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Microbiome Research

The Oklahoma Center for Microbiome Research broadly addresses key principles and questions concerning microbiome structure and function as the underpinnings of One Health. This research center supports and promotes research excellence while facilitating early-stage investigators’ progress towards independence. A key to achieving the objectives and long-term goals is the coordination of research activities, career development, and mentoring. The primary focus of the OCMR is to promote the success of Research Project Leaders in achieving milestones. Research capacity is enhanced by an Anaerobic Microbiology Research Core that provides customized culturomics services, including a novel approach for sequence-guided, targeted culture isolation by using reverse genomics to prepare tagged-nanobodies to surface proteins, paired with anaerobic cell sorting to isolate single living cells.

 

Anaerobic Microbiology Core Facility

The Oklahoma Center for Microbiome Research aims to accelerate cutting-edge multidisciplinary research on microbiome structure and function and facilitate the transition of five new investigators to R01 funding. An Anaerobic Microbiology Research Core is being created so we can reach this overall goal. The Anaerobic Core will provide anaerobic microbiology expertise, instrumentation, and training in anaerobic culturomics, as well as support all five research projects. It is the first entity in Oklahoma to provide customized culturomics services.

 

LEARN MORE ABOUT THE ANAEROBIC MICROBIOLOGY RESEARCH CORE FACILITY

 

Research and Pilot ProjectsLearn about OCMR's five research projects and three pilot projects.

Research Projects

The Oklahoma Center for Microbiome Research consists of five research projects being led by amazing Research Project Leaders.

  • Project 1: Oral pathogen-triggered progression of oral squamous cell carcinoma.
  • Project 2: Engineering host-determinants of novel gut microviruses.
  • Project 3: Characterizing Pathogen-Mediated Production of Secondary Metabolites in the Human Aerodigestive Tract Microbiome.
  • Project 4: The adolescent microbiome-gut-brain axis as a potential target in opioid abuse disorders.
  • Project 5: Exploiting trans‐domain syntrophy for the reduction of obesity using biotherapeutic Christensenella

Pilot Projects

The Oklahoma Center for Microbiome Research consists of three Pilot Projects being led by amazing Pilot Project Leaders.

  • Project 1: Phenotyping gut microbiome contributors to Fragile X Syndrome
  • Project 2: Nasal microbiota-derived extracellular vesicles and their influence on epithelial function in chronic rhinosinusitis
  • Project 3: Modulation of gut-brain axis by Akkermansia muciniphila through unfolded protein response

OCMR Mentors

Supporting each Project Leader is two mentors. Learn more about Oklahoma Center for Microbiome Research's supportive mentors by clicking on their name.
OCMR Mentor OCMR Mentee
Dr. Gerwald Koehler George Huang & Dolores Vazquez-Sanroman
Dr. Lijun Xia George Huang
Dr. Mostafa Elshahed Paul Kirchberger & Subhas Das
Dr. Bentley Fane Paul Kirchberger
Dr. Paul A. Lawson Reed Stubbendieck
Dr. Matthew Traxler Reed Stubbendieck
Dr. Kyle Simmons Dolores Vazquez-Sanroman
Dr. Adel Pezeshki Niki Johnson
Dr. Joy Scaria Niki Johnson
Dr. Lurdes Queimado Vikram Gujar
Dr. Noah Youssef Liz McCullagh

 

Research Mentor's Qualifications

Dr. Mostafa Elshahed

Dr. Elshahed mentors Paul Kirchberger. Dr. Elshahed has a broad range of experience with anaerobes, making him an ideal Mentor for Dr. Kirchberger, the RPL of Project 2, who seeks to establish model systems and characterize Microviridae that infect strict anaerobes. Dr. Elshahed is active on research fronts spanning all three domains of life. He served as PI on an NSF Microbial Observatory grant from 2008 to 2015 and has maintained NSF funding since joining OSU in 2007. His work currently focuses on two main research areas: environmental genomics of novel yet-uncultured microbial phyla, and metabolism, genomics, and biotechnological potential of anaerobic gut fungi. He has successfully mentored 1 Research Assistant Professor, 6 Graduate Students, 3 Post-doctoral Researchers, 2 Laboratory Technicians, 24 Undergraduate Students, and 11 visiting scholars. Dr. Elshahed has published over 100 publications in high impact factor journals. All of his post-doctoral advisees currently hold tenured or tenure-track faculty positions. Five of his graduate students were first generation college students and are experiencing success in industry and academia. For instance, one of Dr. Elshahed’s former graduate students is currently an Assistant Professor at Harvard University’s Brigham and Women’s Hospital in Boston. He provides direct, on-site guidance in project planning, regulatory compliance, anaerobic microbiology, and data analysis to Dr. Kirchberger. He also assists with his publications, grant writing, and interdisciplinary collaborations.

 

Dr. Gerwald Koehler

Dr. Koehler mentors Drs. George Huang and Dolores Vazquez Sanroman, RPLs of Projects 1 and 5. Dr. Koehler’s research focuses on two principal areas: the pathogenesis of fungal infections and the role of the mammalian gut microbiome in health and disease. He also serves as Associate Director for the OCMR on the OSU Center for Health Sciences (OSU-CHS) campus. Dr. Koehler’s knowledge of human and animal microbiomes makes him an excellent choice as Mentor for these two projects, which involve the characterization of microbiome impacts on oral cancer and opioid-induced dysbiosis. Through his past research projects at the Technical University of Munich, the University of Würzburg, the University of California San Francisco, and his current work at OSU-CHS, he has garnered many years of expertise in molecular microbiology, genomics, and bioinformatics (e.g., QIIME 2, mothur). Dr. Koehler has over 25 years of experience in mentoring and training graduate students and post-doctoral researchers. At OSU-CHS he has served on over 60 Graduate Advisory Committees and was the Major Advisor for 12 students. Dr. Koehler has mentored summer undergraduate students in INBRE and TABERC (Tulsa Area Bioscience Education & Research Consortium) programs. Dr. Koehler received Regents’ Distinguished Research Awards in 2016 and 2024 as well as the Regents’ Distinguished Teaching Award in 2015, in part due to his mentoring successes. As the Chair of the OSU-CHS Department of Biochemistry and Microbiology, he advises and mentors six faculty members. As OCMR mentor, he provides direct, on-site guidance in project planning, regulatory compliance, sample collection and processing, next-generation sequencing, and data analysis to Drs. Huang and Vazquez Sanroman. He also advises them in their publication, grant writing, and interdisciplinary collaboration efforts. Dr. Koehler is Dr. Huang’s department chair, and he has been collaborating with Dr. Vazquez Sanroman on several opioid-related microbiome research projects.

 

Dr. Lijun Xia

Dr. Xia mentors Dr. George Huang, RPL of Project 1. He is a Member and Chair of the Cardiovascular Biology Research Program at the Oklahoma Medical Research Foundation (OMRF) in Oklahoma City, where he holds the Merrick Foundation Chair in Medical Research. He brings considerable experience to OCMR because he is PI of the Center for Cellular Metabolism Research in Oklahoma (CMRO) COBRE grant. Dr. Xia represents OMRF in recruiting future pilot and research projects for OCMR and serves as liaison for Research Core synergies. He is PI on three NIH R01 grants. He discovered novel functions of O-glycosylation in platelet function, vascular biology, and intestinal inflammation/tumorigenesis. He published more than 133 peer-reviewed papers in journals such as Nature, Science, and PNAS. Dr. Xia also has expertise in metabolic research. His lab recently reported in Science an essential role for colonic O-glycans in maintaining host-microbiota symbiosis through regulating the structure and metabolic output of the microbiota. His newly funded R01 grant builds on his discovery of a new role of site-1 protease in mannose-6-phosphate-dependent lysosomal enzyme trafficking and lipid metabolism in endothelial cells. He has won numerous awards including most recently the Edward L. Thelma Gaylord Prize for Scientific Achievement from the OMRF. Dr. Xia’s experience leading the CMRO-COBRE and knowhow of host-microbiota interactions are valuable assets to the OCMR and specifically as Mentor to Dr. Huang. He provides guidance in project planning, cellular metabolism, and data analysis.

 

Dr. Paul Lawson

Dr. Lawson mentors Reed Stubbendieck, RPL for Project 4. Dr. Lawson is a Presidential Professor of Microbiology. He relocated to the University of Oklahoma (OU) from the University of Reading, UK, where he spent 14 years as a Senior Research Fellow with the world-renowned microbial taxonomist Dr. M. David Collins. Dr. Lawson’s participation establishes the connection with faculty at OU. Dr. Lawson contributed to a fundamental restructuring of the genus Clostridium. He also described many taxa commonly found in the human microbiome. His work on systematics and taxonomy has contributed a diverse publication record (>200), including more than 25 chapters in Bergey’s Manual of Systematic Bacteriology. In 2011 he founded the “Center for Microbial Identification and Taxonomy” at OU, bringing together seamless use of traditional microbiological and molecular techniques. In 2019 he became a Fulbright Scholar investigating the microbiomes of Lactic Acid bacteria at the University of Technology, Cyprus. Dr. Lawson’s track record establishes him as a world leader in the characterization and taxonomy of anaerobes. He brings this knowledge to the OCMR-COBRE to benefit all the research projects, especially as Mentor to Dr. Stubbendieck. He has successfully mentored over 12 graduate students and 2 postdocs. He provides direct, on-site guidance in project planning, regulatory compliance, and data analysis.

 

Dr. Kyle Simmons

Dr. Simmons mentors Dolores Vazquez Sanroman, RPL of Project 5. Dr. Simmons is an Associate Professor in Pharmacology & Physiology at OSU-CHS and Director of the OSU Biomedical Imaging Center. He is an experienced neuroscientist with over 75 peer-reviewed publications totaling >15,000 citations. He is Co-Director of the Biological Systems Research Core for OSU-CHS’s CIRCA-COBRE, overseeing the collection, analysis, and interpretation of all biosample and neuroimaging data across the CIRCA projects. Dr. Simmons serves as a bridge between OCMR and CIRCA. Dr. Simmons is an internationally recognized expert in body-brain signaling (i.e., ‘interoception’) and its influences on mental health and substance use. As a brain physiology and function expert with a keen interest in microbiome function in the gut-brain axis, Dr. Simmons is well suited to serve as Mentor to Dr. Vazquez Sanroman, whose project seeks to determine the causes of microbiome shifts due to opioid dependency and withdrawal. He provides direct guidance in project planning, regulatory compliance, and data analysis.

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