Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

Figure 2 Multiple host-mediated mechanisms regulate bacterial growth and their activities. These pathways may act against the microbiota in a generalised manner or influence bacteria with distinct properties (blue). A: Substrates from diet are key energy sources for bacterial growth. Changes in feeding pattern will shape the microbiome structure and associated products; B: Ingestion of dietary fibre and osmotically active compounds promotes gut motility. Faster transit rate flushes out slow growing organisms and those without the ability to adhere to the intestines; C: Release of bile in response to dietary fat selects against bile-sensitive bacteria but promotes those with the capacity to obtain energy via anaerobic respiration; D: Mucin secreted by goblet cells physically prevents the penetration of bacteria into gut epithelium, and it also promotes bacteria that utilise mucin as growth substrates; E: Paneth cells in the gut epithelium secrete effector molecules with broad-spectrum antimicrobial activity, e.g. defensins, lysozyme and RegIIIγ, which contribute to the innate barrier against microbial colonisation; F: Migration of flagellated bacteria is inhibited by secretory immunoglobulin A (IgA), which facilitates the exclusion of bacteria at the epithelium; G: When mucin synthesis and release is impaired, pathobionts may penetrate the mucosal epithelium and trigger the inflammatory cascade. Byproducts of inflammation confer a growth advantage for organisms that obtain energy through anaerobic respiration.