The toxicity of three pharmaceutical compounds (caffeine, sulfamethoxazole and carbamazepine) commonly found in municipal wastewater was evaluated by a simple respirometric procedure using mixed microbial culture enriched from activated sludge. Three (SP1, SP2, VM2) microbial cultures were used to assess whether or not the long term exposure to a toxicant could affect microbial resistance. The composition and diversity of bacterial communities were determined by targeting the hypervariable V6–V8 regions of the 16S ribosomal RNA gene using bar-coded pyrosequencing.