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Whole Genome Sequencing and Comparison of Potentially Probiotic Lactobacillus Strains

Abraham, Aaron
Abstract
Lactobacillus is a well-known and ubiquitous genus of bacteria, many species of which are probiotic in nature. While many lactobacilli have been characterized as being probiotic, the cellular mechanisms and genes exerting beneficial effects on the host have not been fully elucidated. The primary objective of this project is to characterize a potential new species of Lactobacillus isolated from prairie voles, with a specific emphasis on probiotic potential. This was assessed by comparative analysis with genomes of known probiotic species of Lactobacillus to determine the presence of genes related to probiosis. This work is based on generating whole genome draft sequences of the vole Lactobacillus strains. The Nextera XT DNA Library Prep protocol was used in conjunction with the Illumina MiSeq system to sequence the samples. The Qiagen CLC Genomics Workbench was employed for de novo assembly of paired sequence reads into sequence contigs. The contig numbers obtained for the Lactobacillus strain PV017, PV019, PV025, PV034, PV037, and PV039 genomes were 53, 42, 54, 109, 164, 90, , respectively. Rapid Annotation using Subsystem Technology (RAST) was used to annotate the draft genomes and identify protein-encoding genes related to potential probiotic characteristics such as adhesion, D-alanylation of lipoteichoic acid, and bile hydrolysis. Psi-Blast queries were performed to determine the closest protein matches to those found in the six strains. Across all categories, PV034 had more distinctive results, indicating that is the most unique of the six strains. Potential directions for future studies include the improvement of the genome assemblies by using long-read sequencing across repetitive regions and functional characterization of probiotic candidate genes in vitro and in prairie voles to confirm probiotic effects.
Date
2018-05-01
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