Fig. 1: Drug supplementation of faecal samples impacts biomass accumulation and microbiota composition.

a, Schematic representation of faecal sample incubations with the drugs entacapone (ENT) and loxapine (LOX). Samples from 6 different donors were mixed and supplemented with 2 different concentrations of each drug (Low and Hi). The H₂O control consisted of medium (in H₂O) without D₂O or DMSO. After 6 or 24 h of incubation, samples were collected for further analyses (Methods). All incubations were performed in triplicates. b, Total microbial cell loads in faecal sample incubations described in a at the start of the incubation (time = 0 h) and after 6 and 24 h, in sM9 medium. Total cell loads were assessed by flow cytometry and are presented in Supplementary Table 1. **P = 0.006, ***P = 0.00015, unpaired two-sided t-test with ‘No drug’ used as the reference. Data represent the mean ± s.e.m. of 3 incubation vials per condition. c,d, Relative (c) and absolute (d) genus abundance profiles of faecal microbial communities incubated for 6 or 24 h as described in b and assessed by 16S rRNA gene amplicon sequencing. Relative and absolute abundance data are presented in Supplementary Tables 3 and 4, respectively. The community composition at 0 h (inoculum) is also shown. All genera present at a relative abundance below 0.025 or absolute abundance below 6 × 10⁶ cells per ml were assigned to the category ‘Other’. Unclass, unclassified. Each bar represents the mean of triplicates. e, Heat map showing the absolute abundance, expressed in log₁₀(cells per ml + 1), of the 25 most abundant ASVs detected across all samples. Each column displays data from one replicate. f, MAGs with 16S rRNA gene sequences matching ASVs shown in e. MAGs were retrieved by metagenomic sequencing of the initial faecal samples using Oxford Nanopore sequencing (Methods and Supplementary Table 8). NA indicates no match of the ASV sequence to each MAG 16S rRNA gene sequence.