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


Columbia Microbiome 16S Boot Camp TrainingRegistration is open! Join us for the next live-stream Microbiome Boot Camp on August 4-5, 2022. 

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 2022 dates: Live-stream, online training August 4-5, 2022; 12:00pm - ~8:00pm 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 August 4-5, 2022 from 12pm EDT - ~8pm EDT (9am PDT - 5pm PDT). Please note this training is not a self-paced, pre-recorded online training.


"Great workshop -- provided excellent background knowledge and a lot of very useful code (while acknowledging the multitude of other tools/options out there in addition to the ones covered here). The learning environment was also good with options to ask questions in large group, small group, or on Slack to suit different preferences." - Faculty member at Brigham and Women's Hospital, 2021

"It's a great opportunity to learn the nuts and bolts of the analysis.  I'm really glad I found the training and was able to sign up." - Government researcher, US Department of Agriculture, 2021 

"Overall, this training was outstanding.  The expertise of the instructors, the material provided and the general approachability of the group was wonderful.  I highly recommend and wish I could take it again in 6-12 months to refresh." - Anonymous Oncology Fellow, 2021

"Very helpful and the best organized workshop I've ever attended. All instructors were not only knowledgeable, but helpful and approachable." - Abbi H., Postdoc at The University of Alabama at Birmingham 

Check out more testimonials here.


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

  Early-Bird Rate (through 6/15/22) Regular Rate (6/16/22 - 7/24/22) Columbia/OSU Discount*
Student/Postdoc/Trainee  $925 $1,025 10% off
Faculty/Academic Staff/Non-Profit Organizations/Government Agencies $1,025 $1,225 10% off
Corporate/For-Profit Organizations $1,225 $1,425 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 the following: 1) your registration category from the table above, 2) if you are paying by credit card, or internal transfer within Columbia, and 3) if an internal transfer, indicate the registration category from the table above, and if grant funds are being used.

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 the following details: 1) full attendee name(s) and applicable registration category from the table above, and 2) payment method (credit card, invoice, wire).

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

Cancellations: Cancellation notices must be received via email at least 30 days prior to the training start date in order to receive a full refund, minus a $75 administrative fee. Cancellation notices received via email 14-29 days prior to the training will receive a 75% refund, minus a $75 administrative fee. 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 <14days prior to the 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. 




Want updates on new Microbiome training details or registration deadlines? Subscribe here.

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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Additional Testimonials

"Taking part in this workshop was an incredible opportunity! As an incoming graduate student, this course provided me with a variety of tools needed to become a more proficient R programmer and effectively explore microbiome research!" - Caroline H., Student at Oregon State University, 2021

"The microbiome course material was presented in a very organized fashion that clarified concepts and methods for microbiome analysis while at the same time providing the latest and most current (timely) information on these topics as well as future directions." - Anonymous Faculty member, 2021

"I've attended other microbiome programs, and this one is probably the best. The R coding tools that we were given are exceptional. I'd highly recommend this course to other colleagues." - Faculty member at Vanderbilt University Medical Center, 2020 virtual training

"This was an excellent training for what I needed. The background information really built into microbiome analysis in a tangible way, and I look forward to having the materials from this course as a resource in the future." - Postdoc at North Carolina State University, 2020 virtual training

"Most well organized and comprehensive workshop I've ever taken. Coming from a different field, I am inspired to incorporate these ideas into my future endeavors." - Student at the University of Chicago, 2020 virtual training

"The instructors were very knowledgeable and thorough with the concepts and ready to answer the questions." - Corporate Staff Member at AbbVie, 2020 virtual training

"Great introduction to learning 16S microbiome analysis in R." Faculty member at Wake Forest University, 2020 virtual training

"All the instructors were great and the hands on practicals were valuable to learning the concepts presented in lectures. I highly recommend this for people who want to learn how to handle and analyze microbiome data." - Student at Emory University, 2020 virtual training

"This was so useful and has made me feel competent to take on my own analyses." - Postdoc at University of California, San Francisco, 2020 virtual training

"This course provided an extensive amount of knowledge of analyzing microbiome data in a friendly and productive manner.  Even though I had little experience of microbiome analyses going in, this course provided me with a wealth of information that I will use throughout my future career." - Student at the University of Iowa, 2020 virtual training

"I prefer trainings that plunge you immediately into how to practically implement what you're learning--this was that type of training. The instructors were very knowledgable and friendly, the R exercises were well thought out, and the online format worked surprisingly well. Overall an excellent course." Faculty member at Georgetown University, 2020 virtual training