Response rate to probiotic treatment is contingent upon species richness
REGRESSION
We next computed alpha diversity using Shannon, Simpson, and taxonomic richness metrics at the phylum, class, order, family, genus, and species levels for all samples. This was done using Wilcoxon tests to compare variation in each of these three metrics between baseline and endpoint for non-responders and responders as well as individuals in the placebo group who both did or did not improve without treatment. Responders were defined as all individuals who received treatment and experienced an increase in WBMs of ≥1. We did not see any association between response to treatment and Shannon or Simpson diversity.However, we found that baseline richness of multiple phylogenetic levels (family, order, class, and phylum, We next stress-tested the ability of richness to discriminate between responders and non-responders using both alternative modeling approaches and a different method for quantifying taxonomic abundance within metagenomes (Kraken2/Bracken as opposed to MetaPhlAn3). We defined responders as individuals who received treatment and experienced an increase in WBMs of ≥1. In addition, to account for potential confounding factors, we tested the association between richness at each phylogenetic level and responder status using a logistic regression approach adjusted for baseline WBMs, sex, and age. The association between responder status and richness was still either significant or trending for all groups (