coli O157:H7, compost samples were individually treated with antimicrobials that targeted gram-positive bacteria (crystal violet), gram-negative bacteria (streptomycin) and eukaryotic species (amphotericin B and cycloheximide) (Fig. 2). The survival of E. coli O157:H7 improved significantly in the presence of the eukaryotic inhibitor cycloheximide and the CFU mL−1 remained relatively constant throughout

the incubation period. No significant differences were observed in the reduction of E. coli O157:H7 compared with the control in the presence of crystal violet, amphotericin B or streptomycin. Statistical comparisons between the slope means between each treatment and the control yielded P=0.578 (crystal violet), P=0.258 (streptomycin), P=0.993 (amphotericin B) and P=0.002 (cycloheximide). These data suggest that cycloheximide-sensitive eukaryotic species were primarily

responsible for the observed decline of E. coli BYL719 Buparlisib order O157:H7. DGGE analysis was used to monitor the shifts in populations in compost samples (Fig. 3). At 25 °C, the banding patterns of fungal species remained similar between cycloheximide-treated and -untreated samples, except for some bands that repeatedly appeared on day 8 and day 10 of the cycloheximide-treated samples. In contrast, a dramatic shift in protist populations was observed at 25 °C between untreated and treated samples (Fig. 3). Notably, none of the prominent bands seen in control compost samples from days 4 to 12 were observed in the lanes for the cycloheximide-treated samples. Protist clone libraries were created from cycloheximide-treated and -untreated compost samples that were incubated at 25 °C.

This set of samples was chosen for further analysis because DGGE results suggested that protists play a more significant role in E. coli O157:H7 decline in our compost model than the fungal species. The numbers of OTUs (observed richness) present in the control library cAMP at day 0 were 19 compared with 17 OTUs in the cycloheximide-treated library (Table 1). The Chao1 estimator (predicted richness) estimated that the two day 0 libraries had 28 and 35 OTUs, respectively. Therefore, we estimate that 68% and 49% of the species present in the control and the cycloheximide-treated samples at day 0 were covered by the clone libraries. libshuff was used to determine the differences between the clone libraries at each time point. Pairwise comparisons between the two day 0 libraries generated P values of 0.58 and 0.67, suggesting that the two libraries are statistically similar (Fig. 4). Similar analyses were performed on days 6, 8 and 12 samples and all control libraries were statistically different from the corresponding cycloheximide-treated sample libraries (Fig. 4). From the blast analysis, days 0, 8 and 12 control libraries were largely composed of the ciliophora Arcuospathidium cultriforme (Day 0) and Onychodromopsis flexilis (Days 8 and 12).