Gut physiology meets microbiome science

Abstract

Research on the gut microbiome has gained high popularity and almost every disease has meanwhile been linked to alterations in microbiome composition. Typically assessed via stool samples, the microbiome displays a huge diversity with a multitude of environmental parameters already identified as contributing to its character. Despite impressive scientific progress, normal microbiome diversity remains largely unexplained and it is tempting to speculate some of the yet unexplained variance is hidden in normal gut physiology. Although a few genome/phenome-wide associations studies have recently highlighted physiological parameters such as stool frequency, known as contributing to microbiome diversity, there is a large knowledge base from decades of basic research on gut functions that can be explored for possible links to stool features and microbiome characteristics. And, when extrapolating findings from faecal samples to the biology in the intestinal lumen or the mucosal microenvironment, gut anatomy and physiology features need to be considered. Similarly, differences in anatomy and physiology between rodents and humans need attention when discussing findings in animals in relation to human physiology and nutrition.

Keywords: diet; gastrointestinal tract; in situ; microbiome; physiology; rodents.

Figure 1

Gastrointestinal tract and it’s neuro-endocrine control system. A multitude of sensor cells with different densities in longitudinal direction coupled to the enteric nervous system (lower part) and the endocrine system with a large repertoire of hormones/mediators (upper part) mediate tight control of every step in intake and processing of food as well as absorption of the constituents embedded into bidirectional communication with peripheral organs and brain.

Figure 2

Bidirectional fluxes of substrates/intermediates (compiled from literature) across the colonic tissue from blood to lumen and vice versa on background of the epithelial morphology that creates a distinct surface compartment between the cells and the colonic lumen hosting the microbial ecosystem.