Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies

Abstract

Complex carbohydrates that escape digestion in the small intestine, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between particular microbes and the host, resulting in metabolic products that influence host gut health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. We found dynamic variations in the microbiome amongst carbohydrate treatments, and over time. Using these data, the MAGs were characterised as primary (0h to 6h) and secondary degraders (12h to 24h). Recent advances in sequencing technology allowed us to identify significant unexplored diversity amongst starch degrading species in the human gut microbiota including CAZyme profiles for novel MAGs.

Effects of Maternal Fortified Balanced Energy-Protein Supplementation on the Mother-Infant Gut Microbiome: A Sub-Study of the MISAME-III Randomized Controlled Trial

“…We observed a significant association between BEP supplementation during the second trimester and a reduction in the abundance of CAG-103 sp000432375, an Oscillospiraceae species that has recently been recognized as responsive to carbohydrates 37 . The overall lesser dependence on carbohydrate metabolism can also be observed in the concerted depletion of genes for the phosphotransferase system and ABC transporters in the maternal metagenomes 38,39 .…”

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

“…Despite evidence of functional redundancy in the gut microbiome [62,63], shifts in CAZyme composition have previously been observed in response to different substrate feeding [64,65]. Likewise, in population-based studies, CAZyme profiles have also been shown to reflect dietary preferences and the type of glycans that microbes encounter in the gut [61,66,67].…”

Modelling the gut microbiota of children with malnutrition:in vitromodels reveal differences in fermentability of widely consumed carbohydrates

“…The growth medium contained 76mL of basal solution, 5 mL vitamin phosphate and sodium carbonate solution, and 1 mL reducing agent. The composition of the solutions used in the preparation of the growth medium is described in detail in Ravi et al (42). A single stock (7 litres) of growth medium was used for all vessels prepared for this experiment.…”