Extended Data Fig. 8: Changes in transcriptional activity in complex microbial communities in response to NAE treatment.

We used a linear model combining profiles of functional activity from both chemostats over time to identify gene families (KEGG orthologies) that were consistently differentially expressed under NAE treatment relative to DMSO controls (at the community level; total n=96 ranging from n=15 to 17 per treatment). The top 100 such orthologies ranked by mean absolute log-scaled fold change in relative expression are shown. Each of these orthologies was significantly differentially expressed under at least one treatment after correcting for multiple hypothesis testing. Pathway–treatment pairs with open circles had FDR q<0.2; those with closed circles had FDR q<0.05, while an “x” indicates that measurements were insufficient to perform the test (FDR q-values derived from nominal two-tailed p-values of the ‘treatment’ coefficient across per-orthology linear regression analyses). While trends were most significant under AEA treatment, effect sizes trended similarly under LEA and OEA treatment as well.