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Extended Data Fig. 2 | Within-individual stability is a major driver
of microbiome differences across measurement types. a, PCoA and
t-SNE embeddings based on Bray–Curtis dissimilarity matrices from
stool species abundances, transcripts, proteins, and metabolites. Marginal
densities are shown for the PCoAs that show disease separation for
some measurements. In the t-SNEs, each subject has been assigned a
different hue, showing that small clusters generally represent individuals’
time courses, as inter-individual differences are the greatest driver
of microbiome variation across measurement types (Fig. 1f). Sample
counts are shown in Fig. 1b. b, Distributions of correlations between
functional profiles, captured as UniRef90^100 gene family abundances^73 ,
measured from paired metagenomes, metatranscriptomes, and
metaproteomes (see Methods). c, Human transcriptional expression was
mostly determined by biopsy location rather than IBD phenotype and
inflammation (n = 249 samples from 91 subjects). Ordination shows PCA
on gene expression levels normalized by library sizes and represented as
CPM. Ellipses indicate 95% confidence regions for the indicated sample
types. d, Principal coordinates plot (Bray–Curtis on OTU profiles) of
community profiles from biopsy samples shows that mucosal microbial
communities do not differ significantly by biopsy location (shape), unlike
human gene expression in epithelial tissue (Fig. 4b).