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.
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.
Cutting-edge tools at Baylor
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.”
Looking ahead: 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.
Funding
The work was supported by the NOMIS Foundation and the Tang Genomics Fund
ABOUT JEREMIAH J “JAKE” MINICH, PH.D.
Jake Minich, Ph.D., joined the Baylor University biology faculty in Fall 2025 from the Salk Institute for Biological Studies, which was founded by Jonas Salk, developer of the first safe and effective polio vaccine. Minich earned a B.S. in biochemistry from Point Loma Nazarene University and an M.S. in molecular biology from San Diego State University. After his master’s studies, Minich lived and conducted research as a Fulbright Scholar in Malawi, Africa. Upon return, he completed his Ph.D. in marine biology at Scripps Institution of Oceanography in the labs of Rob Knight and Eric Allen, where he studied the microbial ecology of mucosal sites in wild and farmed fish. Minich received the prestigious NSF Postdoctoral Research Fellowship in Biology, investigating host-microbe interactions in more than 100 species of marine fish using a combination of microbial sequencing, comparative genomics of fish and fish physiology in Todd Michael’s lab at the Salk Institute.
As a NOMIS Fellow at the Salk, Minich investigated the role of the gut microbiome in infant malnutrition. He developed a new long-read metagenomic sequencing approach where he discovered genetic associations of bacteria with childhood undernutrition including stunting.
ABOUT THE RESEARCH TEAM
In addition to corresponding author Minich, the research team included:
Senior Authors:
- Todd Michael, Ph.D The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies
- Kevin Stephenson, MD Washington University St. Louis School of Medicine
- Rob Knight, PhD, University of California San Diego School of Medicine
- Mark Manary, MD, Washington University St. Louis School of Medicine
Co-authors
- Nicholas Allsing, The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies
- M. Omar Din, Ph.D., Department of Pediatrics, University of California San Diego
- Michael J. Tisza, Ph.D., Department of Molecular Virology and Microbiology, Baylor College of Medicine
- Kenneth Maleta, Ph.D., School of Public Health, Kamuzu University of Health Sciences
- Daniel McDonald, Ph.D., Department of Molecular Virology and Microbiology, Baylor College of Medicine
- Nolan Hartwick, The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies
- Allen Mamerto, The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies
- Caitriona Brennan, Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego
- Lauren Hansen, Department of Pediatrics, University of California, University of California San Diego
- Justin Shaffer, Ph.D., Department of Biology, California State University Fresno
- Emily R. Murray, The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies
- Tiffany Duong, The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies
ABOUT BAYLOR UNIVERSITY
Baylor University is a private Christian University and a nationally ranked Research 1 institution. The University provides a vibrant campus community for more than 20,000 students by blending interdisciplinary research with an international reputation for educational excellence and a faculty commitment to teaching and scholarship. Chartered in 1845 by the Republic of Texas through the efforts of Baptist pioneers, Baylor is the oldest continually operating University in Texas. Located in Waco, Baylor welcomes students from all 50 states and more than 100 countries to study a broad range of degrees among its 12 nationally recognized academic divisions. Learn more about Baylor University at www.baylor.edu.
ABOUT THE COLLEGE OF ARTS & SCIENCES AT BAYLOR UNIVERSITY
The College of Arts & Sciences is Baylor University’s largest academic division, consisting of 25 academic departments in the sciences, humanities, fine arts and social sciences, as well as 11 academic centers and institutes. The more than 5,000 courses taught in the College span topics from art and theatre to religion, philosophy, sociology and the natural sciences. The College’s undergraduate Unified Core Curriculum, which routinely receives top grades in national assessments, emphasizes a liberal education characterized by critical thinking, communication, civic engagement and Christian commitment. Arts & Sciences faculty conduct research around the world, and research on the undergraduate and graduate level is prevalent throughout all disciplines. Visit the College of Arts &
Journal
Cell
Method of Research
Data/statistical analysis
Subject of Research
People
Article Title
Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition
Article Publication Date
9-Sep-2025
COI Statement
T.P.M. is a founder of the carbon sequestration company CQuesta. R.K. is a scientific advisory board member, consultant, has equity, and receives income for BiomeSense, Inc. R.K. is a scientific advisory board member and has equity in GenCirq. R.K. is a consultant and scientific advisory board member for DayTwo and receives income. R.K. has equity in and acts as a consultant for Cybele. R.K. is a co-founder of Biota, Inc. and has equity. R.K. is a co-founder and a scientific advisory board member of Micronoma and has equity. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict-of-interest policies. M.O.D. has equity in GenCirq.