Utilizing “Omics” Tools to Study the Complex Gut Ecosystem

Abstract

In a healthy gut, the immune system tolerates a diverse microbial commensal community avoiding inappropriate inflammation responses and minimizing the presence of pathogens. When the balance between host and microbes is disrupted, risk for disease increases. There is mounting evidence that microbial dysbiosis is a substantial risk factor for common gut diseases including IBS, IBD and colorectal cancer. Understanding this dysbiosis is challenging because of the extraordinary complexity of the gut ecosystem and the tremendous variability between healthy individuals in the taxa that make up the human microbiome. Advances in technology, especially sequencing technology, are beginning to allow for a full description of this complexity. In this review, we consider how new "omics" technology can be applied to the study of the gut ecosystem in human and animal models with special consideration given to factors that should be considered in the design of experiments and clinical trials.

Crosstalk Between the Gut Microbiota and the Brain: An Update on Neuroimaging Findings

“…Furthermore, additional measures of inflammation, immune activation, neurotransmitters, neuromodulators, microbial metabolomics, and intestinal permeability, motility and visceral sensitivity will be useful for elucidating the interactions between the gut and brain. Future studies should also aim to integrate multiple “omics” techniques (69), such as metabolomics and proteomics, to generate a complete picture of host and microbial pathways (Figure 1).…”

Cellular respiration: replicating in vivo systems biology for in vitro exploration of human exposome, microbiome, and disease pathogenesis biomarkers

“…The human body encompasses about 10-times as many bacterial cells as human cells. Therefore, it is reasonable to assume that this 'alien microbiome' (comprised of cells with non-human DNA) influences what is generally presumed to be human-only metabolism (Possemiers et al 2009, Fodor 2014. The gut, pulmonary, dermal, and genito-urinary microbes can be tested separately for metabolic products using isolated strains to determine their contributions to overall biomarker profile of the intact organism (animal or human).…”

The advancements of genomics and data integration in sarcoma research

“…Many researchers are also exploiting the evolutionary nature of cancer from a complex ecosystems perspective, which may shed some light as to how different molecular mechanisms allow cells to fill different necessary niches for cancer adaptation and progression [125][126][127][128][129] .…”