An enhanced domestication method for uncultured bacteria

When environmental bacteria transition to laboratory conditions a process termed domestication the shift from the native environment to a culture medium often reduces cell viability. Consequently most bacteria remain uncultivated using standard techniques leaving the majority of diversity unexplored. Here we introduce an enhanced domestication (EDEN) method for bacterial cultivation which acclimatises environmental bacteria to culture media through a controlled and gradual exposure. To facilitate EDEN we develop a 3D-printable microwell plate incorporating growth chambers exposed to a continuous flow media reservoir. Using metagenomic sequencing we show that EDEN-acclimatised bacterial communities grow as distinct populations with significantly greater diversity and likely-uncultivated taxa compared with standard cultivation methods. In addition EDEN-acclimatised bacterial monocultures show a threefold increase in diversity and a tenfold increase in likely-uncultivated taxa. EDEN also achieves a significant increase in cultivating agarose-encapsulated microcolonies. Finally we demonstrate the utility of EDEN for drug discovery by isolating a novel bacteria exhibiting potent antimicrobial activity against both Gram-negative and Gram-positive multi-drug resistant pathogens.