Unveiling the Gut Microbiome's Role in Inflammatory Bowel Disease
Dr. Li on gut health and how E. Coli influences it.
Recently, I had the privilege of interviewing Dr. Li, a PhD student at the Arthur Lab. Located within the University of North Carolina’s School of Medicine, the Arthur Lab broadly studies the mechanisms by which the human microbiome, which is the community of microorganisms (like bacteria, viruses, and fungi) that live in our intestines, drives intestinal inflammation. Additionally, it explores how this inflammation contributes to the development of other medical conditions such as cancer and fibrosis.
Before his arrival at the Arthur lab, Dr. Li was a microbiologist at the University of Oklahoma where he was studying the environmental microbiome in extreme situations. He also studies bioinformatics, allowing him to learn some analysis techniques that would prove useful in his later studies. After his tenure at the University of Oklahoma, Dr. Li realized that he was interested in specifically studying human health and the microorganisms within our body, specifically the gut microbiome. Dr. Li was interested in the gut microbiome because it contains the most diverse amount of bacteria in the human body. The gut microbiome is absolutely crucial to our health, having a role in both our metabolism and immune system.
In our discussion, Dr. Li and I talked about his recent manuscript that he submitted for publication and his accompanying poster. The overall premise of his project was studying the relationship between inflammatory bowel disease (IBD) and E. coli.
Problem:
The reason behind his study is that patients with IBD often experience a complex and unpredictable disease progression to the point where we cannot foresee what risk patients will face. While it is believed that Adherent-invasive Escherichia coli (AIEC) can perpetuate inflammation, it remains uncertain if these 24-year-old in-vitro findings accurately predict in-vivo mucosal colonization.
I realize that I just threw around a lot of terms, so let me try to elucidate some of this language. AIEC is a specific subgroup of E. coli that has invasive properties, meaning that this strain has the ability to penetrate and spread into organs where they do not typically belong. Furthermore, the last sentence is essentially saying that while we know that the AIEC bacteria are able to colonize and thrive within artificial laboratory conditions using isolated cells or tissues (in-vitro), we do not know if our finding are completely reliable in predicting how these bacteria actually colonize and behave in the gut of living organisms (in-vivo). Finally, mucosal colonization refers to the process by which microorganisms, in this case, E. coli, establish themselves and adhere to the protective lining of the gut. The mucosal surfaces of the gut are lined with mucus, which provides an environment for bacteria to attach and thrive. These adherent bacteria likely interact with the inflamed gut tissue and the surrounding mucosal microbiome. During this interaction, they may influence the immune response and contribute to changes in the gut's microbial composition, leading to a state of dysbiosis
Hypothesis:
Dr. Li and his team hypothesized that the groups of E. coli bacteria that were able to stick to the gut’s mucous lining may share common genetic traits. These adherent E. coli groups could derive from either AIEC or non-AIEC strains.
The team believed that these bacteria could play a significant role in how the gut’s microbial community communicates with the body during inflammatory bowel disease and when the gut’s bacterial balance is disrupted (dysbiosis). Dysbiosis is extremely harmful as it can cause a variety of effects ranging from mild conditions such as cramps, diarrhea, and constipation to more serious chronic conditions. Since your gut microbiome ultimately decides how you overcome these problems, it’s unlikely to produce the best response if it’s in a state of chaos.
The main parts of the experiment consisted of:
The team began by implementing a novel high-throughput barcoding approach to label and track different strains of E. coli. They will then introduce these E. coli strains into mice in order to observe what will happen. They are specifically looking to see which strains cause inflammation.
Throughout the experiment, the team collected the tissues and stools of the mice. They then used two bioinformatic analyses in order to differentiate the AIEC property (AIEC or non-AIEC) and the barcode label (what strain of E. coli it is). The first path (pictured at the bottom) involved targeting the 16s gene and then performing a downstream analysis in order to characterize the whole microbiome community. The latter path involved inserting a barcode into the genome and then checking which E. coli strains persisted in the gut (essentially what barcodes were still found in the mice). Based on their results, they were able to separate which E. coli strains colonized or disappeared in the gut.
Image of showcasing what the team collected and how they analyzed it Finally, they also collected E. coli samples from real patients with IBD to ensure that the mice results matched up with the humans.
After obtaining all of their data, the team concluded that:
Mucosal colonizers are affected by both AIEC and non-AIEC strands. Previously, research groups only focused on AIEC strands. This study advocates for the study of both as they are equally critical in understanding both IDB and dysbiosis.
Continuing in our discussion about mucosal colonizers, the lab found that they appear to be more effective in causing intestinal dysbiosis than the previously defined AIEC phenotype. Targeting these mucosal colonizers could open up new possibilities for treating dysbiosis-associated diseases.
E. coli was significantly more present in the inflamed mice group (Il10) in comparison to the un-inflamed WT group. This shows that the in-vitro studies translated to the in-vivo mouse models.
Through sequencing the barcode of the E. coli strains that persisted in the different mouse groups, the team found that all of the E. coli strains remained present in the WT group while the Il10 group only had 3 or 4 strains.
They also examined the microbiome with and without E. coli in order to see if E. coli affected it in any way. They performed both a broad analysis, seeing if the mere presence of E. coli produced changes, and a more specific analysis in order to see if the number of E. coli strains present affected the microbiome. Their findings concluded that the presence of E. coli did indeed produce changes to the gut microbiome and it did not necessarily matter the number of strains.
Finally, they found what genes were present in the colonized group and not present in the disappeared group. This analysis will help them understand what genes allowed E. coli to survive and influence the gut microbiome and what genes prevent that from happening. In the image below, the darker regions are genes present while the lighter colors represent genes missing. Thus, the lab wanted to identify what genes were dark in the colonized red group and were light in the disappeared blue group. The chart at the lower part of the image gives a clear view of what genes were indeed present. If you see red dots with no corresponding blue dots above, that provides a potential gene of interest.
Despite these astonishing results, the lab still encountered some challenges that could damage the accuracy of their results. The main flaw was that they only tested 7 E. coli strains, meaning that their results may not provide a complete picture, but instead lay the foundation for future and more powerful statistical analyses.
Looking into the future in terms of next steps for this project, Dr. Li mentioned that it would be important to study the pathways that the mucosal colonizers affected and design technology that can regulate those pathways. Furthermore, the main purpose of this study is to establish a new concept in the biomedical field, laying the groundwork for more research. Researchers need to now study both AIEC and non-AIEC strains and how they affect IBD.
Finally, before concluding the interview, Dr. Li and I discussed his future goals. Dr. Li wishes to continue to work on a variety of different projects at the Arthur Lab, using these projects as an opportunity to expand his repertoire. Hopefully, by working on different projects, Dr. Li can gain a better understanding of what else he wants to explore and potentially study. A particular project that Dr. Li was interested in exploring the relationship between our dental health and gut microbiome. He also wishes to expand his knowledge in the biomedical space, exploring fields such as immunology.
Ultimately, this final segment taught me that no matter how far you are in your journey through academia, there is always more to learn and study. There is no need to be certain of what you want to do, especially if you are still in high school or college; after all, you have probably yet to try many of the fields that could potentially become your final field of interest. Another key takeaway from this discussion is that you should be comfortable with change. Who knows what opportunities will arise in your future, and if you are too scared to take them, you could potentially miss out on a wonderful experience.