Unlocking the Secrets of Undernutrition: A Breakthrough in Gut Microbiome Research
A new study published in Cell details a significant advancement in understanding the link between gut microbiome composition and childhood undernutrition. Researchers have created an unprecedented genomic resource and identified key patterns in microbial diversity associated with growth outcomes in children.The team, led by researchers at the Salk Institute and collaborating institutions, leveraged cutting-edge long-read sequencing technology to assemble a thorough library of microbial genomes. This approach yielded 986 complete microbial genomes,a remarkable feat – 50 times more than would have been achievable using customary short-read sequencing methods.According to Jeremiah Minich, the study’s first author, they developed an “efficient, accurate, and cost-effective long-read workflow” allowing them to analyze 10- to 20-fold more human samples than any previous study.
This extensive library, the first of its kind focusing on longitudinal pediatric undernutrition, allowed researchers to identify genetic differences within specific bacterial groups (genera) – Bifidobacterium, Megasphaera, Faecalibacterium, and Prevotella – that correlated with improving or worsening growth in children.However, the most striking finding wasn’t the identification of specific bacteria, but rather a pattern in the stability of their genomes. children exhibiting improved growth showed stable microbial pangenomes (the collective genetic material within a species), while those with faltering growth displayed unstable pangenomes.This suggests that measuring gut microbiome genetic diversity could become a valuable tool for assessing gut health and tracking public health data related to undernutrition.
The study represents four key accomplishments: the collection of a substantially larger number of clinical samples than previous research, the creation of the first longitudinal pediatric undernutrition microbial library, the identification of bacteria and genes linked to undernutrition, and the optimization of a long-read sequencing workflow.
Researchers believe this optimized workflow has broad applications beyond undernutrition research. It can be deployed in field-based molecular laboratories to provide real-time insights into areas like pandemic surveillance, antibiotic resistance, infectious disease, agricultural productivity, environmental monitoring, and biodiversity conservation. This technological advance, they argue, expands the reach of genomics and establishes a new standard for scientific research in the field.
The research was supported by funding from the NOMIS Foundation, tang genomics Fund, National Science Foundation, and U.S. Agency for International Advancement.
Source: Minich, J. J., et al. (2025). Culture-self-reliant meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.Cell. doi.org/10.1016/j.cell.2025.08.020
