Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. In this study, we dissect 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 shows that higher-order interactions counterbalance the negative effect of pairwise interactions on ethanol yield. In addition, we find 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 a beneficial bacterium with the potential to improve sugarcane ethanol fermentation yields by almost 3%. 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. Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production.