Figures & data
Figure 1. This illustrates the overlaps between two key groups of genes, in both humans and their gut bacteria, and key influences on these. While human genes determine key sensitivities, they are greatly impacted by the nature of the gut microbiome. The expression of human genes is impacted strongly by both diet and medication, and these effects might be beneficial or detrimental, depending upon their nature and the specific human genes involved in disease susceptibility. Inflammation, however caused, is likely to have an adverse effect. The gut microbiome is strongly influenced by early life nutrition, and breast feeding plays an important role. Antibiotics may be beneficial, but if used to excess, may be detrimental. Diet is also of key importance, and both probiotics and prebiotics are designed to benefit the gut microbiome.
Figure 2. Potential sequence of in vitro to in vivo studies, including the application of omics technologies. This flow diagram shows a potential approach, working from in vitro studies in tissue culture models, through in vivo studies in animals, to human clinical trials, with the application of omics technologies at several stages. (1) There is increasing use of high-throughput techniques, such as single nucleotide polymorphism (SNP) chips, which enable genome-wide assessment to identify genetic factors which may be linked to a particular disease or health outcome. Relevant SNPs can then be incorporated into suitable in vitro assays (2) in which food compounds can be assessed for their abilities to interact with the SNP of interest and modulate its function. Effective food compounds can then be tested in appropriate animal models (3) which exhibit the relevant phenotype and/or have the SNP of interest (or one in a related gene). This can initially be used to establish if the food has an effect on phenotype and, subsequently a range of omics techniques can be applied, and data derived from them integrated, to better understand the mechanism by which a food may exert its’ effect. Food compounds which show efficacy both in vitro and in vivo may then be suitable as candidates for human studies, both pre-clinically (for example, to assess any possible biomarkers identified in the animal studies (4)) and, finally, clinically, to ascertain a clinically-relevant end-point, such as an improvement of IBD-associated symptoms (5). The Manhattan plot shown in (1) was originally published by Ikram et al. (Citation2010) was obtained from Wikipedia (https://commons.wikimedia.org/wiki/File:Manhattan_Plot.png). This image file is licensed under the Creative Commons Attribution 2.5 Generic license. Reproduced with permission from Ferguson and Barnett (Citation2016).
