Getting Cultured About Bacteria

Help us give a warm welcome to our guest blogger Emily Desmet Ledgerwood, PhD, who shares her experience using uBiome Explorer Kits in her microbiology course at Le Moyne College in Syracuse, New York.

We’re excited to share her hands-on experience in learning how gut microbes shape human health!

We are living in an exciting time in the field of microbiology, a time that, at the very least, is revolutionizing how we perceive microbes as they relate to our health. I’m talking about understanding the implications of our microbiota, and I would argue that it is the biggest advancement in the field since first linking microbes to disease in the late 19th century.

I am a professor of microbiology at Le Moyne College, a small liberal arts college in Upstate New York. Every semester, I give several lectures on the microbiome, detailing what we know about how it is acquired, how we alter it, and how it shapes our health.

I became engrossed with learning how to influence the development of the microbiome when I was pregnant with my daughter.

I would read late into the night (and still do!) about how my daughter might develop fewer allergies if I wash my dishes by hand instead of using a dishwasher because hand-washing is less effective at degerming or how devastating early antibiotic use is to a newborn. I remember being overwhelmed when, just a few days after giving birth, I had a urinary tract infection and had to take a course of antibiotics.

It is funny how just ten years ago I wouldn’t have given it a second thought that I had a completely curable, mild infection that would be gone before I knew it if I just took a quick course of cephalexin. But now, I am crying in the doctor’s office and wondering what this is going to do to my daughter’s fragile gut microbial population and whether it will ever fully recover from this onslaught.

All of this sounds fascinating to me, and like I said, is enough to keep me up late at night reading, but I was having a difficult time reproducing this emotion in my students.

Sure, some of my female students were particularly intrigued, and I envision them recalling the material ten years from now as they learn they will be having a c-section instead of a vaginal birth or struggling with breastfeeding and contemplating formula-feeding their baby.

However, most of my students did not feel the same passion I felt about the microbiome.

The struggle to engage students, many of whom have aspirations to go on to medical school or physician assistant programs, in an area of science that is in the process of transforming medicine as we know it, is what brought me to uBiome. I thought that maybe in allowing my students to sample their own gut microbiome they would gain a greater appreciation for the microbes that inhabit their guts.

And that is exactly what happened.

Students were tasked with analyzing their results and making connections between the bugs in their gut and an aspect of their health that might be linked to a particular microbial population.

One of the first things they noticed is how conflicting the research is. Students were confused to discover that they have a high prevalence of Firmicutes but are, by general standards, considered very lean.

Perhaps instead of the ratio of bacterial populations, the amount of short chain fatty acids produced is a more appropriate measure of leanness? They also learned that the interplay between microbes and their hosts confounds data analysis.  

Allowing students to witness the emergence of a field, forcing them to critically analyze experimental design, was a teachable moment in itself.

Even more fun though was seeing the student’s reactions to their own gut microbiome sequencing results.

I had a student that was lactose sensitive as a child but has since outgrown it. He was pleasantly surprised to find a healthy population of Lactobacillales in his gut that was potentially responsible for his ability to indulge in ice cream.

Another student who has two autoimmune diseases was intrigued to discover that the inflammation fighting genus of bacteria, Akkermansia, is almost non-existent in her gut.

Or the student that discovered the second most prevalent genus of bacteria in her gut was Thalassospira, a marine bacterium capable of degrading naphthalene, an aromatic pollutant that is a component of coal tar. Why this bug makes up nearly 14% of her gut microbiome remains unanswered.

So for the foreseeable future, I will have my students analyze their gut microbiomes as a way to not only get them excited about how gut microbes shape human health, but also to hopefully shed some light on the diversity of college-aged student guts.

Dr. Emily Ledgerwood is an assistant professor of microbiology at Le Moyne College. In addition to teaching and studying the human microbiome in her courses, Dr. Ledgerwood studies host-pathogen interactions of the human virus reovirus, an oncolytic virus that is in phase III clinical trials as a cancer therapeutic for head and neck tumors. She hopes her work will identify key features of tumor cells that can be exploited to improve oncolytic viral therapy.