Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage

Abstract

BackgroundLactobacillus 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.ResultsWhole-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.ConclusionsOur 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.

Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

“…The same phenomenon was observed in Lactobacillus buchneri strains. Nethery et al ( 57 ) suggested that the presence of self-targeting spacers indicates phage escape from immune attack by the CRISPR-Cas system during infection. Alternatively, Nobrega et al ( 58 ) proposed another interpretation that CRISPR-Cas systems accidentally acquire these spacers after these prophages have already been integrated into the bacterial hosts.…”

Advantages and disadvantages of non‐starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics

“…WGS provides a comprehensive picture of all the genome content, allowing the identification of virulence, antibiotic resistance or probiotic/technological‐related determinants (Dong et al., 2019; Mannaa et al., 2019; Nethery et al., 2019; Rodrigo‐Torres et al., 2019; Tyson et al., 2018; Waseem et al., 2017). The quick and reliable identification of microbes responsible for foodborne outbreaks (Gerner‐Smidt et al., 2019) may lead to fast food recalls, contributing to prevent further health risks for the consumers.…”

Comparative genomics of Leuconostoc lactis strains isolated from human gastrointestinal system and fermented foods microbiomes

“…Even though Ln. lactis genome is proportionally small; it has to maintain the capability of rapid and continuous evolution with its essential ecosystem via horizontal gene transfer of plasmids or transduction by phage infectivity [12][13][14]. Moreover, in order to maintain its viability and grow in a changing and highly specific ecosystem, LAB has to balance the maintenance of a strong immune system against bacteriophages, transmissible DNA elements, exogenous plasmids or transposases [14][15][16].…”