Contributed by Carson Ingold

It’s Carson, with more updates from the poop squad and a few late-night philosophical thoughts sprinkled in. As the great Sam Cooke said, “a change is gonna come”, and change indeed has come. Since my last post, I developed and executed experiments based on the founding data of the poop squad. That founding experiment, and the squad’s namesake, investigated the effects of fecal microbiota transplants (FMT) on the gut microbiota composition of a mouse model of inflammatory bowel disorder. The data produced, however, had much more potential for investigation than simply the FMT experiment. We noticed that the inflammatory indexes of the dysbiotic mice showed outcomes comparable to the control mice, in association with high detections of members of the Lachnospiraceae family. This highlighted the potential importance of this family and piqued our research interest. Upon analysis of metagenome-assembled genomes resolving to Lachnospiraceae, we identified genes relating to glutathione metabolism. Glutathione, as an antioxidant, holds a critical role in the inflamed gut. However, the literature did not reflect this function with any specificity. A research question was then formed. We then sought to characterize the potential of Lachnospiraceae and bacterially-derived glutathione metabolism to relieve oxidative stress in the gut. What followed was a barrage of experiments, continually tried and retried to form a body of evidence in support of the anti-inflammatory potential of Lachnospiraceae. Many of these experiments were a version of the Caco-2 co-culture experiments mentioned in my previous blog post. Other experiments involved simple bacterial culture and growth curves. What resulted was a paper that, while it does not prove the anti-inflammatory potential of Lachnospiraceae, it certainly provides another piece in the puzzle of host-microbe interaction in the gut. For more info on Lachnospiraceae and bacterially-derived glutathione, check out the pre-print version of the paper here: Eubacterium rectale detoxification mechanism increases resilience of the gut environment | bioRxiv.

Now, my experiments in Lachnospiraceae have occupied amount of my time and energy in the past year and a half. However, even more personally influential are the thoughts I had surrounding this excursion into scientific investigation. I am confident that I could have had no better opportunity for life learning than the opportunity presented to me as a Lee Lab undergraduate. The Lachnospiraceae project didn’t just teach me protocols about analyzing metagenomic data and bacterial metabolism, though I certainly gleaned some of that information. In daily life as an undergraduate researcher, there was much time spent waiting for the centrifuge to stop spinning or waiting for the anaerobic chamber to finish its cycle. It was in those moments that I learned the most. It’s in the days that I asked “what the hell am I doing here”, that learning happened.

It was at such a time when I learned to view science as an artistic pursuit. Where I once regarded science as an objective field of people with specialized knowledge seeking to apply that knowledge to specific questions, I learned it to be completely reliant on the intuitions and curiosity of the human brain (which is often more intuitive first and logical second) to seek answers to questions exploding with beauty and insight. Then, to share that beauty and insight with others. As strange as it may be, I learned more about art and beauty in the lab than I ever did looking at a painting or listening to a piece of music. Any application of attention to a curious thing, really, could be viewed as artistic. I suppose this way of thinking about scientific investigation was partly informed by the work of the philosopher, Simone Veil, in her work Reflections on the Right Use of School Studies. Attention allows the space for a scientist to let curiosity guide the direction of a project, and desire to drive it forward. This cross-application of knowledge, from one discipline to another, is how understanding and innovation are formed. In the Lachnospriaceae project, much of the inspiration was biochemically motivated, rather than a true expression of pure microbiology. It was born out of true curiosity. This view of science, along with a healthy understanding of attention, now critically informs my intellectual process. Really, from my time in the lab, I had more self-discovery than scientific discovery. I found that my passion, and what I suspect is also true for other scientists, is in finding questions of a truly curious nature and applying true attention to those questions, regardless of the discipline the question could be categorized under. This is an artistic process in that it isn’t a way to create a perfect world, but a way to deal with the fundamentally ambiguous state we live in, and to feed our curious nature.

The Carson that entered college as an 18 year old couldn’t have imagined a better foundation on which to build a meaningful life. My plan is to continue to follow the path that curiosity and the desire for exploration and understanding have laid out for me. I hope you all find something of a curious nature to seek for yourself.

Contributed by Dasik Clouse

Hello all! 

My name is Dasik Clouse. I am a fourth-year undergraduate student here at Kansas State University. I am entering my final semester and will graduate this fall from K-State. I am from a very small town in Kansas called Medicine Lodge. While attending Kansas State, I switched majors only once. Originally, when I first arrived at K-State I had enrolled in the College of business with a major in accounting. Shortly after my second semester, I decided I was very uninterested in accounting and switched majors to general microbiology. This switch was rather unusual to most, as these majors have relatively nothing in common, but I realized that my interest in science had always been much higher than crunching numbers and learning tax law. I have now been with the Lee Lab for almost a year and I will be returning for my third and final semester. 

During my time with the Lee lab, I have received some of the most helpful experiences. Before the lab I had very little idea of what working in a lab was like. I have come to very much enjoy the lab space here at KSU. When I first joined the Lee Lab, I worked under Anna’s watchful eye. Anna cares about the quality of research as much as anyone, and she took the necessary time to teach me different protocols and techniques in the lab. I first learned how to complete DNA extractions, followed by conducting DNA quantification. These protocols are where most of my time in the lab has been spent over the last two semesters. During the spring 2024 semester a new graduate student, Brooke, and I began working together experimenting with DNA extractions. We worked together to improve the DNA extraction protocol for rhizosphere DNA samples to ensure that our quantification results would be the best they could be. 

This lab has taught me so much. Apart from learning techniques and protocols, I have learned how to work as a team in a research setting. There is so much necessary communication needed to operate a research project. All projects can run into roadblocks and problems that no one expects. One of my favorite things to do is being able to problem solve with others and think deeply about how issues can be fixed. Science is a never-ending learning experience, and the Lee lab has been a place where learning never stops. 
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After graduating from Kansas State University, I plan to begin applying for federal and private sector high containment lab research positions. I am very thankful for this lab and the amazing individuals I have gotten to work with. The knowledge and experiences I have gained from this opportunity have set a great foundation for all future opportunities.  

Contributed by Bryttan Adams​

Hello, my name is Bryttan Adams, and I am about to enter my third year at K-State. I joined K-State as a medical laboratory science major, but after a few months working in the Lee lab, I transferred to medical microbiology. I began working in the lab during my second semester of freshman year. A few weeks into the semester, my TA for General Microbiology, Anna, was helping me with a technique when she mentioned the lab. She told me a little about the work she did and proposed that I come work with her. 

Working under Anna has been an amazing experience. She personally took the time to teach me several different techniques and protocols. Working in the lab, I started out by learning DNA quantification, then moved on to DNA extractions, which I became very familiar with. We extracted and measured the DNA from bacteria living in plant rhizospheres across a multitude of samples. During this time, another graduate student was growing hundreds of single-cell isolates, which I helped harvest, extract, and quantify. Additionally, I began learning new techniques, including cell culture of Caco-2 cells, which is one of my favorite things to do in the lab. The following semester, with the support of the lab, I applied for the Johnson Cancer Research Award and was lucky enough to have been selected. 

This opportunity allowed me to work on my own research project, studying Akkermansia muciniphila. Throughout this experience, I learned numerous techniques and skills in both the wet lab and outside of it. This project provided valuable insight into what goes into planning and preparing for experiments, as well as demonstrating the importance of science communication. One of the first experiments I did was a growth curve observation of my bacteria. This opportunity meant I was fortunate enough to come in and measure my cells every four hours for 24 hours. I also began working with a variety of different in vitro tests, including Griess, LDH assays, and wound healing, which were very interesting. Each of these tests was accompanied by its own set of issues and questions, but thanks to the help of graduate students, Sonny, and trial and error, I learned the importance of persistence and problem solving. Following the encouragement and guidance of the Lee Lab, I created posters recounting my project, which I presented at both the Division of Biology’s Undergraduate Research Forum and the campus-wide Undergraduate Research Symposium. Both of these experiences were very exciting. 
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After graduating, I plan to attend graduate school and earn my PhD. The experiences I have gained through both this project and my work in the lab as a whole are invaluable. Every technique I have learned here at the lab will help me be successful in my future research. In this lab, I have learned so much thanks to the continued support from all members.

Contributed by Reece Keller
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​Hello all!
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My name is Reece Keller. I am a third-year undergraduate student here at Kansas State University. I grew up in a small town called Cheney, KS, which resides about 20 minutes west of Wichita. I am currently double majoring in Nutrition and Health and Human Health Biology. While completing my undergraduate courses, I will also concurrently complete a few classes needed to earn a master’s in public health with an emphasis in public health nutrition. After being accepted into K-State’s accelerated BS/MPH program, I was fortunate to be chosen as a recipient for the Kansas Public Health Scholars Scholarship, providing me a “full-ride” to complete my MPH here at Kansas State. After completing my BS/MPH program, I hope to achieve my childhood dream which is to attend medical school to become a physician.
If you would’ve told me that I would end up going to Kansas State, I probably would’ve told you that you were crazy. If you would have told me that I end up being Head Undergrad of Dr. Lee’s bioinformatics research lab at K-State, I probably would’ve laughed in your face. I would be lying if I said that I ever had any intent of working in a research lab. Nonetheless, I have a been a researcher in Dr. Lee’s lab for approximately 14 months and have been head undergrad for about 4 months thus far, and it has been one of the best decisions I’ve ever made.

I first joined the Lee Lab in February 2023, while enrolled in BIOL455, General Microbiology. My recruitment to the Lee Lab happened ever so by chance. Dr. lee’s first year Ph.D. student, Jessica, and I both just happened to “lucky” enough get scheduled for a 7:30am lab time. Jessica and I quickly found out we were complete opposites, which meant we work very well together in the lab! I quickly found a deep respect for her and admiration for her knowledge and expertise.

Jessica and I first started out working together with lots of growth curves. We were still working out the beginning of what she was working on. I was very fortunate to be able to jump right in the wet lab by performing these experiments. The information kept flowing and the knowledge kept coming. Throughout my whole time with the lab, we have done numerous growth curves, media production and plate pouring, cell streak isolation and storage. On top of working on Jessica’s project with her, I have had the privileges of learning other lab techniques such as cell culturing of caco-2 cells, and even DNA extractions of plant rhizospheres. I am grateful to be able to jump in and learn new lab techniques and methods whenever I can.

One of my favorite things in the lab beyond wet lab work has been the leadership skills I’ve been taught. The lab surprised me in November 2023 that I would be taking over as Head Undergrad after the current one had graduated. I had never had such an important leadership role in my life. To say I felt underprepared and undeserving would be an understatement. One of the best things about my job as head undergrad is having the ability to connect and work with everyone in the lab and maintain and build those relationships. Much of my role serves as a point of contact between all the undergraduate students and the grad students and Dr. Lee. I can coordinate between all of them to keep the lab running as a smooth, well-oiled machine. One of the most rewarding parts of my job is that I get to lead by example. If I expect my coworkers in the lab to perform a task up to expectations, or maintain cleaning up to expectations, then I should be able to do it too. I pride myself in providing a good example of what is expected of everyone’s contributions to the lab. This goes beyond maintaining a lab cleaning schedule, attending meetings, or even engaging with everyone to build a good work environment. I hope to show that everyone has a purpose within the lab, and everyone has room to grow in their own way. Everything set aside, we are here to grow, learn, develop, and improve ourselves to prepare us for our futures.

I am beyond grateful to work with such a great group of brilliant minds. Maintenance of these duties while taking on all my other duties of a pre-med student such as volunteering, teaching, gaining clinical experience, shadowing, and my education, are of utmost importance to me!

Contributed by Carson Ingold

​Hello all, my name is Carson and I am currently a second-year medical microbiology student. I joined the Lee Lab last spring and have been working in the lab ever since! I found my way into the Lee Lab via BIOL 455 – General Microbiology, specifically, the required lab component of the course. I had previously become interested in research through some work in a psychology laboratory but found myself looking for a way to mesh the goal-oriented mindset and laboratory setting I fell in love with at the psychology lab, with the interactions of the bacteria I had become fascinated with.

Early in the course, my lab TA, Tanner Richie, gave a short biography, as usual. She mentioned how her research was focused around how changes in the population densities of the human gut microbiome affect health, a topic I remembered being mentioned at Bio Bonanza, and I was most definitely intrigued. After class that day, I asked Tanner for more details on her project. At the time, she was forceps deep collecting mouse fecal samples, for a project investigating the effect of fecal microbiota transplants on two groups of cefoperozone-induced mouse models of inflammatory bowel disorders, one of which was interleukin-10 gene-deficient. I was not too keen on the idea of working with mice again. But the in vivo studies showed that the change in microbial membership in the gene-deficient group was associated with alterations in the nitrogen metabolism of the microbiome. From this finding, Tanner began moving toward modeling the human gut in vitro for a series of nitrate assays and would be culturing HeLa and Caco-2 cell lines for those models. Tanner told me I would be likely be working on the in vitro study. This caught my attention, as I had never worked with cell or bacterial culture.

By the end of my freshman year, I had transitioned from the psychology lab to The Lee Lab, working with Tanner, and cell culture was in full swing. We began the summer culturing both HeLa and Caco-2 cells. The HeLa cells grew as expected and we ran proof-of-concept nitrate assays on a co-culture of HeLa cells and Escherichia Coli. After we proved the co-culture assay would work, the next step is to complete similar assays on the Caco-2 cells, as a truer model of the human gut. Our Caco-2 cultures over the summer had issues with contamination, but after obtaining a new starting culture, we are now closer than ever to being ready for Caco-2 co-cultures.
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Needless to say, I found what I was looking for in a lab!

contributed by Kourtney Rumback
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During the summer before my sophomore year, I was taking a microbiology course and learned how the gut microbiome can impact mental health. Using this knowledge, I proposed to add a microbiome analysis to the rats in my psychology lab, the RTD lab, that was examining how high-fat diets impacted impulsive choice. To propose a project like this required much work and convincing of the graduate students and my PI. I found a research article by Dr. Alexandria Vaughn examining a similar concept, but I was confused about the analytical aspects that goes into microbiome sequencing. From here, I reached out to one of my old professors that I knew quite well, Dr. Ari Jumpponen, who guided me through the process of 16S sequencing and gave me some direction on how to proceed with the project further. At this point I was becoming discouraged due to the cost it would take my psychology lab to be able to extract the DNA independently and to send off the DNA for sequencing. This is when I learned about Dr. Sonny Lee and I reached out to him for collaboration.
After talking to Sonny, I was able to get this project approved by my psychology lab and was able to apply for an Arts & Sciences Undergraduate Research Award, and later, an OURCI award. Due to Covid, I had to postpone this project until my junior year, but this allowed me to work closer with Sonny and was offered a position in his lab. Once the project was up and rolling, I extracted the DNA from 48 rat samples I collected pre-Covid. This was a great opportunity for me to practice my lab techniques and gain more skills with new equipment. The DNA was then prepared and sent to the K-State Genomics lab.
Before I continue more, I want to share about the core project that this analysis stemmed from. In the RTD lab, we wanted to examine how high-fat vs low-fat diets effected impulsive choice. We had 48 rats split into four groups of 12. Group one received a normal chow only, group two received normal chow with Crisco, group 3 received a low-lard commercially produced chow, and group four received a high-lard commercially produced chow. Groups three and four were enriched with vitamins and minerals. We were also curious as to whether fat type can impact impulsivity, hence the Crisco and lard diets. The overall results of this core study were that the rats consuming low fat diets (groups one and three) made more self-controlled choices overall and the high-fat diets (groups two and four) were more impulsive. We also did not see a difference between the two fat types.
The fun part now, after two years of preparation, is finally here: Data! The data analysis portion of this project was by far the most overwhelming and intimidating. It required programs that I was not used to and data sets that were not compatible with Excel. Sonny and Brandi were both great about helping me through this process and making sure I knew exactly what each graph entailed. I received two graphs that were used for this analysis. The PCA clustering plot which places points on a graph to represent each subject’s microbiome composition relative to one another. Within this plot, I was able to see that there was a separation between the two fat types (Crisco vs lard). There was also some evidence of the groups that received high-fat diets being closer together which suggests that their microbiome compositions were more similar. The second graph represented the relative abundance of individual phyla in each sample. Overall, we did not see a significant difference between any of the phyla between groups. This could be due to the high variability of abundance of phyla. Another point to mention is although the relative abundance of phyla was not significant, this does not mean that the phyla have the same identity in each group. Due to this, I would like to further cultivate the remaining samples to see if there is a similarity when examining the specific phyla of interest.
           
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Written by Kourtney Rumback
During my three years of undergrad, I have learned much about taking exams, studying, and how to manage stress. Although these are all important for college success, I was missing a foundational mindset that I finally learned a week before taking my MCAT.
 
For those who do not know me as well, I am Kourtney, a senior majoring in Biology & Psychology. I have been accepted to KU School of Medicine in the Scholars in Rural Health Program. With this program, I am required to meet a certain score on the MCAT and complete other requirements to ensure my position in the school. I took my MCAT on Friday, July 30th for the first time, and will receive my score in a month.
 
I began studying full time for the MCAT in May and ran into multiple obstacles along the way. After months of studying and content review, my score was actually going down and I was far from my needed score for medical school. I experienced self doubt and postponed my test date to later in the summer as I was originally supposed to take it in June. I actually postponed my test twice during this time.
 
To overcome this imposter syndrome I was experiencing, I began to reduce my studying time from 12 hours a day to about 8. I also cut back on my work responsibilities so I had more time to focus on myself and my mental health. At this time, my score started to quickly improve and provided me with hope! Although my score was improving, I still had not crossed the threshold needed to meet the minimum score requirement. This was very difficult for me as I have always received good grades and graduated top of my class in high school. Struggling with academics was not a familiar concept to me.
 
One week before my exam, I was still stuck on this score plateau and had considered pushing my date back again. I was frustrated with my lack of improvement and questioned where I would be using some of this information and it’s relevance to medical school. This mindset quickly changed when one of my psychology professors walked past my office in Bluemont and asked how I was doing. When I expressed my disdain for organic chemistry and the importance of amino acid structures, she changed my outlook of my education. She stated “although you may not directly need this information to be a doctor, being able to know how chemicals react and their structure may make it easier to prescribe medications and know drug interactions, which will overall make you a better doctor.”
 
Having no comment on this, I realized that she was right and that my mindset during my first three years of undergrad was completely wrong. I attended lectures and learned information just for exams and only retained information that I deemed important. This thinking has hindered my ability to succeed on the MCAT and I realized that if I worked harder in my past classes, and cared more about the connection to medicine, the MCAT would have been much easier for me and I wouldn’t have had to work as hard as I did.
 
With this newfound mentality, I came to another conclusion that was critical to my future. I realized that it is okay to fail sometimes. If I do not get the score I need, it is okay, and I can take the test again. If I have to take the test again, it will provide me with another opportunity to learn more about the information I pushed aside the past few years and will ultimately make me a more well-rounded student. This change in attitude made my actual test day much less stressful. It was less of a task to overcome and more of a challenge for me to face.
 
For all of the undergraduate students wondering why some classes are necessary and why we are taught this “unrelated” information, I dare you to find a connection to your desired career. I dare you to look beyond the textbook and find a way to make the information useful for you. If you are able to do this, your college experience will be much more meaningful and worthwhile.

Written by Brandi Feehan
Hey all you posh pigs and piglets! Even with social distancing, stay at home orders and travel restrictions, The Lee Lab has been keeping busy, and I’m excited to introduce myself and share an update on my work. I joined The Lee Lab in January after rotating in the fall 2019 semester to find a good fit for my genetics PhD. I’m no stranger to KSU: I’ll be a triple crown K-State wildcat after my PhD! My passion for pigs and animal health research started in my undergraduate when I interned with Merck Animal Health. During my time at the research facility, I loved working with the pigs, and the experience fueled my enthusiasm to learn and support these animals.
Although I’m new to our lab, we already have some great news: Global Food Systems awarded The Lee Lab a grant to support my swine microbiome studies! So I’ve been lucky enough to be keeping busy collecting fecal samples. I know that doesn’t sound glamorous, but the pigs are adorable, and we are going to make some great investigations to support science surrounding swine production, digestive microbiomes and nutrient utilization. Going to see the pigs is the highlight of my weeks now that we’re home-bound (but let’s be honest the pigs are fun and cute so it’d probably be the highlight anyways). My 10 piggies are very rambunctious and curious; they love distracting me by chewing on my boots or randomly taking off running. Just writing about them has me grinning from ear to ear. Soon I’ll be done with collecting samples and onto lab work, but for now I’m counting down till I get to see my pigs again.
Stay safe everyone!