Human Virome Characterization Center for the Oral-Gut-Brain Axis

University Of California Los Angeles, Los Angeles CA

Investigators

Abstract

Data Analysis and Submission Core: Abstract As an integral component of this Human Virome Characterization Center (HVCC) for the oral–gut–brain axis, the Data Analysis and Submission Core will be responsible for supporting sample tracking via LIMS and performing data management, data analysis, and data dissemination. To support this effort, we will bring together analytical expertise in microbial, viral, and metagenomics experience from the Center for Metagenomics and Microbiome Research (CMMR) at Baylor College of Medicine (BCM) and The Goodman–Luskin Microbiome Center (GLMC) and Technology Center for Genomics and Bioinformatics (TCGB), both at UCLA. Generated datasets will be disseminated to public repositories and the wider Human Virome Program (HVP) community in consultation with the Consortium Organization and Data Coordination Center (CODCC). Our Core will be led by Dr. Sara Joan Javornik Cregeen, the Bioinformatics Team Lead at the BCM CMMR and Assistant Professor of Molecular Virology and Microbiology. She has broad expertise in analysis of microbiome sequencing data and is well-suited to lead this Core. Other Co-Leads for this Core will include Dr. David Elashoff, a Biostatistician at UCLA and leading expert in data analysis, management, and submission systems; Dr. Joseph Petrosino, Professor and Chair of Molecular Virology and Microbiology, Director of the CMMR, and founding member of the NIH Human Microbiome Project (HMP); Dr. Matthew Clayton Ross, Laboratory Director at the CMMR at BCM; Dr. Jonathan Jacobs, Co-Director of the GLMC at UCLA, and Dr. Xinmin Li, Director of the TCGB at UCLA. These Core investigators have far-ranging expertise in molecular genetics, microbial sequencing platforms, and bioinformatics tools for microbiome analysis, as well as data analysis, management, and submission systems. In addition, our Core will include Other Contributing Members with content expertise in various relevant fields, such as artificial intelligence, neuroimaging, and structural biology. The Data Analysis and Submission Core will perform downstream processing and analysis of sequencing data generated by the Biospecimen Analysis Core. Integrated bioinformatics pipelines and close collaboration between our Cores will ensure that primary processing can be completed as soon as the data are generated, which will contribute to the construction of a comprehensive virome database for our HVCC. Moreover, existing pipelines and analysis tools will be updated as new datasets are created, and novel tools will be developed as the need arises. Our Core will further perform integrative analysis of all sequencing and spatio-temporal datasets with available sample metadata to uncover new insights into the factors that shape and alter viral community structure across the lifespan. Prompt data and resource sharing within this HVCC and with the HVP community will be a priority for the Data Analysis and Submission Core, and we will leverage existing local resources and cloud-based tools to ensure broad dissemination of our findings. We will also establish and maintain cross-consortium collaborations with other HVCCs within the HVP and the CODCC.