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

Samanta Michelini, Biju Balakrishnan, Silvia Parolo, Alice Matone, Jane A Mullaney, Wayne Young, Olivier Gasser, Clare Wall, Corrado Priami, Rosario Lombardo, Martin Kussmann

Research output: Contribution to journalArticle

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Abstract

Background: 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.

Results: 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/).

Conclusions: In this study, we applied a benefit-oriented microbiome research strategy for enhanced early-life immune health. We extended from "classical" to molecular nutrition aiming to identify nutrients, bacteria, and mechanisms that point towards targeted feeding to improve immune health in infants around weaning. Here, we present the systems biology-based approach we used to inform us on the most promising prebiotic combinations known to support growth of beneficial gut bacteria ("probiotics") in the infant gut, thereby favorably promoting development of the immune system.

Original languageEnglish
Article number171
Number of pages18
JournalMicrobiome
Volume6
Issue number1
DOIs
Publication statusPublished - 21 Sep 2018
Externally publishedYes

Keywords

  • weaning
  • infant gut bacteria
  • prebiotic feeds
  • natural products
  • Infection
  • Probiotic
  • Systems biology
  • Complementary feeding
  • Infant gut microbiome
  • Reverse ecology
  • Knowledge extraction
  • Prebiotic

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