Childhood stunting, impaired growth caused by chronic undernutrition, affects more than 150 million children worldwide and can lead to lifelong health and cognitive challenges. New research from the Salk Institute highlights the gut microbiome as a promising frontier for tackling this global issue.
In a study of children in Malawi, where nearly one in three are affected by stunting, researchers tracked gut microbes over the course of nearly a year. They found that children whose gut microbiome shifted more over time were more likely to experience poor growth, while those with more stable microbial communities tended to grow better.
To support this work, the team also created the first-ever pediatric undernutrition microbial genome catalog, a library of nearly 1,000 microbial genomes, many of them newly identified. This resource provides scientists with a powerful tool to study how specific microbes affect growth and nutrient absorption.
“By using cutting-edge genome sequencing and pangenomic approaches in a longitudinal design, we were able for the first time to pinpoint specific microbial changes linked to poor growth, opening the door to new diagnostics or therapeutics that could help address a crisis impacting more than 150 million children worldwide,” said senior author Todd Michael, research professor at the Salk Institute.
The study, published in Cell, also found that certain microbial groups, including species of Bifidobacterium and Faecalibacterium, showed genetic differences between children with improving growth and those whose growth faltered. More broadly, the results suggest that microbial genome stability, rather than just the presence or absence of specific bacteria, may be an important marker of gut health.
While this research focuses on children in low-resource settings, the implications reach far beyond. By advancing methods for long-read sequencing, the team demonstrated a way to generate detailed microbial maps that could be applied to other areas of health research, from infectious disease surveillance to personalized nutrition.
For now, the findings underscore the importance of the gut microbiome in growth and development, and they suggest a future where microbiome-based diagnostics might help identify children at risk of stunting and guide new nutritional interventions.
This research was supported by the NOMIS Foundation, Tang Genomics Fund, the U.S. National Science Foundation and the U.S. Agency for International Development.