Ammonia has effects on pathogens and it is usually used to sanitize sewage sludge (Ottoson et al., 2008). Inhibition by ammonia does not depend solely on the concentration of ammonia but it is, also, affected by the conditions of the AD process i.e., temperature and pH, these being the parameters able to modify the equilibrium between toxic-N and non-toxic-N fractions (Ottoson et al., 2008 and Scaglia et al., 2014). The toxic form of ammonia is represented by the free ammonia of which the presence depends, substantially, on the temperature, SKF 96365 and total ammonia concentration (TAN) (Scaglia et al., 2014). AD produces by itself a large amount of ammonia that because of the alkaline pH of the digestate is present in part as free ammonia exhibiting toxic effects (Scaglia et al., 2014). Literature has reported the positive effect of ammonia on pathogen reduction for the mesophilic process at TAN concentration of 6–9 g l− 1 (Ottoson et al., 2008). In effect data of Table 2 indicate a strong increase of the total ammonia content after AD, because of the degradation of organic molecules containing N (Ottoson et al., 2008). TAN ammonia content at the end of the MAD was, on average, 2.11 ± 0.69 g l− 1 (n = 15), to be compared with starting ammonia content of 1.5 ± 0.5 g l− 1 (n = 15), with an increase of TAN of 40% after MAD. TAN content in digestates was far from that reported by Ottoson et al. (2008) to be effective in reducing pathogen content. Nevertheless, by considering pH, TKN, TAN and temperature, toxic ammonia concentrations were calculated ( Scaglia et al., 2014). Results indicated, on average, a toxic ammonia content of digestates of 1.8 ± 1.2 g l− 1 (n = 15) (starting average value was of 0.05 ± 0.1 g l− 1; n = 15) that was much higher than that reported by Ottoson et al. (2008) affecting gram negative pathogens (E. coli, Fecal coliform, Enterobacteriaceae) survival, i.e. 0.42 g l− 1.