Archaeological research yields valuable insights of past communities or civilizations by sifting through the rubbish dumps of ancient dwellings. Microbiome research targeting the gastrointestinal (GI) microbiota communities traditionally uses a similar approach. Feces, the end product of the digestive process that is excreted, are carefully analyzed using very sophisticated methodologies as if feces would hold the treasure trove filled with gold or providing the key for our understanding of the interactions of communities of microbiota with the human body and its relevance for specific diseases.
Microbiome research has taken off with the development and widespread availability of culture-independent high throughput sequencing capabilities and there are high hopes these approaches will enable medicine to answer many burning questions. Indeed, as the technology advances and provides greater scale in time-effective and cost-effective ways, the fields of molecular epidemiology and molecular microbiology further coalesce to reveal associations between the GI microbiome and immune functions, biomolecular activities, or pathogen exclusion, as well as links between the microbiome and diseases such as inflammatory bowel disease,1 autism,2 cancer,3 and even so-called functional GI disorders.4
The rise of human microbiome research over the last three decades coincides with the elucidation of many pathophysiologic concepts for functional gastrointestinal disorders (FGID) including functional dyspepsia (FD) that overlap disordered gastric emptying, impaired funding relaxation, heightened visceral sensory function, psychological factors (or brain-gut factors) and minimal mucosal or systemic inflammation.5 Efforts to elucidate these disease mechanisms were driven by the pressing need to develop therapies for these patients and the emerging pathophysiologic mechanisms mentioned above virtually always initially offering hope that they would allow targeting of underlying disease mechanisms and ultimately provide cure for patients with FGID. Sadly, these expectations are, at best, only partially met. As such, while …
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