Phylogenetics and the human microbiome

TL;DR

This paper reviews the application of phylogenetics to the human microbiome, highlighting methodological differences, current challenges, and the importance of genetic sequencing data in microbiome research.

Contribution

It provides a comprehensive overview of phylogenetic methods tailored to microbiome analysis and discusses unique challenges faced in this emerging field.

Findings

Phylogenetics plays a crucial role in microbiome analysis.

Methodological differences exist between microbiome phylogenetics and traditional applications.

Current challenges include data complexity and methodological adaptation.

Abstract

The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this paper I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.