by Elise Wachspress
Relationships. Trust. Engagement. Leadership. A shared culture.
Often, a thriving community hinges on having a critical mass of members who reliably embody and stand up for these values. A core group that creates an environment where everyone—the weak, the hot-tempered, the shy, the energetic, the weirdos, and even the bombastic egotists—can all get along.
Yes, we are talking about your microbiome. And everyone else’s, for that matter.
Scientists who study the many dysfunctions of the human microbiome are entertaining the idea that gut—and systemic—health rely on a core group of bacteria whose “personalities” foster an environment where diversity can thrive long-term. These “universal colonizers” help smooth the inevitable challenges humans face: birth, development, sickness, even a wildly changing diet or variable climate. And that’s a good thing, because the human body has many different needs best served by a working balance of many different bacteria tunable to changing environmental conditions.
So maybe we should turn our attention from the inevitable “bad guys” who grab all the air time (Strep? Salmonella? Anthrax?) and try to figure out what kinds of bacteria can help the whole microbiome community work well together.
Thanks to research support from the Duchossois Family Institute, A. Murat Eren, known as Meren, is on the search for the foundational bacteria that set the stage for a balanced and happy gut flora. For this complex quest, he has pulled together a similarly diverse group of top citizens in microbiome science: Eugene Chang, MD, a specialist in inflammatory bowel disease; Bana Jabri, MD, PhD, expert in celiac; bioengineer and systems biologist Savas Tay, PhD; microbiologist Howard Shuman, PhD; evolutionary geneticist Luis Barriero, PhD; and epidemiologist Thomas Louie, MD, from the University of Calgary, a world expert in fecal microbiota transplant. (Yes, it is just what it sounds like.)
Identifying universal colonizers in an established gut community is challenging. How does one extract all bacteria living in one single gut environment and figure out which ones could thrive—and help others flourish—in any gut environment?
Meren’s first idea was to take a fecal transplant from one healthy donor, implant the microbiota in different recipients, and track how the bacterial populations change in different individuals. Initial analyses showed that while some of the bacteria colonized only one of their new hosts or none at all, some organisms were quite successful in multiple recipients.
These good colonizers also left their traces in individuals studied through the Human Microbiome Project (HMP), a National Institutes of Health initiative that collects microbiome samples from hundreds of healthy volunteers. But rather than zeroing in on all of the individual species in each sample—an all but impossible task with the available technology—the HMP painstakingly analyzes snippets of genetic code from whole communities of bacteria, generating tremendous amounts of data on the microbial mixtures in each of these volunteers.
This kind of communal sequencing, called metagenomics, has its limits. It’s like trying to recreate a recipe by analyzing all the chemical elements in a fully baked cake. It can work…sort of. With a great deal of user analysis and energy.
Following leads generated from metagenome studies, Meren’s team is working with some newer technologies, including a cutting-edge “long-read sequencing” approach which can look at much longer—and thus more uniquely identifiable—stretches of DNA. They also, thanks to Dr. Louie, now have access to a collection of potential colonizers much larger than their original “healthy patient #1.”
Even with the long-read sequencer, the work will depend on a lot of computational expertise. But Meren, whose group continues to hone anvi’o, an advanced, open-source analysis and visualization software that integrates many types of microbial data, has the team for the job. Meren’s leadership in creating anvi’o, a dynamic and unified work environment for data exploration, manipulation, and reporting, is empowering researchers with lesser bioinformatics skills to access and make use of many publicly available datasets, thus accelerating progress by the entire microbiome science community.
Now Meren and his team, especially graduate student Andrea Watson, senior research tech Karen Lolans, and post-doctoral scientist Florian Trigodet, PhD, are using their new long-read sequencing devices to zero in on some of the microbes who seem to have interesting stories to share. The aim is to identify the kind of microbial citizens who fosters a diverse gut community and thus helps their human hosts thrive.
Elise Wachspress is a senior communications strategist for the University of Chicago Medicine & Biological Sciences Development office
