An extended reconstruction of human gut microbiota metabolism of dietary compounds

Abstract

Understanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex problem. However, when applied to nutritional questions, a major issue in existing reconstructions is the limited information about compounds in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of diet metabolism in the human gut microbiota. AGREDA adds the degradation pathways of 209 compounds present in the human diet, mainly phenolic compounds, a family of metabolites highly relevant for human health and nutrition. We show that AGREDA outperforms existing reconstructions in predicting diet-specific output metabolites from the gut microbiota. Using 16S rRNA gene sequencing data of faecal samples from Spanish children representing different clinical conditions, we illustrate the potential of AGREDA to establish relevant metabolic interactions between diet and gut microbiota.

Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis

“…Green tea has numerous health benefits due to its rich polyphenolic content. More recent in-vitro and in-vivo scientific studies have further supported the role polyphenols in modulating gut microbiota [35,36]. The rich polyphenols in green tea are of great interest for drug discovery and widely known for their hypocholesteremic, antibiotic, anticarcinogen and hypoglycaemic properties [37][38][39][40].…”

Development of an Unified Food Composition Database for the European Project “Stance4Health”

“…One of the milestones of personalized nutrition is to understand the health level of the gut microbiota of a given patient. The S4H FCDB generated data will also be completed with the use of AGREDA [99], an extended reconstruction of diet metabolism by the human gut microbiota. The S4H FCDB will also introduce commercial products, incorporating allergens and different scores as used in Open Food Facts [16].…”

Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods

“…Universal metabolic databases, such as KEGG 15 or the Model SEED database 16 , store reactions from species not present in the gut microbiota, and pathway extraction is not direct. In a previous work 17 , we addressed this issue and developed AGREDA 17 , an extension of AGORA 18 , the most comprehensive collection of metabolic reconstructions for the human gut microbiota. AGREDA 17 provides a better description of the metabolic pathways of dietary compounds, including 114 phenolic compounds of Phenol-Explorer 19 , the largest database of phenolic compounds in the literature.…”

“…In a previous work 17 , we addressed this issue and developed AGREDA 17 , an extension of AGORA 18 , the most comprehensive collection of metabolic reconstructions for the human gut microbiota. AGREDA 17 provides a better description of the metabolic pathways of dietary compounds, including 114 phenolic compounds of Phenol-Explorer 19 , the largest database of phenolic compounds in the literature. However, there is still substantial room for improvement.…”

“…We provide details as to the reactions, metabolites and species involved in the proposed pathways and evaluate their chemical and biological plausibility. Then, we integrate these predicted reactions with our previous metabolic reconstruction of the human gut microbiota, AGREDA 17 , and systematically analyze the metabolic capabilities acquired in the extended reconstruction. We assess the impact of our improvements in the metabolic processing of various foods detailed in the Phenol-Explorer database 19 , finding previously undetected connections with output microbial metabolites.…”