An enhanced domestication method for uncultured bacteria

Abstract When environmental bacteria transition to laboratory conditions, a process termed domestication, the shift from the native habitat to a culture medium often reduces cell cultivability. Consequently, most bacteria remain uncultured using standard techniques, leaving the majority of their 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 integrated with a continuous-flow media reservoir. Using amplicon sequencing, we show that EDEN-acclimatised bacterial polycultures grow as distinct populations with significantly greater diversity and likely-uncultured taxa compared with standard cultivation methods. Similarly, EDEN-acclimatised bacterial monocultures show threefold greater diversity and tenfold more likely-uncultured taxa. EDEN also doubled the cultivability of agarose-encapsulated microcolonies. Finally, we demonstrate the utility of EDEN by isolating a previously uncultured bacterium exhibiting broad-spectrum antimicrobial activity against drug-resistant pathogens.