Genomic insights into persistence, antibiotic resistance, and intraspecific diversity of lactic acid bacterial contaminants at corn dry-grind fuel ethanol facilities

Authors: Qi, Yunci; PATEL, MAULIK - Oak Ridge Institute For Science And Education (ORISE); Lu, Shao; Skory, Christopher

Submitted to: Journal of Bioresource Technology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/16/2025
Publication Date: 6/20/2025
Citation: Qi, Y., Patel, M.H., Lu, S.Y., Skory, C.D. 2025. Genomic insights into persistence, antibiotic resistance, and intraspecific diversity of lactic acid bacterial contaminants at corn dry-grind fuel ethanol facilities. Journal of Bioresource Technology. https://doi.org/10.1016/j.biortech.2025.132836.
DOI: https://doi.org/10.1016/j.biortech.2025.132836

Interpretive Summary: Bacterial contamination is a common problem in commercial fuel ethanol fermentation facilities resulting in lowered ethanol yield and profits. These contaminants are difficult to control and persist even with application of antibiotics and costly facility shutdowns for cleaning. In this project, ARS scientists from Peoria, Illinois, sequenced the genomes of over 100 bacterial strains collected from a U.S. Midwest corn dry-grind fuel ethanol production facility. These strains were specifically selected based on their ability to inhibit production of ethanol by brewer’s yeast. Analyzing these genomes helps researchers to better understand how these bacteria have adapted to the fuel ethanol fermenter environment, how they gained resistance to the commonly used antibiotic virginiamycin, and the difference between the worst contaminants and their relatively harmless relatives. This research is important for helping researchers develop better methods to control contamination during fuel ethanol production.

Technical Abstract: During fuel ethanol production, fermenter tanks are persistently contaminated by lactic acid bacteria (LAB), lowering ethanol yields and causing costly shutdowns for cleaning. In this study, whole-genome sequencing was conducted for 156 Lactiplantibacillus plantarum, Levilactobacillus brevis, Limosilactobacillus fermentum, and Limosilactobacillus mucosae isolates previously obtained in a two-year longitudinal study at a U.S. Midwest corn dry-grind fuel ethanol production facility. Striking similarity between genomes for isolates collected during different years reveal the strong ability of LAB strains to persist in bioethanol fermentation facilities. Furthermore, comparison of bioethanol contaminant genomes and previously published genomes in the same species from other environments showed a smaller, closed pangenome for bioethanol contaminants, indicating their specialization for this niche. Additionally, 39 genomes contained a putative plasmid or transposable element encoding for resistance to the antibiotic virginiamycin, frequently used by fermentation facilities to control LAB contamination. Finally, comparison of L. fermentum isolates that strongly inhibited Saccharomyces cerevisiae fermentation and less inhibitory isolates suggest there may be genetic and metabolic changes underlying these differences. To our knowledge, this study represents the first large-scale genomic analysis for LAB contaminants of bioethanol production, providing new insights into the biology of industrial microbial contaminants that have enormous economic impact.