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Nat Commun ; 12(1): 4728, 2021 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-34354065


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.

Dieta , Microbioma Gastrointestinal/fisiologia , Redes e Vias Metabólicas , Modelos Biológicos , Algoritmos , Criança , Fenômenos Fisiológicos da Nutrição Infantil , Dieta Mediterrânea , Fermentação , Microbioma Gastrointestinal/genética , Humanos , Técnicas In Vitro , Lens (Planta)/química , Valor Nutritivo , RNA Ribossômico 16S/genética , Espanha
Nutrients ; 13(7)2021 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-34199047


The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow's milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization.

Fermentação , Congelamento , Microbioma Gastrointestinal , Animais , Bovinos , Criança , Fezes/microbiologia , Armazenamento de Alimentos , Microbioma Gastrointestinal/genética , Humanos , Masculino , Microbiota , Leite , Projetos Piloto , RNA Ribossômico 16S/genética