Understanding microbial community dynamics to improve optimal microbiome selection

Abstract Background Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. Results Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. Conclusions The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.