Abstract
Predicting the metabolic behavior of the human gut microbiota in different contexts is one of the most promising areas of constraint-based modeling. Recently, we presented a supra-organismal approach to build context-specific metabolic networks of bacterial communities using functional and taxonomic assignments of meta-omics data. In this work, this algorithm is applied to elucidate the metabolic changes induced over the first year after birth in the gut microbiota of a cohort of Spanish infants. We used metagenomics data of fecal samples and nutritional data of 13 infants at five time points. The resulting networks for each time point were analyzed, finding significant alterations once solid food is introduced in the diet. Our work shows that solid food leads to a different pattern of output metabolites that can be potentially released from the gut microbiota to the host. Experimental validation is presented for ferulate, a neuroprotective metabolite involved in the gut-brain axis.
Highlights
The study of nutrition has become increasingly concerned with human metabolism and the individualized human metabolic responses to diet
Networks associated with data collected after 7 months and 1 year of birth are clearly separated from data taken after 1 week and 1 and 3 months
This significant change is related with the introduction of solid food, between 4 and 6 months after birth, which modifies nutritional patterns and, the input exchange reactions in the reconstructed networks
Summary
The study of nutrition has become increasingly concerned with human metabolism and the individualized human metabolic responses to diet. The colon is the major site for the gut microbiota’s ‘co-metabolic’ activity, which enhances the efficiency of energy harvest from foods and influences the synthesis, bioavailability, and function of nutrients (Tremaroli and Bäckhed, 2012). This activity produces different beneficial compounds that regulate host health, such as short chain fatty acids (SCFAs), polyphenol metabolites, neuroactive chemical species, etc
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