Microbiome Data Analytics Boot Camp

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. This workshop specifically trains participants in the use of the R programming environment for the analysis of microbiome sequence data, including the implementation of the DADA2 and phyloseq software packages. It will also introduce introductory concepts and methods in the generation and analysis of shotgun metagenomic data.

By the end of the boot camp, 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
• Introduction to machine learning in microbiome data
• Phylogenetic analysis

Summer 2026: The Microbiome Data Analytics Boot Camp is a livestream, remote training. With instructors on the west coast, the Boot Camp will take place over live, online video on September 2-3, 2026 from 12pm EDT - ~8pm EDT (9am PDT - 5pm PDT). Please note this training is not a self-paced, pre-recorded online training.

Investigators from any institution and from all career stages are welcome to attend, and we particularly encourage trainees and early-stage investigators to participate. There are three requirements to attend this workshop:

1. Each participant must have an introductory background in statistics.
2. Each participant must be familiar with R.
3. Each participant must have a computer with either Chrome or Firefox installed (latest update).

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 are available for the Microbiome Boot Camp.

"This is a great course if you plan to analyze microbiome data, and also if you just want to understand microbiome analyses. The course material is an excellent mix of biology and data analysis, and the instructors are super knowledgeable and helpful." - Faculty Member at University of Massachusetts, 2025

"The Boot Camp exceeded my expectations. I left feeling confident in trying the newly learned material on my own (under the guidance of a mentor). It was thorough with ideal teaching techniques from short lectures to the guided practical workshop optimizing learning." - Postdoc at Oregon Health and Science University, 2025

"The course significantly improved my understanding of the generation and analysis of microbiome data and the practicals provided real-time examples to solidify the knowledge in the lectures. The instructors were very knowledgeable, and excellent teachers." - Faculty Member at University of Florida, 2025

"The Microbiome Boot Camp was thoughtfully designed and executed to present principles and demonstrate them with curated and guided practicals using R. The instructors were highly knowledgeable, thorough and communicable, leading to a highly productive and informative boot camp." - Research Associate at University of Hawaii at Manoa, 2024

"The code this training provides you with would be worth it on its own, but the fact that you also get to interact with knowledgeable masters of the field who explain the code and also walk you through the biological concepts makes this course extraordinary!" - Student at Boston University, 2024

"I gained in-depth knowledge about the latest methodologies and techniques for microbiome research, including data analysis and interpretation. This training has equipped me with advanced skills to enhance my research in gut microbiome studies." - Research Assistant at Oregon State University, 2024

"'Exceeded expectations' is definitely true. This training was extremely valuable. I feel I have the tools to do a complete start to finish analysis. The added benefit of talking to instructors about their views and experience on study design and other R/data analsyis questions was so appreciated. If the quality of workshops is this good for all SHARP programs, I want to sign up for them all! Thank you so much!" - Faculty member at University of Hawaii, 2023

"What a fantastic course, providing you with a foundational/fundamental framework to conduct microbiome analysis including: R-code scrips to plug and play with your own data and useful resource references. The team was amazing and very helpful." - Faculty member at Western University of Health Sciences, 2023

"As a microbiome newbie, the course was extremely comprehensive and provided me with the necessary tools to support my exploration and research in this area. The tools were excellent, and the instructors were very clear and supportive." - Faculty member at Rutgers School of Public Health, 2023

"This training was both insightful, challenging, and supportive! All of the instructors were great at explaining the complex topics related to 16S sequencing and analysis as well as machine learning." - Student at Oregon State University, 2023

Registration Fee is based on your category and includes course material, which will be made available to all participants both during and after the conclusion of the training.

2026 Registration Category Rates: 

• Student/Postdoc/Trainee: 
  • Early-bird rate: $995 
  • Regular rate: $1,195 
• Faculty/Academic Staff/Non-Profit Organizations/Government Agencies: 
  • Early-bird rate: $1,195
  • Regular rate: $1,395 
• Corporate/For-Profit Organizations: 
  • Early-bird rate: $1,395 
  • Regular rate: $1,595 

$200 early-bird discount is automatically applied if you register before the June 15 deadline.  

• $200 Early-bird Discount: This is automatically applied if you register before the June 15 early-bird deadline.  
• 10% Columbia Discount: This is valid for any active student, postdoc, staff, or faculty at Columbia University. If paying by credit card, use your Columbia email address during the registration process to automatically have the discount applied. If paying by internal transfer within Columbia, see below.  
• 10% Mailman Alumni Discount: This is valid for any individual who graduated from the Columbia University Mailman School of Public Health. To access the Mailman Alumni discount and receive a registration code, please email sharp_program@cumc.columbia.edu your graduation year and degree.  
• Group discounts are available for organizations sending 5+ participants. Please contact us directly at sharp_program@cumc.columbia.edu for more information.  

If paying by internal transfer within Columbia, submit this Columbia Internal Transfer Request form (link to form coming soon) to receive further instructions. Please note: filling out this form is not the same as registering for a training and does not guarantee a training seat.

If you would prefer to pay by invoice/check, please submit this Invoice Request form (link to form coming soon) to receive further instructions. Please note: filling out this form is not the same as registering for a training and does not guarantee a training seat.

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 less than 14 days 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, gather registration details, and provide materials. Should the substitute fall within a different registration category (e.g. you are a faculty member and they are a postdoc), 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.