Microbiome Data Analysis in Population-based Studies [ESP81]

Detailed information about this course:

Description

Faculty: Carolina Medina-Gomez, PhD, Luba Pardo-Cortes, PhD, Robert Kraaij, PhD & others

Our understanding of the link between the human microbiome and health outcomes is rapidly expanding. The microbial communities that inhabit the human body affect cellular responses and shape many aspects of our physiology, playing a critical role in health and disease processes. From an epidemiological perspective, microbiome data analysis aims at elucidating the composition of microbial communities, their variation in response to environmental triggers and ultimately, their involvement in human health outcomes in the population. Thanks to the advances in next-generation sequencing technology, microbiome profiling is now within reach of large epidemiological studies, bringing up new challenges for the analysis of microbiome data. This course seeks to provide students with their first experience with real microbiome datasets, giving them the opportunity to learn about quality control, prepare datasets for analysis, and finally, carry out typical analytical tasks, such as comparing microbial diversity and composition, clustering samples and computing associations. Uniquely, this course will also cover aspects of study design offering examples for population-based studies on gut, oral, vaginal and skin microbiome studies. The course will comprise theoretical lectures (by local experts and guest speakers) together with hands-on interactive practical sessions.

Participants of this course should be familiar or become familiar with R-programming language, before the start of the course.

Topics covered:

• Research questions and design of a microbiome study
• Technical and analytical applications for the analysis of gut, oral, vaginal and skin microbiome.
• Sequencing techniques, data types (16S, metagenomics)
• Sample size and power in context of multidimensional and dynamic microbiome data
• Creation and pre-processing of microbiome data
• Estimating microbial evenness and diversity
• Testing differential "relative" and "absolute" abundance, including compositional approaches
• Association analysis of microbiome data in relation to health outcomes in human populations
• Critical review of literature and real-life examples of disease (Acne, caries/periodontitis, diabetes, vaginosis)

Objectives

At the end of the course participants will be able to:
• Recognize the role of microbiome determinants in human health and disease processes
• Get acquainted with the methodology used for microbiome research in population-based settings
• Draw research questions and appraise the properties of microbiome study design
• Characterize methods used to sample the microbiome across distinct bodily systems
• Describe the process of microbiome dataset creation and quality control
• Understand how to extract species and function counts from sequencing data
• Comprehend the definitions of microbiome richness, evenness and diversity
• Correlate diversity and microbial composition with health and disease outcomes
• Understand how to perform and interpret associations with taxonomic features

Participant profile

Healthcare professionals, clinical and fundamental researchers working with microbiome profiling (e.g., skin, oral, gut, vaginal) and health and disease outcomes within population—based settings or planning to carry-out a project using these techniques and approaches.

Assessment

Attendance