Industrial bioethanol production, crucial for sustainable energy, suffers from suboptimal efficiency due to bacterial contamination. This study investigates the microbiome across all process steps in two Brazilian biorefineries over three timepoints. Using shotgun metagenomics and cultivation, researchers identified beneficial and detrimental bacteria, linking improved outcomes to higher yeast-to-bacteria ratios. A microbial gene catalogue revealed bacteria-specific pathways affecting performance, with *Limosilactobacillus fermentum* overgrowth significantly lowering yields. Temperature emerged as a key driver of strain-level dynamics. Improved microbial management could significantly enhance this US $60 billion industry.

Felipe Senne de Oliveira Lino, Shilpa Garg, Simone S. Li, Maria-Anna Misiakou, Kang Kang, Bruno Labate Vale da Costa, Tobias Svend-Aage Beyer-Pedersen, Thamiris Guerra Giacon, Thiago Olitta Basso, Gianni Panagiotou, Morten Otto Alexander Sommer