Microbiome Data Analytics Boot Camp: Planning, generating, and analyzing 16S rRNA gene sequencing surveys


Microbiome Boot Camp Training Workshop 1080The most recent live-stream Microbiome Boot Camp was July 30-31, 2020. Join the email list below to hear about the next training.

The Microbiome Data Analytics Boot Camp is a two-day intensive training of seminars and hands-on analytical sessions to provide an overview of 16S rRNA gene sequencing surveys including planning, generating and analyzing sequencing datasets.

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Microbiome Boot Camp OVERVIEW

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.


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. 


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.


Training scholarships are available for the Microbiome Boot Camp.


COVID-19 Update: The Microbiome Data Analytics Boot Camp will no longer take place in person due to the COVID-19 pandemic. With instructors on the west coast, the Boot Camp will instead be a live-stream, remote training that takes place over live, online video on July 30-31, 2020 from 12pm EDT - 7pm EDT (9am PDT - 4pm PDT). Please note this training is not a self-paced, pre-recorded online training.


COVID-19 Update: With the training being offered virtually, we are passing along any and all costs saved to attendees.

  Early-Bird Rate (through 5/15/20 5/22/20) Regular Rate (5/16/20 5/23/20 - 7/15/20) Columbia/OSU Discount*
Student/Postdoc/Trainee  $975 $825 $1,175 $975 10% off
Faculty/Academic Staff/Non-Profit Organizations $1,175 $975 $1,375 $1,125 10% off
Corporate/For-Profit Organizations $1,375 $1,125 $1,575 $1,275 NA



*Columbia/OSU Discount: This discount is valid for any active student, postdoc, staff, or faculty at Columbia University or Oregon State University. To access the Columbia/OSU discount, email ColumbiaSHARP.Microbiome@gmail.com for instructions. For the Columbia employees, please specify if you are paying by credit card, or internal transfer within Columbia.

Invoice Payment and Group Registrations: If you would prefer to pay by invoice/check, or would like to pay for a group of registrants, please email ColumbiaSHARP.Microbiome@gmail.com with details.

Registration Fee: This fee includes course material, which will be provided to all participants after the workshop. Lodging and transportation are not included. 

Cancellations: For summer 2020, no administrative fees will be assessed due to the evolving COVID-19 situation. Cancellation notices must be received via email at least 14 days prior to the workshop start date in order to receive a full refund. Please email your cancellation notice to ColumbiaSHARP.Microbiome@gmail.com. Due to workshop capacity and preparation, we regret that we are unable to refund registration fees for cancellations after these dates, unless a new COVID-19 restriction is implemented that impedes virtual attendance, in which case any registration cancellation <14 days prior to a training related to COVID-19 restriction beyond your control (institutional policy, shift in work responsibilities, etc.) will be fully refunded and no administrative fee will be assessed. Because of the significant resources required to develop these trainings, you will be asked to submit supporting documentation (e.g. employer email notice, local regulations, etc.) for any COVID-19 related cancellation <14 days before a given training.

If you are unable to attend the training, we encourage you to send a substitute within the same registration category. Please inform us of the substitute via email at least one week prior to the training to include them on attendee communications, updated registration forms, and materials. Should the substitute fall within a different registration category your credit card will be credited/charged respectively. Please email substitute inquiries to ColumbiaSHARP.Microbiome@gmail.com. In the event Columbia must cancel the event, your registration fee will be fully refunded. 





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Questions? Email the Microbiome team here.

The Microbiome Boot Camp is hosted by the Columbia SHARP Program at the Mailman School of Public Health, Oregon State University's College of Public Health and Human Services, and Oregon State University's College of Science.

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