A study of the molecular mechanisms underlying the response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics

Doctoral thesis (2018)

The human gastrointestinal tract (GIT) microbiome plays essential roles in maintaining human health. A variety of diseases including colorectal cancer (CRC) are associated with microbial dysbiosis ... [more ▼]

The human gastrointestinal tract (GIT) microbiome plays essential roles in maintaining human health. A variety of diseases including colorectal cancer (CRC) are associated with microbial dysbiosis. Administration of microbial isolates associated with health benefits (e.g. prebiotics) together with specific dietary components (e.g., probiotics) may find application as supportive therapeutic options in the treatment and management of CRC. Although microbiome-modulating therapeutics hold great promise, such approaches are presently not formally integrated into treatment plans. To obtain better understanding of combined pre- and probiotic regimens in relation to CRC, the present study was dedicated to investigate the effects of selected prebiotics on the proliferation of CRC primary cells and conventional CRC-cell lines, the effects of prebiotics on the growth and metabolism of selected probiotic strains, and the combinatorial/synbiotic effects of selected pre- and probiotics on CRC proliferation. In addition, this work established the in vitro gut-on-a chip HuMiX model with a simulated high-fibre medium for co-culturing human and microbial cells in HuMiX. Furthermore, the anti-carcinogenic combinatorial effects of dietary fiber (e.g., prebiotics), and GIT bacteria (e.g., probiotics) were evaluated using human GIT transcriptomes and metabolomes in HuMiX. An integrated in vitro and in silico modeling approach was finally established to decipher the complex cross-talk between gut bacteria, dietary components and human host cells. My results demonstrate that in stark contrast to the individual pre- or probiotic treatments, the synbiotic regimen of the probiotic Lactobacillus rhamnosus GG and dietary fiber results in the down-regulation of genes involved in pro-carcinogenic pathways and drug resistance (e.g., ABC transporters) and reduced levels of the oncometabolite lactate. Distinct ratios of organic and short-chain fatty acids are produced during the simulated regimens. Treatment of primary CRC-derived cells with a molecular cocktail reflecting the synbiotic regimen attenuated self-renewal capacity. The developped integrated in vitro and in silico modelling approach provides mechanistic insights into the interplay between pre- and probiotics and elucidation of the microbiota-host relationship. In summary, my dissertation work illustrates the potential of HuMiX to be used for nutritional studies and more precisely for studying the underlying mechanisms of the effects that dietary components (e.g., dietary fiber) and probiotics have on CRC-derived cells. Thereby, this dissertation work highlights the potential for formulating efficacious dietary supplements including synbiotics in the context of therapeutic regimens for microbiome-linked diseases in the future. [less ▲]

A study of the molecular mechanisms underlying teh response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics

Poster (2017)

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

in Nature Biotechnology (2016)

Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of ... [more ▼]

Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available. AGORA reconstructions can integrate either metagenomic or 16S rRNA sequencing data sets to infer the metabolic diversity of microbial communities. AGORA reconstructions could provide a starting point for the generation of high-quality, manually curated metabolic reconstructions. AGORA is fully compatible with Recon 2, a comprehensive metabolic reconstruction of human metabolism, which will facilitate studies of host–microbiome interactions. [less ▲]

The human gut microbiome in health: establishment and resilience of microbiota over a lifetime

in Environmental Microbiology (2016), 18(7), 21032116

With technological advances in culture-independent molecular methods, we are uncovering a new facet of our natural history by accounting for the vast diversity of microbial life which colonizes the human ... [more ▼]

With technological advances in culture-independent molecular methods, we are uncovering a new facet of our natural history by accounting for the vast diversity of microbial life which colonizes the human body. The human microbiome contributes functional genes and metabolites which affect human physiology and are, therefore, considered an important factor for maintaining health. Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various body habitats, most notably within the gastrointestinal tract (GIT). Relatively high levels of variation have been described across different stages of life and geographical locations for the GIT microbiome. These observations may prove helpful for the future contextualization of patterns in other body habitats especially in relation to identifying generalizable trends over human lifetime. Given the large degree of complexity and variability, a key challenge will be how to define baseline healthy microbiomes and how to identify features which reflect deviations therefrom in the future. In this context, metagenomics and functional omics will likely play a central role as they will allow resolution of microbiome-conferred functionalities associated with health. Such information will be vital for formulating therapeutic interventions aimed at managing microbiota-mediated health particularly in the GIT over the course of a human lifetime. [less ▲]