In the Gut: Therapeutic Discovery in the Microbiome

The Fifth Annual Microbiome Symposium: Microbes, Metabolomics, and Modern Diseases highlighted the synergy of the Children’s Hospital of Philadelphia and University of Pennsylvania scientific community to produce incredibly novel and exciting research.

Hosted by the PennCHOP Microbiome Program, the Nov. 8 symposium brought experts from the fields of microbiology, immunology, gastroenterology, cell and molecular physiology, and pathology together with a common goal: to share developments from their labs with the end game of improving outcomes for individuals with chronic disease.

Larry Jameson, MD, PhD, executive vice president, University of Pennsylvania Hospital System and dean of the Perelman School of Medicine, welcomed attendees to the packed Gaulton Auditorium.

“It’s terrific to see a five-year anniversary for this symposium,” Dr. Jameson said. “While we are all graciously serving as hosts for the microbiome, we have about 15 clinical trials underway, some with therapeutic intervention,” noting the implications of microbiota research throughout the lifespan.

David Piccoli, MD, chief of the Division of Gastroenterology, Hepatology, and Nutrition at CHOP, credited the “marvelous work” by the Program’s leaders to create an environment where shared resources drive innovative breakthroughs. Co-directors of the PennCHOP Microbiome Program, Perelman School of Medicine, University of Pennsylvania include Robert Baldassano, MD, director of the Center for Pediatric Inflammatory Bowel Disease at CHOP, and a professor of Pediatrics at Penn; Daniel Beiting, PhD, assistant professor, University of Pennsylvania School of Veterinary Medicine; Gary D. Wu, MD, an academic investigator in childhood obesity research at CHOP, and Ferdinand G. Weisbrod Professor in Gastroenterology, and director, Penn Center for Nutritional Science and Medicine at Perelman School of Medicine; and Frederic D. Bushman, PhD, an academic investigator in childhood obesity research at CHOP, and professor and chair, Department of Microbiology, at the Perelman School of Medicine.

A Mosaic of Microbes

Dr. Bushman introduced Jessica Mark Welch, PhD, associate scientist, Marine Biological Laboratory, Woods Hole, Mass., and acknowledged a difference in their approach to laboratory analysis of microbiota samples: “When we’re working [with a sample], we try to beat the bejesus out if it; Jessica takes a more gentle approach, studying the interaction in situ.”

And what Dr. Mark Welch has gleaned from those observations comprised her lecture, “Spatial Organization in the Human Microbiome at Micron Scales,” pertaining mostly to the human mouth and gut. A method she created with colleagues, Combinational Labeling and Spectral Imaging – Fluorescent in situ Hybridization (CLASI-FISH), enables simultaneous imaging and identification of most microbes in complex natural samples.

“We applied this method to the human oral microbiome,” Dr. Mark Welch explained. “The human oral microbe is complex, but most of these taxa are site-specific — plaque below and above the gum line, tonsils, throat, saliva, tongue, hard palate, cheek, gums — these locations are in constant communication but hold very different bacteria.”

With specially designed probes. Dr. Mark Welch and her team scrutinize the intimate spatial associations among these taxa and consider whether they are competing with each other, synergizing, or engaging in other ecological associations. Spatial relationships and growth of certain taxa create conditions in which other taxa can thrive.

The ability to see a variety of morphological structures that show a range of growth, such as how the rate at which the body sheds epithelial cells correlates to the different bacteria in areas of the mouth, could provide some ideas of where to look to study specific bacteria.

Combatting Enteric Bacterial Infection

The next speakers focused on host-pathogen interactions specific to Clostridium difficile infection. Michael C. Abt, PhD, assistant professor of microbiology, Perelman School of Medicine, presented “Host Immunity Modulates Efficacy of Microbiota-Based Therapy in Treatment of Clostridium difficile Infection.” His research interests lie in host-pathogen interactions and how microbiota are impacting the dynamic host-pathogen relationship, particularly with enteric bacterial infection and multidrug resistant pathogens.

“There is an urgent need for alternative strategies,” Dr. Abt noted. “Resistant bacteria are on the rise, but antibiotic development has decreased. C. difficile is a continued urgent public health threat that is costly for health systems and for patients.”

The current standard treatment is for patients to receive prophylactic antibiotics, which increases the risk for C. difficile due to alterations in the gut microbiota, then for the patient to receive more antibiotics to address the infection. But that doesn’t treat the underlying cause — the lack of microbiota diversity — which can lead to multiple infectious episodes that may become life-threatening.

This is where fecal microbiota transplantation (FMT) comes into play. FMT restores microbiota diversity, and it has been shown to be effective. A current mouse model provided promising results: When the treatment group was given antibiotics then subjected to C. difficile and subsequently treated with FMT, inflammatory genes were reduced, and the microbe environment was brought back to baseline.

“We still don’t know how it works,” Dr. Abt said, “but it comes into the intestinal environment and clears C. difficile.”

Among the “knowns” are that the host’s immune status supports FMT engraftment and contributes to therapeutic efficacy. This is critical to the development of microbiota-based therapies for inflammatory bowel disease (IBD), allergies, cardiovascular disease, cancer, obesity, and neurobiological disorders.

“We’re studying a system in which we know microbiota therapy works, and now we must understand the how and use that as a scaffold and blueprint to develop therapeutic intervention,” Dr. Abt concluded.

Joseph P. Zackular, PhD, assistant professor in the Department of Pathology and Laboratory Medicine at the Perelman School of Medicine and CHOP Research Institute, is taking on C. difficile from another angle with his lab’s research into how environmental and nutritional changes could be contributing to an uptick in patients acquiring enteric infections without prior antibiotic treatment.

During his lecture, “Pathogen-Microbiota Interactions During Clostridium difficile Infection,” Dr. Zackular detailed his work with dietary zinc and nutritional immunity in C. difficile infection. Dietary metals, while essential to survival and important cofactors, also aid bacteria and pathogens. Dr. Zackular investigated the hypothesis that zinc alters gut microbiota, and his results showed that a high zinc diet created a competitive advantage for certain bacteria such as enterococcus, which thrive in a C. difficile-infected gut. Additional research into how enterococcus and C. difficile interact during infection is underway, and Dr. Zackular thinks the combination of these bacteria could potentially exacerbate disease.

Microbiology and the Microbiome

Maayan Levy, PhD, assistant professor of microbiology, Perelman School of Medicine, discussed her work with the inflammasome in “Intestinal Epithelial Cell Functions in Host-Microbiome Interactions.” Dr. Levy’s interest in the importance of microbiota in health and disease led her to focus on the inflammasome, guardian of the microbiota, believed to be activated by the host as well as bacteria.

Communication between the microbiome and host occurs between secreted metabolites, yet little is known about how the epithelial cells, which mediate this interaction, sense microbial metabolites, and initiate regulatory responses. Her work has involved setting up an automated screening system to identify new metabolites that can be used as modifiers of epithelial integrity.

“Microbial metabolites remain largely unexplored,” Dr. Levy said. “We know the function of very few of them.”

Dr. Levy discussed her recently published work, with first author Christoph A. Thaiss, PhD, assistant professor of microbiology at the Perelman School of Medicine, that investigated the effect of hyperglycemia on intestinal barrier dysfunction and risk for enteric infection.

The researchers demonstrated in mouse models that hyperglycemia drives intestinal barrier permeability and leads to an influx of microbial products and dissemination of enteric infection. Treatment of hyperglycemia, intestinal epithelial-specific GLUT2 deletion, or inhibition of glucose metabolism restores barrier function and bacterial containment.

In humans, systemic influx of intestinal microbiome products correlates with individualized glycemic control; these results link hyperglycemia and intestinal barrier function with the infectious and inflammatory consequences of obesity and diabetes.

“We are exploring the intestinal niche, one of the most interesting systems in the human body, to identify new therapies,” Dr. Levy noted, adding that goals for her ongoing research include identifying host factors that control host-microbiome interactions and new microbiome signals that influence immunity to discover implications for inflammatory diseases.

Kathryn E. Hamilton, PhD, researcher in the Center for Pediatric Inflammatory Bowel Disease at CHOP and assistant professor of pediatrics at the Perelman School of Medicine, presented “Understanding Intestinal Epithelial Cell Responses in Inflammatory Bowel Disease.” In an excellent example of the multidisciplinary nature of microbiome research, Dr. Hamilton noted that very little of her presentation dealt with the microbiome directly, and she sought the questions and insight of her colleagues as the work of her lab began to intersect with immunology.

Her recently published work examines the role of RNA binding proteins, specifically IMP1, as essential regulators of intestinal development and cancer. Results demonstrate that IMP1 acts as a posttranscriptional regulator of gut epithelial repair post-irradiation and colitis, in part through modulation of autophagy. The next steps in her research aim to learn about intestinal epithelial stem cells by studying patients directly to determine if stem cells are aberrantly or permanently altered in patients with IBD.

Dr. Hamilton is working to apply these results to ongoing research in children with Very Early Onset IBD. These patients often present with more severe disease than older patents, and patient-derived enteroids and colonoids are proving to be helpful in understanding how epithelial cells contribute to the pathogenesis of IBD.

“Epithelial stem cell cultures can create primary cell lines and are a powerful tool when studying diseases like IBD,” Dr. Hamilton said. “My dream is to find a link between the IMP1 and antigen presentation phenotype.”

Implications for research into the depths of the microbiome have far-reaching potential. We look forward to the exciting developments researchers will share at next year’s symposium (date to be determined).