New research led by Baylor University’s Jeremiah J “Jake” Minich, Ph.D., assistant professor of biology, reveals that the stability of gut bacteria in early life plays a critical role in whether children thrive or struggle with undernutrition – a global health challenge affecting millions.
Published in the journal Cell, the study introduces a novel method for capturing the complete genomes of gut microbes, offering unprecedented insight into how bacteria shape childhood growth.
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Using advanced long-read DNA sequencing, Minich followed children in the African nation of Malawi for nearly a year, building a catalog of nearly 1,000 complete bacterial genomes from their gut microbiomes.
Minich and his research team at the Salk Institute found that children who grew steadily maintained stable bacterial populations, while those with slower growth had gut bacteria that shifted over time.
“This tells us that gut health isn’t just about what children eat,” Minich said. “If the microbial community is unstable, nutrients may not be absorbed properly – even if food is available. Our work suggests that the gut microbiome could be a predictor of which children are at risk for undernutrition, allowing for earlier and more effective interventions.”
From mothers to children
The study also highlighted the importance of microbes passed from mothers during birth. Specific bacteria were found to vary significantly between villages, suggesting geography and culture strongly shape gut ecosystems, Minich said. These findings underscore the need for global diversity in microbiome research.
Baylor University has recently made an investment in a state-of-the-art benchtop, long-read DNA sequencer (PacBio Vega)– the first of its kind at a Texas University. Minich said the instrument allows researchers to capture far longer and more accurate stretches of DNA, opening doors for discoveries in gut health and environmental monitoring.
“This tool gives us resolution we’ve never had before,” Minich said. “It’s like switching from blurry vision to a telescope – you suddenly see details that were invisible.”
Prevention, not just treatment
Minich envisions the work leading to low-cost diagnostics that can flag children at risk of undernutrition before symptoms emerge.
“Just like maternal HIV testing helps protect newborns, microbiome screening could one day guide preventative care for moms and babies,” he said.
The work was supported by the NOMIS Foundation and the Tang Genomics Fund
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