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This book is dealing with approaches to activate silent biosynthetic pathways and with the structure elucidation of fungal bioactive natural products focusing mainly on antibiotic and cytotoxic activities. As microbial interactions represent a significant factor for activation of silent biosynthetic pathways, an approach to maximize chemical diversity of endophytic fungi through coculture of fungi and bacteria was undertaken. In addition, inhibitors of histone deacetylases (HDAC) and DNA methyltransferases (DMATs) were also used to induce the secondary metabolite production of endophytic fungi. Moreover, investigation of bioactive metabolites from endophytic fungi under axenic culture conditions led to the isolation of the antibiotic compound neosartorin and of the new atropisomers diaporthemin A and B.