The fate of antagonistic microorganisms and antimicrobial substances during anaerobic digestion of pig and dairy manure

► We studied the effects of anaerobic digestion (AD) on the characteristics of pig manure and dairy manure that are related to disease suppressiveness. ► AD had no significant impact on the numbers of fluorescent pseudomonads and Bacillus sp. ► Total phenolic, VFA and total sugar in manures were decreased by AD, while the contents of humic substance and ammonia were increased. ► FTIR spectra of the manures are similar to humin while spectra of anaerobically digested slurry (ADS) are similar to humic acid and fulvic acid. ► AD had different influences on the content of amino acid in pig manure and dairy manure, results obtained indicated that the key inhibitory factors of ADS might be attributed to ammonia and humic substances.