the importance of the scientific process in investigating unknown questions—a key component of any CURE (Auchincloss et al. 2014; Spell et al. 2014). Variations in the probiotic content of kefir may ultimately affect the health benefits conveyed by consuming the product, whether produced commercially or by the user. Analysis of these variations provides a learning opportunity for the students in which the health benefits of specific types of probiotics, as well as the disease connection, can be discussed. Importantly, educating students on these topics illustrates to them how truly interconnected microorganisms are not only with disease states but also with everyday functions of the human body system.

In the ‘Fermentation Revival in the Classroom’ course module, students conducted a 6-week study in order to investigate the identity and quantity of unique probiotic species found in various sources of kefir, including homemade (prepared by the students) as well as commercial. Through collaboration with one another, students collected raw data, analyzed the results and presented their findings. One of the greatest benefits provided to the student by participating in a CURE, such as the one described here, is that it creates an authentic hands-on research experience for the student in a classroom setting (Shortlidge, Bangera and Brownell 2017). In this CURE, students utilize the scientific process by asking questions, building hypotheses and designing studies. In addition, students gain a better understanding of key microbiological concepts, such as the process of fermentation, the significance of the human microbiome and the connection between gut health and disease. This CURE challenges our pre-health students by encouraging them to think outside of the boundaries of ‘traditional’ or modern-day medicine.

The effectiveness of a CURE in achieving the desired learning outcomes should be determined using best practices in assessment (Shortlidge and Brownell 2016). To determine if our course module was an effective way to introduce key microbiological principles and techniques, establish important connections between information and real-world application and stimulate interest in microbiology and the scientific process, student responses to pre- and post-study surveys were collected and analyzed in order to assess student knowledge and attitudes. Survey results from all participating microbiology course sections were combined (n = 267).

MATERIALS AND METHODS

Curriculum design

‘Fermentation Revival in the Classroom’ was taught over the course of six 3-hour lab periods in an undergraduate microbiology course. Both students from a primarily undergraduate institution (Francis Marion University; n = 83) and a major research university (University of Florida; n = 184) participated in this study. While most students were pre-health majors, their academic status, educational experience and background varied extensively. During each lab period, the instructor gave a brief introductory lecture on relevant microbiological topics and laboratory concepts (Table 1). The students then performed various laboratory techniques, reinforcing information presented in the lecture with hands-on experience. In most undergraduate microbiology courses, many of these topics are also covered in a traditional classroom setting. Therefore, these concepts are not being introduced to the students for the first time through this CURE. Rather, the laboratory experience is an opportunity to emphasize and reinforce these concepts with tangible technical applications. Students participated in reflection through group presentations of their results, bioinformatic analysis, literature review, conclusions and significance.

Table 1.

Course-based Undergraduate Research Experience (CURE) overview.

Lab	Microbiological topics	Laboratory concepts	Hands-on experience and techniques
1	Introduction/Overview	Sterilization	Prepare homemade kefir
	Process of fermentation	Fermentation
	Types of fermentation	Starter cultures
	What is kefir?	Kefir grains
2	History of fermented products	Introduction to bacterial enumeration	Prepare serial dilutions
	Cultural connection	Dilution (and dilution factors)	Inoculate agar plates with dilutions
		Serial dilution	Spread sample with cell spreader
		Aseptic technique	Incubate agar plates at 37°C
		Culture medium
		Inoculation
		Incubation
3	Probiotics (definition)	Bacterial enumeration (continued)	Analyze microbial growth
	Probiotics (function)	Too numerous to count (TNTC)	Count colonies
	Natural sources	Too few to count (TFTC)	Calculate microbial densities (CFU/mL)
	Artificial sources	Colony-forming units (CFU)	Perform streaking for isolation
		Mixed vs. pure cultures	Incubate agar plates at 37°C
		Isolating a pure culture
4	Human microbiome	Differential stains	Perform a Gram stain
	Gut health	The Gram stain (theory)	Extract DNA from microbial cells
		DNA extraction (theory)	Quantify DNA concentration
		Spectrophotometry	Setup PCR reactions
		A260/A280 ratio	Run PCR program
		PCR (theory)
		16S rRNA gene (prokaryotes)
		18S rRNA gene (eukaryotes)
5	Gut-brain axis	PCR purification (purpose)	Purify PCR products using kit
	Mental health	Gel electrophoresis (theory)	Load gel with sample of PCR product
	Emotion and cognition	Gel imaging	Separate DNA by size using electrophoresis
		DNA sequencing (general)	Visualize DNA bands using gel imaging system
		Sanger sequencing (theory)	Sanger Sequencing by bioinformatics core
6	Health benefits of probiotics	Bioinformatics	Align sequences using NCBI BLAST
	Disease connection	Primary literature	Identify genus/species of isolates
	Commercial regulation of probiotics	Communicating science	Perform literature search using PubMed
			Analyze results and compile data
			Prepare and give presentation

Experimental design

The organization and order of techniques performed in this study are presented in Table 1. Detailed experimental materials and methods are provided in the supplemental material. Briefly, students prepared serial dilutions of kefir samples, inoculated MRS and PDA agar plates with those dilutions. After incubation, students determined the concentration of bacteria and yeast in the kefir samples by calculating CFU/mL. Pure cultures were isolated using the streak plate method, and unique colonies were characterized and Gram stained by the students. Students extracted DNA from these isolates, and a region of the 16S or 18S rRNA sequence in bacterial and yeast samples, respectively, was amplified via PCR. Upon purification and analysis by gel electrophoresis, the PCR-amplified nucleotide sequences were determined by Sanger sequencing. Finally, students aligned these unique sequences with a curated database using the NCBI Basic Local Alignment Search Tool (BLAST) to determine species identity.

Assessment of student learning and attitudes

Student knowledge, as well as changes in attitudes, were assessed based on their responses to pre- and post-study surveys. These assessments were created and published using Qualtrics software (complete surveys are provided in the supplemental material). This study was approved by the University of Florida's Institutional Review Board (IRB)—protocol #2014-U-429 and the Francis Marion University's IRB—protocol #Lyles-01-19-2015-001.

RESULTS AND DISCUSSION

Lab 1: an introduction to kefir and the fermentation process

During the first lab period, an overview of the course module was presented (Table 1). Students learned about the biochemical process of fermentation, as well as different types of fermentation and their utilization by distinct groups of microorganisms. Students were introduced to the fermented milk beverage known as kefir. The process of preparing kefir was presented, including discussions about sterilization procedures, starter cultures and kefir ‘grains᾿—a complex matrix of polysaccharides, bacteria and yeasts. In order to provide the students with a sense of ownership in the scientific process and hands-on experience with fermentation, the students prepared their own fermentation jars containing kefir grains and whole or skim milk. The resulting homemade kefir samples were used in downstream analysis.

Lab 2: the history of fermentation and plating serial dilutions

During the second lab period, students learned about the history of fermented products. Next to dehydration, fermentation is the oldest method of food preservation. Aside from practicality, fermentation became more prevalent over time as it also conveyed a vast array of new flavors and textures to common foods and beverages (Farnworth 2008). As added health benefits of fermented products continue to be discovered, these foods and beverages only grow more popular. The association of particular fermented products with various cultures was also discussed.

The laboratory concepts presented during Lab 2 focused on an introduction to the process of microbial enumeration. Students gained a foundational understanding of the importance of aseptic technique, dilutions and dilution factors, the use of culture medium for growing microorganisms, the use of selective culture medium for inhibiting or favoring growth, how to inoculate culture medium and setting the appropriate conditions for optimal growth during incubation. To reinforce these concepts with hands-on experience, students worked in pairs to prepare serial dilutions of a kefir sample and inoculate MRS and PDA agar plates with each dilution using the spread plate technique.

Lab 3: probiotics and microbial enumeration

During the third lab period, students learned about probiotics—living microorganisms that are beneficial to human health. Prophylactic consumption of probiotics has been shown to contribute to overall increased health and disease prevention by improving or restoring the gut microbiota (Pandey, Naik and Vakil 2015; Hill et al. 2018). Artificial sources of probiotics are becoming increasingly prevalent in many commercial products, such as dietary supplements. However, probiotics are naturally occurring and commonly found in fermented foods and beverages, such as yogurt, sauerkraut, kimchi, kombucha and kefir (Rezac et al. 2018).

Our discussion of the process of microbial enumeration continued in Lab 3. Students gained an understanding of how to count colonies, the concept of a colony-forming unit (CFU), how to calculate the concentration of microorganisms in terms of CFU/mL based on the number of colonies, sample volume and dilution factor; the difference between a mixed culture and a pure culture and the process of isolating a pure culture. To reinforce these concepts with hands-on experience, students worked in pairs to analyze the microbial growth on their agar plates from the previous week, count colonies and calculate microbial densities as CFU/mL. Data collected and analyzed by the students revealed that the concentration of bacteria (from MRS plates) and yeast (from PDA plates) varied in commercial kefir versus homemade kefir, as well as amongst various types and brands of kefir (Fig. 1). As expected, negative controls (pasteurized whole and skim milk) revealed no detectable viable bacteria or yeast. The necessity of controls in experimental design was emphasized here. In general, commercial kefir samples contained a greater quantity of microorganisms, with Lifeway strawberry kefir containing the highest concentration of bacteria and yeast. Students proposed that the increased concentration of sugar in the flavored kefir may supply additional carbohydrate sources for fermentation, supporting the robust growth of these microorganisms. This was an excellent point and a remarkable display of student learning in which the students applied knowledge acquired during lecture (regarding the fermentation process) to explain an observation made during a hands-on laboratory experiment. Lastly, students inoculated new agar plates using the streak plate method in order to isolate pure cultures for further analysis.

Figure 1.

Concentration of bacteria and yeast in kefir. The concentrations of bacteria (blue) and yeast (orange) in kefir samples and controls were determined by inoculating MRS and PDA agar plates, respectively, with serial dilutions of samples. Plates were incubated at 37°C for 48 h, and those with 30–300 colonies were counted. Data represent the average colony-forming units per mL (CFU/mL), with standard deviation. Sample size: Lifeway Kefir, Plain (n = 6); Lifeway Kefir, Blueberry (n = 5); Lifeway Kefir, Strawberry (n = 2); Evolve Kefir, Blueberry (n = 2); Homemade Kefir, Whole Milk (n = 3); Homemade Kefir, Skim Milk (n = 3); Kefir Grains, Whole Milk (n = 2); Kefir Grains, Skim Milk (n = 2); Whole Milk Control (n = 2) and Skim Milk Control (n = 2).

Lab 4: the human microbiome and molecular identification techniques

During the fourth lab period, students learned about the significance of the human microbiome and gut health. The human microbiome is comprised of the microorganisms that exist in and on the human body. Specifically, the gut microbiota functions to support the immune system and assist in the digestion of food (Brestoff and Artis 2013). Maintaining the necessary balance of beneficial microorganisms in the body, especially in the gastrointestinal tract, has been shown to improve overall health and protect the body from harmful pathogens (Surendran Nair, Amalaradjou and Venkitanarayanan 2017).

The laboratory concepts presented during Lab 4 focused on molecular identification techniques. Students gained an understanding of differential staining techniques, how to perform a Gram stain, the cell wall components of Gram-negative and Gram-positive bacteria, how DNA is extracted from microbial cells, how to determine DNA concentration using spectrophotometry, the meaning of the A₂₆₀/A₂₈₀ ratio, the theory behind PCR, the difference between conserved and variable nucleotide sequences and why analysis of the 16S and 18S rRNA gene is useful for identification of bacterial and yeast species, respectively. To reinforce these concepts with hands-on experience, students worked in pairs to analyze the microbial growth on their streak plates from the previous week. Unique, isolated colonies representative of pure cultures were selected for further analysis. Colony morphology was recorded, and a Gram stain was performed by the students to determine cell morphology and Gram stain reaction. The students extracted DNA from the microbial cells and determined DNA concentrations using a microplate spectrophotometer. Following a guided protocol, students set up and ran individual PCR reactions containing a primer set targeting either the 16S or 18S rRNA sequence in bacteria or yeast, respectively.

This lab was especially valuable to the learning experience of the students as they learned not only how to perform key microbiological and molecular techniques but also the theory behind those techniques. Too often students are taught how to perform a technique, and while they go through the motions of the procedure, they never gain a full understanding of the ‘how’ and ‘why’ of what they are doing. How does the technique work, at a cellular, molecular, or chemical level? How does this help to accomplish a particular goal? Why does the procedure generate a certain type of result over another? Understanding the theory behind the procedure, performing the technique hands-on and then observing the results creates a meaningful, full-circle learning experience for the students.

Lab 5: the gut–brain axis and DNA analysis

During the fifth lab period, students learned about the gut–brain axis and how it is influenced by different species of microorganisms. The gut–brain axis is a bidirectional communication system between the nervous system and the gut microbiota that affects mental health, emotion, cognition, pain, obesity and many other disease states (Liu, Cao and Zhang 2015). Importantly, recent studies show that the activity of the gut–brain axis can be modulated by the introduction of probiotics (Kim et al. 2018). Recalling information from previous lectures, students are able to use their knowledge of probiotics, the human microbiome and gut health as a framework for understanding the complexity of the gut–brain axis.

The laboratory concepts presented during Lab 5 focused on methods for DNA analysis. Students gained an understanding of how to purify PCR products and why this is a necessary step for downstream analysis, the theory behind gel electrophoresis, the development of DNA sequencing and how it has changed science, and the theory behind Sanger Sequencing. To reinforce these concepts with hands-on experience, students worked in pairs to purify their PCR products from the previous week. They loaded a gel, observed gel electrophoresis and imaged the gel in order to visualize their PCR products. Students learned how to determine the size of a DNA fragment by comparing it to a DNA ladder. This provided a convenient opportunity to discuss the importance of standards in scientific experimentation. After confirming the appropriate size of their PCR products, students prepared and submitted DNA samples for Sanger sequencing to a bioinformatics core facility.

Lab 6: disease connection, bioinformatics and communicating science

During the sixth and final lab period, students learned about the connection between disease states and gut health, peer-reviewed research on perceived health benefits associated with probiotics, and commercial regulation of probiotic products. Although some questions regarding causation versus correlation remain, dysfunction of the gut microbiota has been associated with a wide range of conditions, including inflammatory bowel disease, antibiotic-resistant infections, autism, depression, Parkinson's disease, Alzheimer's disease and more (Morgan and Huttenhower 2012; Kim et al. 2018). Recent studies suggest that maintaining the appropriate balance of beneficial microorganisms in the gastrointestinal tract may play a role in prevention and treatment of certain diseases (Surendran Nair, Amalaradjou and Venkitanarayanan 2017). For example, in human clinical trials, probiotic supplementation reduced the risk of developing Clostridium difficile-associated diarrhea in both adults and children (Lau and Chamberlain 2016). In addition, the introduction of select probiotics resulted in improved insulin sensitivity in clinical trials with patients with type II diabetes (Saez-Lara et al. 2016). However, further studies are required to elucidate the underlying mechanisms of how probiotics affect such disease states. It is important for our pre-health professional students to understand both the value and the limitations of such investigative clinical studies and health management strategies.

The laboratory concepts presented during Lab 6 focused on identification of the unknown microbial species. Students gained a general understanding of the field of bioinformatics, how large databases are maintained and available bioinformatics tools. Students then used these tools to analyze the 16S or 18S rRNA sequences of their microbial isolates from kefir. Specifically, students aligned these unique sequences with a curated database of sequences using BLAST. Search results were used to determine the identity of the unknown species based on sequence similarities. Based on this information, students found that while the overall species diversity (the number of unique microbial species present) was comparable in commercial and homemade kefir, species isolated from commercial kefir were predominantly bacterial (95%) and species isolated from homemade kefir were predominantly yeast (77%; Table 2). Students hypothesized that the diversity of yeast species in commercial preparations may be reduced in order to decrease carbon dioxide gas produced as a byproduct of alcohol fermentation. This would in turn minimize the buildup of pressure inside the bottle and increase the shelf life of the product. This was another exceptional display of student learning in which the students applied knowledge acquired during lecture (regarding biochemical processes of different types of fermentation) to explain an unexpected observation made during a hands-on laboratory experiment.

Table 2.

Microbial identification of isolated species from kefir.

Source	Species	Type	Isolates
Commercial	Lactobacillus casei 1 , 2	B	10
	Lactobacillus fermentum 4	B	2
	Lactobacillus paracasei 1 , 2 , 3	B	11
	Lactobacillus rhamnosus 1 , 3 , 4	B	8
	Staphylococcus caprae 3	B	1
	Staphylococcus epidermidis 1 , 4	B	2
	Staphylococcus warneri 1	B	1
	Pichia cecembensis 3	Y	2
Homemade	Enterococcus faecium 5	B	7
	Enterobacter ludwigii 5	B	1
	Klebsiella michiganensis 5	B	1
	Lactobacillus kefiri 5	B	2
	Streptococcus thermophilus 5	B	1
	Kluyveromyces marxianus 5	Y	4
	Pichia cecembensis 5 , 6	Y	35
	Saccharomyces cerevisiae 5	Y	1
	Saccharomyces unisporus 5	Y	1

¹Lifeway kefir, plain

²Lifeway kefir, blueberry

³Lifeway kefir, strawberry

⁴Evolve kefir, blueberry

⁵Homemade kefir, whole milk

⁶Homemade kefir, skim milk

B = Bacteria

Y = Yeast

Although high concentrations of bacteria and yeast were detected in kefir (Fig. 1), the associated health benefits imparted by consuming fermented products like kefir are due to the activities of probiotic species, specifically (Pandey, Naik and Vakil 2015). Therefore, it was necessary to investigate the activities and potential health benefits associated with the species isolated from our kefir samples. Students were taught how to properly search for and retrieve peer-reviewed articles from primary literature databases (such as PubMed). They then performed their own literature searches and compiled the results. Students found that the most common species isolated from commercial kefir, Lactobacillus paracasei, is known to inhibit the growth of cariogenic microbes, such as Streptococcus mutans, and reduce visceral hyperalgesia (Verdu et al. 2006; Chuang et al. 2011). Also prevalent in commercial kefir, Lactobacillus casei has been implemented in the treatment of colitis (Lee et al. 2015) and helps reduce the risk of developing allergies, such as asthma and atopic dermatitis (Kalliomaki et al. 2001; Johansson et al. 2011). Prevalent in homemade kefir preparations, students found that Enterococcus faecium is known to inhibit the growth of pathogens, such as Listeria monocytogenes and Staphylococcus aureus (Barbosa et al. 2014). Interestingly, the most common species detected in homemade kefir, Pichia cecembensis, was originally isolated from a decaying papaya fruit (Bhadra et al. 2007). It was first detected as a component of kefir grains in 2011 (da C. P. Miguel et al. 2011), although potential health benefits conveyed by this species as a probiotic microorganism have not yet been explored. This provides an interesting avenue for future student projects.

Several students also pointed out that the microbial species isolated from the commercial kefirs in this study varied considerably from the species advertised by the brands (Table S1, Supporting Information). This presented an opportunity to discuss the commercial regulation of probiotics. Despite probiotic products gaining a significant commercial presence in recent years, there remains little to no regulation by organizations such as the Food and Drug Administration (FDA; de Simone 2019). Consequently, the contents of various types and brands of probiotic products may vary significantly, as was observed in this study (Table 2). The discussion of this topic with pre-health students has broad, relevant implications and provided an opportunity to pose important questions about related topics, such as the regulation of drug manufacturing and bioequivalent drugs (generic versus brand-name). Limitations of this study, as well as physical and chemical requirements for growth of microorganisms, were also discussed. While the cultivation of certain species, such as anaerobic or fastidious bacteria, may be inhibited by common laboratory growth conditions, this finding still raises important questions regarding impacts to consumers and provides additional investigative opportunities for future student projects.

Finally, the importance of communicating science was emphasized. Relevant topics, such as knowing your audience, preparing a poster or oral presentation and public speaking skills were discussed. Students then worked in groups to prepare and give a short presentation on their findings. Through this didactic method, students are learning by teaching their peers—a common practice in educational theory in which the teacher's own learning is improved because they are required to retrieve information that they have previously studied (Koh, Lee and Lim 2018). The value of this reflective pedagogical approach is that it brings the student learning experience full-circle and helps them to achieve a deeper understanding of the nature of science (Bautista and Schussler 2010).

Assessment

Student responses to pre- and post-study surveys were collected and analyzed in order to assess student knowledge, perceptions and attitudes. Improving student knowledge of the topics presented was an important educational outcome of this CURE. In order to evaluate the accomplishment of this aim, questions regarding knowledge of these topics were asked, and student responses were analyzed (Fig. 2). It should be noted that a decrease in student participation was observed in the post-study survey as compared to the pre-study survey. This was likely due to a lack of incentive, as the post-study survey was administered at the end of the semester after final grades were submitted. Administering the post-study survey earlier and/or incentivizing participation would likely mitigate this issue in future iterations of this CURE. In the pre-study survey, the majority of students (63%) indicated that they were not familiar with the topics of fermentation, probiotics and the human microbiome (Fig. 2A). After participation in this study, the majority of students reported that they had personally read about, taken a class that taught, or conducted research on the topics of fermentation (40% increase), probiotics (84% increase) and the human microbiome (70% increase; Fig. 2A). In addition, student perception of their learning experience in this study was markedly positive, as the vast majority of students (98%) self-reported that their knowledge of probiotics and fermented foods had improved due to their participation in this CURE (Fig. 2B). Although an increase in student knowledge of the gut–brain axis was observed, only 45% of students self-reported that they were aware of the gut–brain axis post-study (Fig. 2C). In future iterations of this CURE, it will be important to spend more time emphasizing the importance of the gut–brain axis in order to bridge this learning gap. Taken together, these data support the improvement of student knowledge regarding these topics due to participation in this CURE.

Figure 2.

Assessment of student knowledge. Several questions were asked as part of both a pre- and post-study survey in order to assess differences in student knowledge regarding specific topics as a result of participation in this course-based undergraduate research experience. Orange (pre-study) and blue (post-study) bars represent the percentage of total students that selected each corresponding answer. (A) Students answered three questions: ‘How would you describe your familiarity with the human microbiome? (Select all that apply)’, ‘How would you describe your familiarity with probiotics? (Select all that apply)’ and ‘How would you describe your familiarity of fermentation as it pertains to fermented foods and fermented beverages? (Select all that apply)’ with a response of ‘I am not familiar with this topic’, ‘I have personally read about this topic’, ‘I have taken a class that taught this topic’, ‘I have conducted research on this topic’ or ‘Other’ including an option to offer a written explanation. Total responses received: pre-study (n = 213), post-study (n = 43). (B) As part of the post-study survey, questions were asked to assess the students’ perceptions of changes in their own knowledge as a result of participation in this course-based undergraduate research experience. Students reacted to the following statement: ‘My knowledge on the topics of probiotics and fermented foods has improved due to my participation in this project’ with a response of ‘Strongly disagree’, ‘Disagree’, ‘Somewhat disagree’, ‘Neither agree nor disagree’, ‘Somewhat agree’, ‘Agree’ or ‘Strongly agree’ (n = 43). (C) As part of both the pre- and post-study surveys, students answered the question: ‘Are you aware of the gut–brain axis?’ with a response of ‘No’, ‘I have heard of it’ or ‘Yes’. Total responses received: pre-study (n = 213) and post-study (n = 43).

Stimulating student interest in the topics presented was also an important aim of this CURE. Students were asked if they think consuming fermented foods could be important for their own health. Prior to participation in this study, just over half of the students responded ‘yes’. Post-study, a 60% increase in students responding ‘yes’ was observed (Fig. 3A). In addition, 95% of students agreed that they want to learn more about probiotics and their health benefits (Fig. 3B), and 71% agreed that they are interested in making their own fermented products at home (Fig. 3C). These data provide support for the positive impact of this CURE in stimulating student interest in the topics presented, as well as fostering positive student attitudes towards new and unfamiliar concepts. By participating in this CURE, students gained knowledge and skills that can be applied in both their professional and personal lives.

Figure 3.

Assessment of student attitudes. Several questions were asked as part of both a pre- and post-study survey in order to assess changes in student attitudes towards the topics covered in this course-based undergraduate research experience. (A) Students answered the question: ‘Do you think consuming fermented foods could be important for your own health?’ with a response of ‘No’, ‘Maybe’ or ‘Yes’. Total responses received: pre-study (n = 213) and post-study (n = 43). (B) Students reacted to the following statement: ‘I want to learn more about probiotics and their health benefits’ with a response of ‘Strongly disagree’, ‘Disagree’, ‘Somewhat disagree’, ‘Neither agree nor disagree’, ‘Somewhat agree’, ‘Agree’ or ‘Strongly agree’ (n = 43). Responses of ‘Strongly disagree’, ‘Disagree’ and ‘Somewhat disagree’ were combined and presented as a single data point titled ‘Disagree’. Responses of ‘Somewhat agree’, ‘Agree’ and ‘Strongly agree’ were combined and presented as a single data point titled ‘Agree’. (C) Students reacted to the following statement: ‘I am interested in making my own homemade kefir, yogurt or other fermented foods’ with a response of ‘Strongly disagree’, ‘Disagree’, ‘Somewhat disagree’, ‘Neither agree nor disagree’, ‘Somewhat agree’, ‘Agree’ or ‘Strongly agree’ (n = 43). Responses of ‘Strongly disagree’, ‘Disagree’ and ‘Somewhat disagree’ were combined and presented as a single data point titled ‘Disagree’. Responses of ‘Somewhat agree’, ‘Agree’ and ‘Strongly agree’ were combined and presented as a single data point titled ‘Agree’.

CONCLUSIONS

A course-based undergraduate research experience (CURE) designed to integrate key microbiological principles and techniques was successfully implemented in an undergraduate microbiology laboratory course. ‘Fermentation Revival in the Classroom’ followed an inquiry-based pedagogical approach in which students use the scientific process to investigate an unknown question with no predetermined outcome. This learning experience focused on broadly relevant topics such as fermentation, the human microbiome, probiotics, the gut–brain axis and health benefits of consuming fermented products. Both student knowledge and attitudes towards the topics covered improved due to participation in this CURE. However, student learning gains could be strengthened in future iterations of this research experience by spending additional time on complex and unfamiliar topics, such as the gut–brain axis. Additionally, incentivizing completion of the post-study survey may increase participation and strengthen the interpretation of data regarding the student learning experience. Overall, this CURE stimulated interest in microbiology and conveyed knowledge and skills that will benefit the students both personally and professionally. Importantly, the ease of implementation and adaptability of this CURE make it an accessible resource for all instructors and students at many different levels of education.

FUNDING

This work was supported by the Academic Programs Section (APS) of the Association of Public Land-Grant Universities (APLU) [Innovative Teaching Award]; the National Institute of General Medical Sciences (NIGMS) [South Carolina IDeA Networks of Biomedical Research Excellence (INBRE)] and Francis Marion University [Ready to Experience Applied Learning (REAL) Program].

Conflicts of Interest

None declared.