Microbiome Core & Metabolomic

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The UCSD Microbiome Core

Microbiome research has become dependent on powerful tools, such as amplicon, metagenomic and metatranscriptomic sequencing, along with metaproteomics and metabolomics to understand microbial taxonomic and functional metabolism in myriad ecosystem, from cellular biochemistry to global ecology. Central to the application of this research are high-throughput, cost effective, standardized protocols to reliably process the hundreds thousands of samples that constitute modern microbiome investigations.

The microbiome is defined as a community of microorganisms which resides within an ecosystem. Microbiome's are dynamic, constantly changing due to external factors that influence the composition, transcription and metabolic output in ways that can be used to characterize and diagnose variance in a system. The application of multi-omic technologies is not limited to human-microbiome studies, but can be leveraged to investigate soil and plant processes, or marine and sediment interactions, animal and insect microbial dynamics, and even atmospheric processes. Understanding this delicate biological, genetic and metabolic equilibrium, and especially disturbance to that balance, require detailed investigation of the composition of a microbiome (rRNA amplicon and shotgun metagenomic sequencing), the transcriptional activity of its genes (metatranscriptomics), and the resulting proteomic and metabolite profile. Robust investigation also requires the ability to combine these tools using consistent, high-throughput protocols with automated technologies that minimize bias. Finally, by supporting the isolation of microorganisms from diverse environmental samples to create a culture library, and to quantify DNA and RNA markers with quantitative PCR, this suite of tools provides a comprehensive experimental platform to further research in any environment.

Our Mission is to provide academic, government and industry researchers with innovative, timely and reliable microbiome sample processing and generation of DNA, RNA and metabolomic data through lab service and recharge agreements to advance understanding of diverse global microbiome communities, coordinating with other Cores and CMI to provide seamless project completion.

Our Staff