Project description:Purpose: To understand the metabolic mechanism of Lactobacillus salivarius Ren in raffinose Methods: Samples of Lactobacillus salivarius Ren grown in glucose and raffinose were sequenced on the Illumina Hiseq platform. Three independent biological replicates were generated, including a total of six samples. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample. Overall design: Lactobacillus salivarius Ren is cultured in MRS medium with carbon source as glucose and raffinose
Project description:Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbor at least one megaplasmid which encodes functions contributing to contingency metabolism and environmental adaptation. RNA-seq transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel long and unusually abundant non-coding RNA (lancRNA) encoded by the megaplasmid and which represented more than 75% of total RNA-seq reads after depletion of ribosomal RNA species. The expression level of this 550 nt lancRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time, and was also expressed during intestinal transit in a mouse. This lancRNA sequence is specific to the L. salivarius species, however among 45 L. salivarius genomes analyzed, not all (only 34) harbored the sequence for the lancRNA. This lancRNA was produced in 27 tested L. salivarius strains but at strain-specific expression levels. High-level lancRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lancRNA identified altered expression levels of genes in a number of pathways but a definitive function of this new long non-coding RNA was not identified. This lancRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon. Overall design: L. salivarius UCC118 wild-type vs 2 mutants (ΔlancRNA and ΔlancRNA ΔHTH), in exponential and stationnary growth phases
Project description:This experiment compared the gene expression profiles of Lactobacillus salivarius UCC118 (wild type, control) and UCC118 with the SrtA gene deleted. Following exposure of both strains to Caco-2 epithelial cells.