Extended Data Fig. 4: FGFP DADA2 data summaries. | Nature Microbiology

Extended Data Fig. 4: FGFP DADA2 data summaries.

From: Genome-wide associations of human gut microbiome variation and implications for causal inference analyses

Extended Data Fig. 4

Rank ordered mean percent abundance (a) and prevalence (b) for each observed phylum, in the FGFP cohort. Prevalence is defined as the proportion of individuals in the cohort containing a rarefaction read assigned to a taxon, in this instance a phylum. Data for this plot can be found in Supplementary Table 3. (c) A scatter plot of the nMDS, β-diversity for the quality-controlled FGFP cohort. Individuals are colored by their defined enterotype, and boxplots illustrating the enterotype structure across the two nMDS (β-diversity) axes are presented. The stress level, of forcing the individual level data into two axes, in the nMDS analysis is presented in the lower right-hand corner of the scatter plot. Dashed lines are equidistant guidelines. Each box plot presents the mean, first and third quantiles, and 95% confidence intervals of the data distribution. The sample sizes for each enterotype class is Bact1 = 793, Rum = 660, Bact2 = 418, Prev = 388, as presented in Supplementary Table 2.

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