I Study Poop: Adventures from Scientists on the Front Line

It’s been a LONG time brain-gut lovers. We were knee deep in snow last time I posted, and have now emerged into sunshine! Summer means ice cream, relaxation, and more time for blogging, so expect to be hearing more from me.

As a welcome back to the blogging life, today we are going to hear the science story of a brain-gut researcher from the great state of Illinois – grad student Katherine Durham-Maki – whom I met during a recent workshop for microbiome bioinformatics – QIIME2.

Tell us about yourself

Hey there, my name is Katherine Durham-Maki and I am a third-year PhD student at University of Illinois at Chicago (UIC) working with Dr. Anne Fink. I study at the Center for Narcolepsy and Sleep Research in the College of Nursing. I also work as a cardiac electrophysiology nurse practitioner at the Jesse Brown Veterans Affairs (VA) Medical Center, which is conveniently across the street. I enjoy the opportunity to connect clinical care with bench science as questions and issues that arise in the clinic provide continuous inspiration!

How did you come to the study of poop?

It was actually a bit unexpected; I had a long-time interest in epigenetics and how the environment affects DNA expression in the pathogenesis and mechanisms of disease. I had been reviewing the literature looking for connections between shift work and blood pressure and came across previous research looking at the influence of the microbiome on extra-intestinal disease. The director of the DNA services here UIC, Dr. Stefan Green, is especially interested in the microbiome and works with several groups focusing on circadian derangement and the beautiful bacteria of the gut. The pieces started to fit together, and as I dove deeper in the literature I became hooked! As I work on the bioinformatics and analysis of my (very) preliminary data that informed the sampling times for my dissertation, I am overwhelmed, amazed and excited for the multitude of information that comes from the microbiota. Luckily, I somehow convinced Dr. Green to serve as a member of my dissertation committee, and so he has been a great resource as I navigate this area of research.

How long have you been working in the field?

I am basically the definition of a novice in this field, but I am loving how I learn more every day. As a cardiology nurse practitioner at the VA I have been interested in the cardiovascular health of veterans for a long time. My brother is currently in the military service on active duty and happens to work night shift so when I read about increased cardiovascular risk and increased blood pressure with shift workers, I wanted to study a possible mediator that may be targeted in the future. More and more evidence points to the microbiome as a system that is synergistic with the cardiovascular system. A number of studies have shown that gut changes occur before blood pressure changes in genetically modified hypertensive rats, and that the hypertensive phenotype can be transferred to other animals via Fecal Microbiome Transplantation (FMT). I am very early in my investigative process, but I truly believe there is so much discovery potential now through increased accessibility of high throughput sequencing and analysis methods.

Tell us about your poop study

As I mentioned previously, I am very interested in the active duty and veteran military population. Sleep is chronically fragmented during deployment as a result of extended/rotating-schedule assignments and because of light exposure during rest periods. These factors dysregulate circadian rhythms and can potentially cause altered sleep architecture during recovery sleep (sleep after the shift work period). My advisor has previously shown in rat models where sleep is fragmented, that blood pressure increases significantly. My dissertation research focuses on two hypotheses, in rats: (1) that the duration of sleep fragmentation correlates with pathological alterations in the gut microbiome topography, (2) that specific microbiome changes correlate with increased blood pressure. I hope to someday grow this research to the study of non-pharmacologic interventions that can be used during deployments that reduce acute and chronic effects of sleep fragmentation on cardiovascular health. As I am just starting my data collection, I don’t know exactly where this work will lead, but that is why science is exciting!


Who are some researchers that really inspire you?

Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA gene and allowed scientists to identify and study bacteria that previously weren’t able to be easily cultured in the lab. I believe their work was paramount to where we are today in this field and therefore they should be recognized.

Santisteban et al, 2017: This is the article that changed everything for me. This research was done in a systematic and eloquent way to show mechanisms linking the gut to the brain & cardiovascular system. I highly suggest you give the article a read if you have any doubt that our physiologic systems are all interconnected (although I believe I am preaching to the choir here).

I also love the work that Martin Blaser and Rob Knight have done to get knowledge about the microbiome out to the general public and students that are new to the field (like me). Rob Knight has put out a vast assortment of accessible information about the microbiome through his books, online course and online videos. I have listened to Blaser & Knight’s audiobooks two times (each!) cover to cover because I think the information is that important. It still boggles my mind that a percent of the American public is so anti-vaccine but yet they gobble down antibiotics like they are candy. I also think Jack Gilbert has done a great job in explaining how “dirt is good”. I think much of the previous scientists work has aligned with ideas things I believed to be true in the past, but didn’t have the evidence to back up. Read: get your hands dirty and stay away from antibiotics (unless completely necessary).

What is next for you?

I am currently working on my data collection and teasing out the challenges of recording rodents with telemetry long-term. As I complete my doctoral research, I am constantly on the lookout for educational opportunities and future postdoc locations in microbiome-neuro-cardiovascular research. I also want to expand my training in the field of chronobiology and sleep science. My goals for my PhD are to master this type of animal model/recording, data management and collection techniques of fecal sampling, and learn how to run the bioinformatics and statistics on my microbiome data independently. From there I hope to have opportunities in my next phase of learning to incorporate new technologies and research techniques, so I am well equipped to continue this work independently in the future. As I believe interdisciplinary work is essential for gaining perspective on relevant clinical questions, I hope to continue to collaborate with scientists from various disciplines in my research endeavours.

What weird and wonderful things have you had to deal with since working in the brain-gut world?

Well, I now feel that I am a rat-poop aficionado and can spot a fresh pellet from a mile away (haha). If I had a dollar you every weird look I receive when I explain my dissertation research (you collect WHAT?), I would be able to finance all of my genetic analyses. I will admit, I didn’t fully understand that vast amount of information that can be obtained from fecal samples when I first started. Now I look at those little guys with a newfound respect; they are like keys to unlock our future understanding of health and disease. I also never had an appreciation for the important of microbial diversity and the influence of diet and lifestyle choice on health/disease. That is why this area is so exciting—new links and discoveries are constantly being made. Although some still need to be backed by controlled experiments and may be only associational at this point, there is an enormous potential for future research.

What is your favorite Brain-Gut fact?

Did you know there is a pathway from the gut to the paraventricular nucleus in the brain, which is directly responsible for controlling sympathetic discharge (fight-or-flight response) in our body? This is one mechanism how alterations in the gut may affect blood pressure and heart rate response. This was shown by adding a retrograde tracer-virus to the stomach and imaging the cells of the brain. I may be biased, but I think that is fascinating!

How can people learn more about you/get involved in your work?

I am currently working on an animal model but hope to expand my research to shift-workers in the military and civilian populations in the future, so stay tuned. In the meantime, I would love any opportunities to collaborate on manuscripts, projects or to get involved in a community of people share a common love of bacteria! Please reach out because I would love to connect with you!



Research Gate

Google Scholar


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s