{"id":11760,"date":"2021-12-10T12:59:12","date_gmt":"2021-12-10T17:59:12","guid":{"rendered":"http:\/\/sites.bu.edu\/urbanarch\/?page_id=11760"},"modified":"2021-12-15T15:14:47","modified_gmt":"2021-12-15T20:14:47","slug":"integrated-metagenomic-and-metabolomic-core-information-for-urban-arch-newsletter","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/urbanarch\/integrated-metagenomic-and-metabolomic-core-information-for-urban-arch-newsletter\/","title":{"rendered":"Integrated Metagenomic and Metabolomic Core"},"content":{"rendered":"<figure id=\"attachment_11761\" aria-describedby=\"caption-attachment-11761\" style=\"width: 169px\" class=\"wp-caption alignright\"><a href=\"\/urbanarch\/files\/2021\/12\/Shirish.png\" style=\"font-size: 16px;\"><img loading=\"lazy\" src=\"\/urbanarch\/files\/2021\/12\/Shirish.png\" alt=\"\" width=\"159\" height=\"144\" class=\"wp-image-11761\" \/><\/a><figcaption id=\"caption-attachment-11761\" class=\"wp-caption-text\">Shirish Barve, PhD, Principal Investigator, University of Louisville<\/figcaption><\/figure>\n<p>The Integrated Metagenomics and Metabolomics Core (IMMC) will provide a platform that interconnects Projects 1 and 2. Specifically, IMMC will provide high-quality, metagenomics and targeted metabolomics data, to be integrated with the probiotics randomized clinical trial and clinical cohort outcomes for Projects 1 (RCT) and 2 (Cohort), respectively. The IMMC has already acquired relevant metagenomics and metabolomics data that support the experimental rationale and study design for Projects 1 and 2. To ensure optimal scientific output from the study samples, the IMMC has implemented standardized procedures for collection of samples from Projects 1 and 2 study sites, and established logistics to coordinate shipment of samples for analysis, manage inventory, and enable tracking of chain of custody.<\/p>\n<p>For Project 1, IMMC &#8211; sub-core 1 will conduct state of the art metagenomics analysis of fecal samples collected from study participants receiving probiotics supplementation, to profile the changes in the gut microbial communities. The culture-independent molecular methods will consist of 16S rRNA gene and whole genome shotgun (WGS) metagenomic sequencing that provide the most comprehensive microbiota profiling. Rigorous sequence data analysis will utilize a set of advanced computational algorithms, according to taxon-based or function-based data matrices. IMMC- sub-core 2 will conduct targeted metabolomics analysis of plasma\/serum (Projects 1 and 2) to monitor host and gut-microbiota metabolomes.<\/p>\n<figure id=\"attachment_11762\" aria-describedby=\"caption-attachment-11762\" style=\"width: 156px\" class=\"wp-caption alignright\"><a href=\"\/urbanarch\/files\/2021\/12\/Smita.png\"><img loading=\"lazy\" src=\"\/urbanarch\/files\/2021\/12\/Smita.png\" alt=\"\" width=\"146\" height=\"168\" class=\"wp-image-11762\" \/><\/a><figcaption id=\"caption-attachment-11762\" class=\"wp-caption-text\">Smita Ghare, Ph.D, Co-Investigator, University of Louisville<\/figcaption><\/figure>\n<p>The IMMC will collaborate with Projects to develop meaningful study designs, implement effective sample collection and storage strategies, generate high-quality metagenomics and targeted metabolomics data, computationally summarize these data and support interpretation of the results. It will implement high-quality techniques, along with quality control standards, that produce meaningful results in a timely fashion. The IMMC will also standardize data generation methods across studies to enable integration across Projects and uncover robust discoveries.<\/p>\n<p>&nbsp;<\/p>\n<p>To accomplish these goals the IMMC has established the following <strong>aims<\/strong>:<\/p>\n<ol>\n<li>Employ metagenomic approaches to generate and analytically summarize project microbiome data.<\/li>\n<li>Perform targeted metabolomics analyses to profile plasma\/serum metabolites.<\/li>\n<li>Manage specimen and data biorepository and facilitate transfer between research Projects.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>The Integrated Metagenomics and Metabolomics Core (IMMC) will provide a platform that interconnects Projects 1 and 2. Specifically, IMMC will provide high-quality, metagenomics and targeted metabolomics data, to be integrated with the probiotics randomized clinical trial and clinical cohort outcomes for Projects 1 (RCT) and 2 (Cohort), respectively. The IMMC has already acquired relevant metagenomics [&hellip;]<\/p>\n","protected":false},"author":16853,"featured_media":0,"parent":0,"menu_order":100,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/pages\/11760"}],"collection":[{"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/users\/16853"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/comments?post=11760"}],"version-history":[{"count":10,"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/pages\/11760\/revisions"}],"predecessor-version":[{"id":11887,"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/pages\/11760\/revisions\/11887"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/urbanarch\/wp-json\/wp\/v2\/media?parent=11760"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}