Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries

Felipe Senne 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 and Morten Otto Alexander Sommer ()
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Felipe Senne Oliveira Lino: Technical University of Denmark
Shilpa Garg: Technical University of Denmark
Simone S. Li: Technical University of Denmark
Maria-Anna Misiakou: Technical University of Denmark
Kang Kang: Leibniz Institute for Natural Product Research and Infection Biology
Bruno Labate Vale da Costa: Escola de Engenharia de Alimentos da Universidade de Campinas
Tobias Svend-Aage Beyer-Pedersen: Technical University of Denmark
Thamiris Guerra Giacon: Departamento de Engenharia Química da Escola Politécnica da Universidade de São Paulo. Universidade de São Paulo
Thiago Olitta Basso: Departamento de Engenharia Química da Escola Politécnica da Universidade de São Paulo. Universidade de São Paulo
Gianni Panagiotou: Leibniz Institute for Natural Product Research and Infection Biology
Morten Otto Alexander Sommer: Technical University of Denmark

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Bioethanol is a sustainable energy alternative and can contribute to global greenhouse-gas emission reductions by over 60%. Its industrial production faces various bottlenecks, including sub-optimal efficiency resulting from bacteria. Broad-spectrum removal of these contaminants results in negligible gains, suggesting that the process is shaped by ecological interactions within the microbial community. Here, we survey the microbiome across all process steps at two biorefineries, over three timepoints in a production season. Leveraging shotgun metagenomics and cultivation-based approaches, we identify beneficial bacteria and find improved outcome when yeast-to-bacteria ratios increase during fermentation. We provide a microbial gene catalogue which reveals bacteria-specific pathways associated with performance. We also show that Limosilactobacillus fermentum overgrowth lowers production, with one strain reducing yield by ~5% in laboratory fermentations, potentially due to its metabolite profile. Temperature is found to be a major driver for strain-level dynamics. Improved microbial management strategies could unlock environmental and economic gains in this US $ 60 billion industry enabling its wider adoption.

Date: 2024
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DOI: 10.1038/s41467-024-49683-2

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