Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentations

Abstract Microbial communities affect several natural processes, from nutrient cycling to human health. Nevertheless, the mechanisms of interaction between microorganisms and their influence on community functions are not well understood. Sugarcane ethanol fermentations represent a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. In this study, we dissected the microbial interactions in sugarcane ethanol fermentation by combinatorically reconstituting every possible combination of species, comprising approximately 80% of the biodiversity in terms of relative abundance. Functional landscape analysis showed that higher-order interactions counterbalance the negative effect of pairwise interactions on ethanol yield. In addition, we found that Lactobacillus amylovorus improves the yeast growth rate and ethanol yield by cross-feeding acetaldehyde, as shown by flux balance analysis and laboratory experiments. Our results suggest that Lactobacillus amylovorus could be considered an industrial probiotic with the potential to improve sugarcane ethanol fermentation yields by more than 10%. These data highlight the biotechnological importance of comprehensively studying microbial communities and could be extended to other microbial systems with relevance to human health and the environment.