NTB-T02

• Date: Thursday, September 15th
• Time: 17:00 to 20:00 CEST
• Format: Virtual

• Violeta Larios-Serrato, Winter Genomics (México)
• Maira Nayeli Luis-Vargas, Winter Genomics (México)
• Karla Ruiz, Winter Genomics (México)
• Kenya Contreras, Winter Genomics (México) – Helper

This tutorial will cover the essential aspects of the microbiome alpha diversity: rarefaction and some alpha diversity metrics. Alpha diversity measures the microbiome diversity in individual samples. However, some other metrics (i.e. Shannon, Inverse Simpson and Pielou) are used to study the different properties of the microbiome communities. We will use R and Rstudio to learn and identify whether to rarefy and calculate other metrics to compare samples (richness, diversity, dominance) and plot the results in great charts.

Life sciences professionals interested in microbiome 16S and/or metabarcoding projects.

• Basic knowledge of R and RStudio, like data frames, file import and package installation. 
• Basic principles of sequencing.

20

R and RStudio (at least 4.0 version) should be installed. Attendees will need a desktop or laptop computer (not tablets or notebook-type laptops) with at least 4 GB RAM. 

• Project description: in this topic, we will explain how a 16S rRNA microbiome project is performed, starting from the experimental part to the bioinformatic data analysis. (15 min)
• File import: the student will learn how to import datasets that will be used during the workshop. (15 min)
• Rarefaction: explanation of what rarefaction is, how the algorithm works and its implications in microbiome 16S rRNA analyses. We will construct a rarefaction curve of the data using R programming language. (1h)
• Alpha diversity index: creation of the following graphs that are commonly used that facilitate the analysis of 16S microbiome data (1.5h)
  • Dot plots
  • Box plots
  • Alpha diversity metrics (Shannon, Simpson, Pielou)
  • Hypothesis tests

TIME	CONTENT
17:00 – 17:15	Project description. In this topic, we will explain how a 16S rRNA microbiome project is performed, starting from the experimental part to the bioinformatic data analysis
17:15 – 17:30	File import. The student will learn how to import datasets that will be used during the workshop
17:30 – 18:30	Rarefaction. Explanation of what rarefaction is, how the algorithm works and its implications in microbiome 16S rRNA analyses. We will construct a rarefaction curve of the data using R programming language
18:30 – 20:00	Alpha diversity. Creation of the following graphs that are commonly used that facilitate the analysis of 16S microbiome data: – Dot plots – Box plots – Alpha diversity metrics (Shannon, Simpson, Pielou) – Hypothesis tests