Track alpha and beta diversity dynamics of viral/microbial communities

Overview

Teaching: 120 min
Exercises: 0 min

Questions

• What is compositional data?

• How to do compositional data analysis?

• What is Hill Number?

Objectives

• Compositionality

• Hill number of alpha divesity

Basic ecology

Watching:

• Alpha Diversity Microbiome Discovery 7: Alpha Diversity
• Beta Diversity Microbiome Discovery 8: Beta Diversity

Compositional data and analysis

Compositionality

• Definition: a D-part composition is positive real vector of D components describing the parts of some whole. It only carries relative information between the parts.
• Three principles of compositional data (analysis)
  • Scale invariance
  • Permutation invariance
  • Subcompositional coherence

Reading:

• Microbiome Datasets Are Compositional: And This Is Not Optional (Gregory B. Gloor et al fmicb 2017)
• A field guide for the compositional analysis of any-omics data (Thomas P Quinn et al GigaScience 2019)
• Exploring MGS Bias (Ryan Moore)

Watching:

• Compositionality Microbiome Discovery 19: Compositionality
• Compositional data analysis Compositional Data Analysis Approaches to Improve Microbiome Studies: from Collection to Conclusions

Alpha diversity

Reading:

• Estimating diversity in networked ecological communities Amy D Willis et al Biostatistics 2022
• Hill number as a bacterial diversity measure framework with high-throughput sequence data Sanghoon Kang et al nature 2016

Differential abundance and correlations

Reading:

• Understanding sequencing data as compositions: an outlook and review Thomas P Quinn et al bioinformatics 2018
• propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysiss Thomas P. Quinn et al Biostatistics 2022

Acknowledgement

The content and material of the course today is heavily based on the MCAW-EPSCoR Microbial Community Analysis Workshop by Viral Ecology and Informatics Lab in the University of Delaware.

Key Points

• Next Generation Sequencing data is compositional and should be analyzed using compositional data analysis methods

• Hill number is linear and more intuitive than original alpha diversity measures