Microbiome Core

To accomplish this goal, the BEES Sub-Core leverages existing institutional resources at UofC and UIC in microbiome analysis, metabolomics, proteomics, genomics and bioinformatic services. To enable streamlined access to these varied services by CACHET members and provide advice on appropriate experimental design and resource utilization, each BEES Sub-Core has a Center-supported Facilitator who is the director of that institutional facility core and a subject-matter expert. In addition to providing guidance and priority access to CACHET members, they will provide training to CACHET investigators who wish to master these technologies, particularly young investigators and those new to the fields. The BEES Sub-Core uses the Office of Shared Research Facilities cores (OSRF) central web-based ordering system at UofC for services and subsidy/co-pay requests which enables efficient turnaround time for all CACHET members on both campuses. This system permits tracking of subsidized services and Core/Unit utilization in a centralized database for efficient metrics analysis of facility usage and outcomes.

Leadership

Ashley has been the Metabolomics Platform Director for the Host-Microbe Metabolomics Facility (HMMF) within the Duchossois Family Institute (DFI) at the University of Chicago since April 2021. Her career has focused on the study of host-microbe interactions mediated by microbial factors, specifically within inflammatory bowel disease (IBD). Following her Chemistry PhD work in untargeted metabolomics and analytical chemistry from Indiana University (mentor Dr. Erin E. Carlson), she completed her post-doctoral work at the University of Chicago with Dr. Dionysios A. Antonopoulos and Dr. Eugene B. Chang where she quantitatively and qualitatively explored peptides and metabolites from continuous microbial culture, IBD patients and murine model systems. She currently serves as a Scientific Advisor on the GIRF AB since 2020. In the DFI – HMMF, Ashley and the amazing HMMF team members (Jessica Little, PhD; Mary McMillin, BS; David Moran, MS, MPH; Michael Mullowney, PhD; Amber Rose, MS) are dedicated to providing targeted and untargeted metabolomics platforms to the host-microbe community to elucidate and define disease state-specific metabolite profiles for the discovery of early detection and prevention strategies as well as the discovery of novel treatments.

Anitha Sundararajan received her PhD from Montana State University in 2011 from the Center for Biofilm Engineering and the Department of Microbiology. For her dissertation, she studied two metabolically diverse organisms and how they sense and respond to different environmental stressors to optimize metabolism.  During this time, she developed and optimized several techniques to cultivate and harvest anaerobic biofilms (under microaerophilic conditions) with defined oxygen concentrations. For her post-doctoral training, she took up a position at the National Center for Genome Resources (NCGR), a sequencing service provider and a biotech company.  Here, she was trained on Illumina and Pacific Biosciences sequencing platforms and is well versed with library preparation workflows for DNA and RNA. Here at DFI she wishes to combine her microbiology background with her genomics experience and build a core that offers different services to support DFI’s mission, i.e. to investigate the gut microbiome and its implication(s) in a range of human diseases using -omics approaches.

Key Accomplishments

• Trained Argonne Microbiome Core staff and developed specimen receipt protocols for EHS studies;
•  Streamlined and refined microbiome sequencing assays, sample collection, processing procedures and bioinformatics pipelines for profiling gut and saliva microbiome in population studies;
• Established protocols and collection procedures for air sample microbiomes from South Chicago households;
• Provided microbiome profiling services to eight studies led by CACHET members, including three funded by the CACHET Pilot Project Program;
• Recruited Dr. Eric Pamer to assume Microbiome Core Leader position upon Dr. Gilbert’s departure;
• With establishment of the DFI, CACHET launched a collaborative arrangement for DFI to assume the role of CACHET Microbiome Core, with a focus on translational EHS research;
• DFI purchased four new state-of-the-art MS systems dedicated to microbial metabolite profiling;
• Recruited Dr. Chaubard of DFI as CACHET Facilitator for Metabolomics Core, particularly for EHS research;
• Established collaborative arrangements to leverage pre-existing and high-functioning institutional genomics and bioinformatics core facilities at UofC to augment the new BEES Sub-Core services for CACHET members; key services for CACHET investigators will be provided at “in-house” service rates with subsidized co-pay support available for justified EHS research.