Figure 5.
Harmonizing amplicon and shotgun metagenomic data
(A) The principal coordinate analysis (PCoA) Emperor plot of the harmonized ASV/genome Greengenes 2 weighted UniFrac distances with both the amplicon and shotgun data analyzed using the Greengenes 2 database (n = 1,772 subjects; 3,544 data points) is shown.
(B) An Emperor plot using unweighted UniFrac, which only assesses for presence-absence of taxa, is shown. For both Emperor plots, the PERMANOVA results for the platform and subject are shown in the lower right-hand corner.
(C) A logistic regression forest plot is shown that considers three participant characteristics within the GOLD cohort: sex (men vs. women), obesity (BMI 18.5–25 vs. >30), and relocation (US-born vs. recent immigrants, i.e. those that immigrated after 55 years of age). Each of the three main outcomes is modeled using the ratio of the two top bacterial predictors based on ANCOM W-stat (see Figure S2). Each of the models is adjusted for age, collection center, Hispanic background, and healthy eating index (AHEI2010). Each point and associated bar represent the exponentiated beta coefficient (i.e., OR) and the associated 95% and 90% confidence intervals (thinner and thicker lines, respectively). Color of bars indicates the dataset used to model the outcomes: green represents the original 16S sequencing set; blue indicates the full shotgun set (samples overlapping with 16S and those unique to shotgun analysis); and yellow represents a combination between the original 16S amplicon set and the newly sequenced shotgun set (i.e., shotgun samples that do not overlap with16S). Numbers to the right of the forest plot show the numerical values of the exponentiated beta coefficients, confidence intervals, and associated p values.