Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

: Armstrong George, Cantrell Kalen, Huang Shi, McDonald Daniel, Haiminen Niina, Carrieri Anna Paola, Zhu Qiyun, Gonzalez Antonio, McGrath Imran, Beck Kristen L, Hakim Daniel, Havulinna Aki S, Meric Guillaume, Niiranen Teemu, Lahti Leo, Salomaa Veikko, Jain Mohit, Inouye Michael, Swafford Austin D, Kim Ho-Cheol, Parida Laxmi, Vázquez-Baeza Yoshiki, Knight Rob

Publisher: Cold Spring Harbor Lab Press, Publications Dept

: 2021

: Genome Research

: GENOME RESEARCH

: GENOME RES

: 31

: 11

: 2131

: 2137

: 7

: 1088-9051

: 1549-5469

DOI: https://doi.org/10.1101/gr.275777.121

The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.