The gut microbiome and early-life growth in a population with high prevalence of stunting

Ruairi C. Robertson, Thaddeus J. Edens, Lynnea Carr, Kuda Mutasa, Ethan K. Gough, Ceri Evans, Hyun Min Geum, Iman Baharmand, Sandeep K. Gill, Robert Ntozini, Laura E. Smith, Bernard Chasekwa, Florence D. Majo, Naume V. Tavengwa, Batsirai Mutasa, Freddy Francis, Joice Tome, Rebecca J. Stoltzfus, Jean H. Humphrey, Andrew J. Prendergast and Amee R. Manges (amee.manges@ubc.ca)
Additional contact information
Ruairi C. Robertson: Queen Mary University of London
Thaddeus J. Edens: Devil’s Staircase Consulting
Lynnea Carr: University of British Columbia
Kuda Mutasa: Zvitambo Institute for Maternal and Child Health Research
Ethan K. Gough: Johns Hopkins Bloomberg School of Public Health
Ceri Evans: Queen Mary University of London
Hyun Min Geum: University of British Columbia
Iman Baharmand: University of British Columbia
Sandeep K. Gill: University of British Columbia
Robert Ntozini: Zvitambo Institute for Maternal and Child Health Research
Laura E. Smith: Zvitambo Institute for Maternal and Child Health Research
Bernard Chasekwa: Zvitambo Institute for Maternal and Child Health Research
Florence D. Majo: Zvitambo Institute for Maternal and Child Health Research
Naume V. Tavengwa: Zvitambo Institute for Maternal and Child Health Research
Batsirai Mutasa: Zvitambo Institute for Maternal and Child Health Research
Freddy Francis: University of British Columbia
Joice Tome: Zvitambo Institute for Maternal and Child Health Research
Rebecca J. Stoltzfus: Goshen College, Goshen
Jean H. Humphrey: Johns Hopkins Bloomberg School of Public Health
Andrew J. Prendergast: Queen Mary University of London
Amee R. Manges: University of British Columbia

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Stunting affects one-in-five children globally and is associated with greater infectious morbidity, mortality and neurodevelopmental deficits. Recent evidence suggests that the early-life gut microbiome affects child growth through immune, metabolic and endocrine pathways. Using whole metagenomic sequencing, we map the assembly of the gut microbiome in 335 children from rural Zimbabwe from 1–18 months of age who were enrolled in the Sanitation, Hygiene, Infant Nutrition Efficacy Trial (SHINE; NCT01824940), a randomized trial of improved water, sanitation and hygiene (WASH) and infant and young child feeding (IYCF). Here, we show that the early-life gut microbiome undergoes programmed assembly that is unresponsive to the randomized interventions intended to improve linear growth. However, maternal HIV infection is associated with over-diversification and over-maturity of the early-life gut microbiome in their uninfected children, in addition to reduced abundance of Bifidobacterium species. Using machine learning models (XGBoost), we show that taxonomic microbiome features are poorly predictive of child growth, however functional metagenomic features, particularly B-vitamin and nucleotide biosynthesis pathways, moderately predict both attained linear and ponderal growth and growth velocity. New approaches targeting the gut microbiome in early childhood may complement efforts to combat child undernutrition.

Date: 2023
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DOI: 10.1038/s41467-023-36135-6

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