Reprogramming of community metabolism by prebiotics and medicinal herbs Metagenome

Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here we used in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic medicine, followed by 16S rRNA sequencing. We applied genome reconstruction of enumerated communities to compare and contrast the structural and functional impact of prebiotics and medicinal herbs, the latter possessing higher complexity of sugars and sugar linkages. In so doing, we examined the relationships between discrete variations in sugar composition and sugar linkages associated with each prebiotic to drive changes in microbiota composition, catabolism of glycan substrates. The restructuring of microbial communities with glycan substrates reprograms community metabolism and its potential impact on host physiology. We analyzed sugar fermentation pathways and products predicted to be formed and prebiotic and herb-induced changes in vitamin and amino acid biosynthesis and degradation. These results highlight the utility of combining genome reconstruction methodology with 16S rRNA community profiles to enable insights pertaining to community metabolism. This process also provides a rational means for prioritizing in vivo analysis of prebiotics and medicinal herbs in vivo to test hypotheses related to therapeutic potential in specific diseases of interest.