What is it about?

Taxonomic and functional annotation studies of metagenomic reads are nowadays more on trend. Phylogenetic diversity analysis, on the contrary, got more out of fashion, hence less microbiome studies use it nowadays to study microbial communities. However, the study of microbial communities is heavily hindered by its compositional nature, and while taxonomic and functional annotation tend to suffer more from compositionality's drawbacks, phylogenetic diversity analysis is more robust to it. So, we pulled PD out of the drawer, and used it to analyze our dataset. We found signals of aging, piglets' intrinsic factors such as day of birth, breed, and litter effects, and mild effects of intramuscularly administered antibiotic, and oral probiotic, on the gut microbiome of post-weaning piglets.

Featured Image

Why is it important?

Our study is important because it's a reminder to the scientific community of the strength of phylogenetic diversity analysis to study microbial communities. From a biological signal perspective, our study is a reminder of host intrinsic factors as confounding factors to the sought signal.


I hope this article is a reminder of the compositionality drawbacks of microbial communities studies and it inspires other researchers to make use of phylogenetic diversity analysis.

Daniela Gaio
University of Zurich

Read the Original

This page is a summary of: Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig, PLoS ONE, June 2022, PLOS, DOI: 10.1371/journal.pone.0270372.
You can read the full text:

Open access logo



The following have contributed to this page