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Research Project: Improved Processes for the Preservation and Utilization of Vegetables, Including Cucumber, Sweetpotato, Cabbage, and Peppers to Produce Safe, High Quality Products with Reduced Energy Use and Waste

Location: Food Science Research

Title: Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage

item NETHERY, MATTHEW - North Carolina State University
item DAUGHTRY, KATHERYNE - North Carolina State University
item HENRIKSEN, EMILY - North Carolina State University
item Johanningsmeier, Suzanne
item BARRANGOU, RODOLPHE - North Carolina State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/12/2019
Publication Date: 11/27/2019
Citation: Nethery, M.A., Daughtry, K.V., Henriksen, E., Johanningsmeier, S.D., Barrangou, R. 2019. Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage. Biomed Central (BMC) Genomics. 20:902.

Interpretive Summary: Lactobacillus buchneri, a common non-pathogenic bacterium, can cause spoilage of fermented cucumbers and other foods due to its unique metabolism. Conversely, this microbe is beneficial to stabilizing silage and has been proposed for use in several biotechnological applications. Whole genome sequences of several unique strains of L. buchneri were generated and analyzed to provide a deeper understanding of the universal and strain specific genetic characteristics of this microbe.

Technical Abstract: Background: Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on the application. The ability to metabolize lactic acid into acetic acid and 1,2-propandiol makes L. buchneri invaluable to the ensiling process, however, this metabolic activity leads to spoilage in other applications, and is especially damaging to the cucumber fermentation industry. This study aims to augment our genomic understanding of L. buchneri in order to make better use of the species in a wide range of applicable industrial settings. Results: Whole-genome sequencing (WGS) was performed on seven phenotypically diverse strains isolated from spoiled, fermented cucumber and the ATCC type strain for L. buchneri, ATCC 4005. Here, we present our findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes, L. buchneri CD034 and NRRL B-30929. Overall, we see ~ 50% of all coding sequences are conserved across these ten strains. When these coding sequences are clustered by functional description, the strains appear to be enriched in mobile genetic elements, namely transposons. All isolates harbor at least one CRISPR-Cas system, and many contain putative prophage regions, some of which are targeted by the host’s own DNA-encoded spacer sequences. Conclusions: Our findings provide new insights into the genomics of L. buchneri through whole genome sequencing and subsequent characterization of genomic features, building a platform for future studies and identifying elements for potential strain manipulation or engineering.