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Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage.

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.

SUBMITTER: Nethery MA

PROVIDER: S-EPMC6881996 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The objective of this study was to assess the impact of Saccharomyces cerevisiae in combination with Lactobacillus buchneri on the fermentation characteristics, aerobic stability, nutritive value, and microbial communities of corn silage. Whole crop corn (39% DM) was either uninoculated (Control) or inoculated with S. cerevisiae and L. buchneri at the following concentrations: S. cerevisiae 104 cfu/g fresh forage (S4), S. cerevisiae 105 cfu/g (S5), S. cerevisiae 104 cfu/g + L. buchneri 105 cfu/g (S4L5), and S. cerevisiae 105 cfu/g + L. buchneri 104 cfu/g (S5L4), and ensiled in mini silos for 118 d, followed by 7 d of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages. Saccharomyces cerevisiae, L. buchneri, and total yeast, fungal, and bacterial communities in silage were estimated using quantitative PCR. Composition of bacterial and fungal communities during ensiling and aerobic exposure was measured using 16S rDNA and ITS sequencing, respectively. In the first 7 d of ensiling, the concentration of lactic acid rapidly increased (P < 0.01) in all silages, with the pH declining to 4.0 (P < 0.001) and thereafter remaining stable (P = 0.23). Although S4L5 contained a higher (P = 0.03) concentration of acetic acid than Control, other fermentation characteristics were did not differ among terminal silages. Inoculation with S. cerevisiae had no detrimental effect on the aerobic stability of silage, whereas L. buchneri did not prevent spoilage as the pH across all silages averaged 8.0 after 7 d of aerobic exposure. Total yeast (P = 0.42), bacterial (P = 0.13), and fungal (P = 0.89) communities were not altered by the inoculants after ensiling or aerobic exposure. Sequencing identified temporal shifts of bacterial and fungal communities during ensiling and aerobic exposure. Concentrations of S. cerevisiae and L. buchneri in all inoculated silages remained greater (P < 0.01) than Control after ensiling, with numbers of S. cerevisiae increasing after 7 d of aerobic exposure. Bacterial communities in silages inoculated with S. cerevisiae and L. buchneri clustered separately from other silages, an observation that was not apparent for fungal communities. Our findings suggest that aerobic exposure could potentially increase the abundance of S. cerevisiae with probiotic properties in corn silage just prior to feeding.

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Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage.

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