[Paper Review] ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization

Yang Chen, Jiahao Mai+4 more|arXiv (Cornell University)|Mar 18, 2023

Gut microbiota and healthBiochemistry, Genetics and Molecular Biology7 citations

TL;DR

ggpicrust2 is an R package that enables extensive differential abundance analyses and publishable visualizations for PICRUSt2 predicted functional profiles.

ABSTRACT

Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA analysis is one of the most popular and a cost-effective method to profile the microbial compositions, marker-gene sequencing cannot provide direct information about the functional genes that are present in the genomes of community members. Bioinformatic tools have been developed to predict microbiome function with 16S rRNA gene data. Among them, PICRUSt2 has become one of the most popular functional profile prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference tools are available to test the differences in pathway abundances between comparison groups. We have developed ggpicrust2, an R package, to do extensive differential abundance(DA) analyses and provide publishable visualization to highlight the signals.

Motivation & Objective

• Motivate the need to move beyond taxonomic only analyses to functional profiling in microbiome studies.
• Provide a tool to test differences in pathway abundances between comparison groups using PICRUSt2 predictions.
• Offer publishable visualization capabilities to highlight signals in functional profiles.
• Leverage PICRUSt2 outputs to enable robust downstream differential analysis in R.

Proposed method

• Integrates PICRUSt2 predicted functional profiles into an R framework.
• Implements extensive differential abundance analyses for functional pathways.
• Provides statistical testing capabilities to compare pathway abundances across groups.
• Includes visualization functions suitable for publication to highlight significant signals.
• Designed to facilitate analysis and interpretation of microbiome functional profiles.
• Relying on established PICRUSt2 predictions as input for downstream inference.

Experimental results

Research questions

• RQ1 Can ggpicrust2 reliably detect differences in pathway abundances between predefined sample groups using PICRUSt2 predictions?
• RQ2 What are the most informative visualizations for communicating differential signals in predicted functional profiles?
• RQ3 How does ggpicrust2 facilitate integration of functional profiling with downstream microbiome analyses in R?

Key findings

• ggpicrust2 enables extensive differential abundance analyses on PICRUSt2 predicted functional profiles.
• The package provides visualization tools intended to produce publishable figures highlighting signals.
• It focuses on functional pathway-level inference derived from 16S rRNA data via PICRUSt2.
• The work addresses the need for state-of-the-art inference tools for pathway abundance differences.
• The package aims to fill gaps in tools for testing differences in functional profiles rather than just taxa abundances.