A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

Microbiome
Samanta MicheliniMartin Kussmann

Abstract

Weaning is a period of marked physiological change. The introduction of solid foods and the changes in milk consumption are accompanied by significant gastrointestinal, immune, developmental, and microbial adaptations. Defining a reduced number of infections as the desired health benefit for infants around weaning, we identified in silico (i.e., by advanced public domain mining) infant gut microbes as potential deliverers of this benefit. We then investigated the requirements of these bacteria for exogenous metabolites as potential prebiotic feeds that were subsequently searched for in the natural product space. Using public domain literature mining and an in silico reverse metabolic approach, we constructed probiotic-prebiotic-food associations, which can guide targeted feeding of immune health-beneficial microbes by weaning food; analyzed competition and synergy for (prebiotic) nutrients between selected microbes; and translated this information into designing an experimental complementary feed for infants enrolled in a pilot clinical trial ( http://www.nourishtoflourish.auckland.ac.nz/ ). In this study, we applied a benefit-oriented microbiome research strategy for enhanced early-life immune health. We extended from "classic...Continue Reading

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Citations

Sep 8, 2021·Frontiers in Cell and Developmental Biology·Silvia ParoloRosario Lombardo
Sep 24, 2021·Nature Reviews. Microbiology·Anelize BauermeisterPieter C Dorrestein
Sep 29, 2021·Journal of Biochemical and Molecular Toxicology·Rahagir SalekeenKazi Mohammed Didarul Islam

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Software Mentioned

Perl script
Pubtator
R package
CoreNLP API
DNorm
ModelSeed
NetSeed
NetCooperate
bStyle
RevEcoR

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