Muehlbauer Research Lab

The overarching goal of our laboratory is the identification of the molecular mechanisms by which commensal bacteria regulate wound healing responses of intestinal stem cells specifically in inflammatory bowel disease, colitis-associated colon cancer and necrotizing enterocolitis. The ultimate long-term clinical and translational research goals are to develop pharmacologic treatments directed at the modulation of the microbiome based on the molecular mechanisms found through our research.

Current studies

Colitis-associated colorectal cancer

Despite the increasing implementation of colonoscopy screening and advances in chemotherapeutic and biological agent-based therapies, colorectal cancer (CRC) remains one of the most common and deadliest malignancies in the United States. The American Cancer Society estimates approximately 140,000 new CRC cases and over 50,000 CRC-related deaths nationwide in 2014. CRC includes hereditary, sporadic, and colitis-associated CRC (CAC). CAC represents a severe medical complication for patients with inflammatory bowel diseases (IBD), and often shows rapid progression, poor response to treatment and high mortality.

Substantial evidence points to an essential role of the intestinal microbiota in CRC/CAC pathogenesis.  Perhaps the strongest link between bacteria and CRC development in humans came from the study on Fusobacterium nucleatum, a hydrogen sulfide (H2S)-producing bacterium (HSPB). The mechanism by which Fusobacterium nucleatum promotes carcinogenesis is unclear but virulence factors such as FadA and Fap2 were shown to regulate cellular proliferation and host immune response respectively.  In addition, we previously demonstrated that inflammation triggers the expansion of enteric E.coli, which can promote the development of colonic tumors when the bacteria carries the genotoxic island pks. This suggests that host inflammation and microbial-derived molecules play a critical role in carcinogenesis.

In collaboration with the group of Dr. Alain Stintzi (U. Ottawa), we reported a link between HSPB and new onset of Crohn’s disease in a pediatric population (Nat. Comm. Nov 2016). Our data also suggested that H2S is an important contributor to A. parvulum-induced colitis in the Il10-/- mouse model. New and exciting unpublished preliminary data showed increased intestinal tumorigenesis in germ-free Apcmin/+;Il10-/-  mice associated with A. parvulum plus SPF compared to mice associated with SPF biota only.  H2S is an important mediator of many biological processes and can be pro- or anti-inflammatory depending on its concentration and the particular circumstance. Importantly, H2S exerts genotoxic effects on mammalian cells and is considered pro-carcinogenic. A recent study showed that cancer cell-derived H2S promotes tumor development.

We currently test the hypothesis that host-derived and bacterial-generated factors promote A.parvulum induced colitis-associated colon cancer.

The ongoing project already won two prizes for Junior Faculty at the University of Florida.

Necrotizing Enterocolitis

Necrotizing colitis (NEC) is a disease affecting mostly preterm babies. Up to 10% of babies born below 1500g develop NEC with a 50% mortality. Once triggered it leads to irreparable death of the intestines. Antibiotic use and the resulting microbial dysbiosis have been linked to the development of NEC. On the other hand it has been demonstrated that babies who develop NEC have a bloom in Proteobacteria together with an upregulation of the TLR4 receptor, a receptor for the bacterial wall product lipopolysaccharide (LPS). The exact mechanism is unknown but is thought that barrier dysfunction in NEC allows bacterial translocation which then leads to an overactive immune response in a susceptible host. Interestingly breast-feeding has been shown to protect from NEC by potentially fostering the growth of beneficial Lactobacilli. Our hypothesis is that a healthy microbial ecosystem can provide protection from the development of NEC. Our laboratory is currently investigating how the microbial ecosystem from NEC and healthy babies affects intestinal stem behavior.

Inflammatory Bowel Disease

Inflammatory bowel diseases (IBD) consist of two main manifestations, ulcerative colitis (UC) and Crohn’s disease. Although the etiology of IBD is unknown, it is generally recognized in the research field that abnormal inflammatory responses observed in patients involve host genetic factors and the intestinal microbiota. To date ~200 genes have been linked to IBD. Numerous animal models of colitis failed to develop intestinal inflammation when reared into germ-free conditions, but will rapidly develop the disease when returned into specific pathogen free (SPF) conditions (conventionalized). Therefore it is clear that the microbiota plays a central part in the etiol­ogy of IBD.

The human colon plays host to as many as 15,000 to 36,000 bacterial species, amounting to over 100 trillion bacteria. The microbiota and its associated prokaryotic-genome is an inte­gral part of the host and uniquely contributes to various biological processes such as maturation and development of the mucosal immune system, metabolic capacity, and intestinal epithelial cell (IEC) proliferation/differentiation. Interestingly, at the phylum level, the human and murine microbiota are similar with Firmicutes (64%), Bacteroides (23%), Proteobacteria (8%) and Actinobacteria (3%) representing most of the microbial consortia. Importantly, microbial composition is influenced by various biological conditions such as inflammation, infection, antibiotic treatment and diet.

It is reasonable to speculate that changes within the microbiome and its enormous metabolic capacity could affect the hosts ability to maintain homeo­stasis. Indeed, the metabolic capacity (metabolome) of this community practically amounts to that of the liver. The focus of our research is to understand how the bacterial metabolome regulates the intestinal stem cell niche and innate lymphoid cells during disease and healthy state.

Lab Personnel

Marcus Muehlbauer

Marcus Muehlbauer M.D., Ph.D.

Program Director & Assistant Professor

Michael Dougherty

Michael Dougherty has a Masters degree in Biology and is currently overlooking and managing all the ongoing projects in the laboratory. Michael previously conducted research on the phenology and genetics of the tick vector of Lyme disease, Ixodes scapularis, and its associated bacterial pathogens. His current research focuses on the interactions between the gut microbiome, intestinal stem cells and innate lymphoid cells and its implications for wound healing, inflammatory bowel disease and colitis-associated colorectal cancer.

Oleksandr “Sasha” Kudin

Oleksandr “Sasha” Kudin is a physician-scientists currently enrolled in a neonatal-perinatal fellowship at UF. His main interest is how the microbiota affects intestinal stem cell behavior in babies suffering from Necrotizing Enterocolitis (NEC). He plans on pursuing an academic career that allows him to be involved in the development of treatments from “bench” to “bedside”.

 Wenbin Liu

Wenbin Liu is a physician who is currently working as a medical advisor and scientist for Johnson & Johnson Medical (China) Ltd. Dr. Liu joined the laboratory to focus on a project studying how the colitis-associated bacterium Atopobium parvulum fosters the development of colorectal cancer.

Subhankar Samal

Subhankar Samal is an internal medicine-pediatrics board certified physician currently appointed as assistant professor of medicine at UF. He joined the laboratory in January 2017. His area of interest is “The role of bacteria in regulating the stem cell niche during wound healing/necrotizing enterocolitis.”

Davis J Roddenberry

Davis J Roddenberry is currently a sophomore pursuing a degree in microbiology with a minor in Business Administration at the University of Florida. He won honorable mention at the state science fair for studying how the brain interprets optical illusions. Davis is responsible for genotyping the laboratories mouse colonies and has his own project focusing on how bacteria regulate innate lymphoid cells. Davis will attend Medical School with a focus on basic research.

Arjun Panicker

Arjun Panicker is a senior at Buchholz High, who also won the national championship in math. He joined the lab to learn basic techniques like RNA/Protein isolation, real-time PCR, Western blots and intestinal stem cell cultures early in his career. His goal is to attend medical school with a special interest in basic research.