The Microbiome Core Facility at UNC is a science-based recharge facility that has served the center, the university, and external entities since it was established in 2009. The core was taken over by the CGIBD in 2011 and was not included in the prior application. The Core provides support to investigators from experimental planning to quantification and phylogenetic identification of host-associated microbiome components. The Core initially offered Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis as its main service. However, it has transitioned to offering amplicon sequencing as Next Generation Sequencing (NGS) has become more cost effective and providing additional support for informatics by giving investigators the relative abundance and phylogenetic assignments of microbes. Other services include quantitative PCR, clone library creation, consulting and research support. Additionally, with support of UNC-ITS Research Computing and using the UNC Kure cluster the Core offers 1) amplicon sequencing bioinformatics pipeline that removes low-quality sequences, clusters reads into Operational Taxonomic Units (OTUs) with an average percent identity of 97%, and assigns taxonomy to OTUs, 2) metrics of community diversity including Shannon diversity, 3) distance metrics between samples based on Unifrac distance, and 4) PCoA clusters of samples based on distance metrics and/or user metadata. During the next year we aim to establish three new services: lllumina barcoding and library preparation, RNA-seq on microbial communities, and a Microbionie Screening Assay (MSA).The MSA will be developed based on reported microbiome data in collaboration with the Advanced Analytics Core, and will provide quantitative abundance of the most common phyla and OTUs reported in the human and murine gut. The MSA will provide a more accurate quantification of bacteria (compared to sequencing) using a 48.48 Dynamic Ai-ray Integrated Fluidic Circuits instrument which combines 48 gene-specific primer sets with 48 samples to run 2,304 simultaneous qPCR reactions. We intend to develop the MSA for species level identification of taxa that cannot be identified by sequencing of only the 16S rRNA gene. The proposed services have been requested by users and reflect the demand of our users for both 16S rRNA sequencing and new assays that yield more information than can be produced by single-gene 16S rRNA surveys. As a science-based facility, the Core requires highly trained personnel with a background in molecular biology, microbiology, and bioinformatics, capable of advising researchers new to the field and able to keep up with the current technology, specifically next generation sequencing methods. To support the planned expansion of services, the Core has added Dr. Anthony Fodor as Associate Director of Bioinformatics to advise users on the best bioinformatics approach to microbiome data analysis and hypothesis testing. He will oversee our continuing efforts to automate our 16S amplicon analysis pipeline to produce the most benefit for our users.
The microbiota is the community of microorganisms that live in or on the human body. It is becoming increasingly clear that the microbiome (the microbiota's collective genomic information) contributes to GI health and disease. In order for the CGIBD to fulfill its mission, it is imperative that CGIBD members have access to state-of-the-art methods for analyzing microbial communities in the context of GI health and disease. The UNC Microbiome Core, a facility almost solely dedicated to the analysis of host-associated microbiota, has assisted 66 principal investigators from CGIBD and elsewhere on 157 projects since it was established as a recharge facility in 2009. Many of the completed projects were relevant for human GI related diseases like necrotizing enterocolitis (NEC), irritable bowel syndrome (IBS), and colorectal adenomas.
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