Summer 2020 dates: Live-stream, online training July 30-31, 2020; 12:00pm-7:00pm EDT
Amplicon sequencing of taxonomic marker genes such as the 16S rRNA gene in bacteria has been used over the last two decades to survey the microbiota of myriad environments. From soil to aquatic to human systems, 16S rRNA amplicon sequences are widely used to characterize the diversity and composition of the gut microbiome, discover novel microbes, and define how specific microbes link to environmental or host traits of interest. As a result, 16S rRNA amplicon surveys have proven invaluable in efforts designed to uncover the potential contribution of microbiomes to critical ecological and health processes.
This two-day intensive workshop will provide a rigorous introduction to the theory and methodology underlying the design, generation, and analysis of Amplicon Sequence Variant (ASV) based investigations of microbial communities. The workshop will introduce state-of-the-art techniques using the R language and environment. A team of leading experts in microbiome data analytics and statistics will offer a hands-on experience in learning how to implement these techniques by integrating publicly available data and R packages to explore and understand some of the pitfalls and information drawn from 16S rRNA data analysis.
By the end of the workshop, participants will be familiar with the following topics:
-The theoretical basis underpinning 16S rRNA investigations
-Methodologies for generating 16S rRNA sequence data
-16S sequence data quality control
-Amplicon sequence variant inference
-Taxonomic annotation
-Biodiversity estimation
-Principal Component Analysis and PERMANOVA
-Taxon-covariate correlation and regression modeling
Investigators at all career stages are welcome to attend, and we particularly encourage trainees and early-stage investigators to participate.
PREREQUISITES AND REQUIREMENTS
There are three prerequisites and requirements to attend this workshop:
1.Each participant must have an introductory background in statistics
2.Each participant must be familiar with R and a basic UNIX command line interface.
3.Each participant must have a laptop with either Chrome or Firefox installed (latest update). Additionally, participants need an SSH client (e.g., terminal for Mac or putty for Windows) installed on their machine prior to the first day of the workshop. SSH clients are available for free download and installation on Mac, PC, and Linux devices.
INSTRUCTORS
Maude David, PhD, Assistant Professor, Department of Microbiology & Department of Pharmaceutical Sciences at Oregon State University. Dr. David’s laboratory studies gut-brain interactions to understand how the gut microbiota can impact our behavior. Her laboratory also works on identifying bottlenecks in microbiome data exploration and has been developing new biocomputing methods to improve sequencing data annotation and analysis. Her interest lies in using machine learning algorithms to extract meaningful information from massive datasets already publicly available such as the Human Microbiome Project.
Thomas Sharpton, PhD, Associate Professor, Department of Microbiology & Department of Statistics, Oregon State University. Dr. Sharpton applies systems biology tools to understand how nutritional and chemical exposure impacts the structure and function of the vertebrate gut microbiome, and how these impacts affect human health. He has published over 50 manuscripts pertaining to the bioinformatic analysis of microbial genomic and metagenomic data and directs the Oregon State University Microbiome Initiative. His current research includes defining how the microbiome modulates environmental exposure over lifespan, mining the gut microbiome for novel pharmaceuticals, and developing analytical resources to define how the microbiome links to health and disease.
SCHOLARSHIPS
Training scholarships are available for the Microbiome Boot Camp.