Project description:We have developed a microfluidics-based in vitro model of the human gut allowing co-culture of human and microbial cells and subsequent multi-omic assessment of the effect of the co-culture on the host transcriptome. We compare the transcriptional changes induced in the human epithelial cell line, Caco-2 after co-culture with Lactobacillus rhamnosus GG or a consortium of Lactobacillus rhamnosus GG and Bacteroides caccae.
Project description:The data set consist of three different sources. 1) All files with ecoli_* derive from a pure culture of Escherichia coli K-12 (MG1655). 2) All files with SIHUMI_standard_* derive from a mixed culture of 8 bacteria (SIHUMIx) Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Clostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655) and Lactobacillus plantarum (DSMZ 20174). A standard proteomic protocol was used for purification. 3) All files with SIHUMI_small_* derive from the same bacteria culture as second source in contrast a variety of different proteomic protocols were used to enhance enrichment of small (<100 AS) Proteins. The goal of the project was to design a workflow to quickly prioritize novel protein candidates. The workflow was designed to be robust in a meta-omics context and facilitate the integration of transcriptomic and other information on a genomic level. The MS-data from the first source was used to test the workflow under well controlled conditions, namely in pure culture and near complete annotation. The workflow was used with data from the second source to see if good results can be produced in a mixed culture. To enhance the chances of finding novel proteins we incorporated the data from the third source.
Project description:We used a whole-genome microarray based on the sequenced strain Lactobacillus sakei 23K to study ribose catabolism in three Lactobacillus sakei strains by screening for differentially expressed genes when grown on ribose compared to glucose
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with oleuropein. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile shows that Lactobacillus plantarum WCFS1 adapts its metabolic capacity to acquire certain carbohydrates and repress the expression of genes involved in fatty acid biosyntheis. The transcriptomic datasets also revealed the downregulation of genes related to the biosynthesis of capsular polysaccharides and genes coding for ABC-type transporters. In addition, induction of oligopeptide permeases is also part of the response of Lactobacillus plantarum WCFS1 to oleuropein.
