Fig. 2: Metabolic activity of drug-incubated single-microbiome cells measured by deuterium incorporation via SRS.
From: The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration
a, Representative SRS images of a mixture of 6 faecal samples incubated with the indicated drugs for 6 h, as depicted in Fig. 1. Top: %CDSRS distribution images. Bottom: C-H for biomass visualization (log scaled). %CDSRS scaling: minimum 0, maximum 20%. b, Single-cell %CDSRS values in each analysed sample (see also Supplementary Table 9). Violin plots illustrate summary statistics (median, first and third quartiles, with whiskers representing the minimum and maximum values within 1.5× the interquartile ranges from the first and third quartiles). Number of measured cells per sample are indicated on the x axis (cell n). **P = 0.0043, ***P = 5.2 × 10−12, **** P < 2 × 10−16, two-sided Wilcoxon test using ‘No drug’ as the reference. c, Drug-incubated faecal samples (at 6 h) were hybridized with fluorescently labelled oligonucleotide probes targeting E. coli (Ecol_268), Streptococcus and Lactococcus species (Strc_493), Clostridium sp900539375 (Clostridium sensu stricto 1, Clo_648), Ruminococcus bromii (Brom_2036), B. uniformis (Buni_1001) and P. dorei (Bado_374) (Supplementary Table 10). For each targeted group, top rows show representative images obtained by overlay of transmitted light (Trans) and fluorescence intensity (FISH). Bottom rows show the corresponding SRS images (displaying %CDSRS) for the FISH-targeted microbes (%CDSRS values of other microbes are not displayed for the sake of visibility). Scale bar, 10 μm. For a and c, we reproducibly detected analogous differences when measuring at least one additional batch of samples. d, Bubble plot denoting the fold change (FC, represented as log2FC) in activity levels (calculated as %CDSRS) for the taxa targeted by FISH and incubated with drugs relative to ‘No drug’ incubations at 6 h (Supplementary Table 11). e, Bubble plot denoting the FC in absolute abundances for the taxa targeted by FISH and incubated with drugs relative to ‘No drug’ incubations, as determined by DeSeq2 at 6 h (Supplementary Table 5). In d and e, P values were obtained using the Wald test and corrected for multiple testing using the Benjamini–Hochberg method.
