The drug discovery process is a starving machine requiring constant feeding with new chemical compounds. Synthetic or natural scaffolds: what are the best sources? While synthetic molecules are rapidly generated by combinatorial chemistry, they show lower chemical diversity than their natural counterparts. A significant fraction of known natural products is issued from microbial secondary metabolism; however, more than 95% of bacterial organisms remain unexploited as a source of active chemical compounds due to their cultivation difficulties. Recent technological advances in metagenomics have provided reliable access to chemicals of these hidden bugs, thus opening up new opportunities for feeding the machine.