Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition

Jeremiah J Minich¹, Nicholas Allsing², M Omar Din³, Michael J Tisza⁴, Kenneth Maleta⁵, Daniel McDonald⁴, Nolan Hartwick², Allen Mamerto², Caitriona Brennan⁶, Lauren Hansen³, Justin Shaffer⁷, Emily R Murray⁸, Tiffany Duong², Rob Knight⁹, Kevin Stephenson¹⁰, Mark J Manary¹¹, Todd P Michael¹²

Affiliations

¹ The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: jeremiah.minich@gmail.com.
² The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
³ Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
⁴ Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
⁵ School of Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi.
⁶ Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA 92037, USA.
⁷ Department of Biology, California State University, Fresno, CA 93740, USA.
⁸ The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA.
⁹ Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA; Department of Computer Science, University of California, San Diego, La Jolla, CA 92037, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92037, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92037, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: robknight@ucsd.edu.
¹⁰ Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA.
¹¹ Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address: manarymj@wustl.edu.
¹² The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA 92037, USA; Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA; Science and Conservation, San Diego Botanical Garden, Encinitas, CA 92024, USA. Electronic address: tmichael@salk.edu.

PMID: 40930091
DOI: 10.1016/j.cell.2025.08.020

Free article

Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition

Jeremiah J Minich et al. Cell. 2025.

Free article

. 2025 Nov 13;188(23):6666-6686.e25.

doi: 10.1016/j.cell.2025.08.020. Epub 2025 Sep 9.

Authors

Affiliations

¹ The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: jeremiah.minich@gmail.com.
² The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
³ Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
⁴ Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
⁵ School of Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi.
⁶ Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA 92037, USA.
⁷ Department of Biology, California State University, Fresno, CA 93740, USA.
⁸ The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA.
⁹ Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA; Department of Computer Science, University of California, San Diego, La Jolla, CA 92037, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92037, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92037, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: robknight@ucsd.edu.
¹⁰ Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA.
¹¹ Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address: manarymj@wustl.edu.
¹² The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA 92037, USA; Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA; Science and Conservation, San Diego Botanical Garden, Encinitas, CA 92024, USA. Electronic address: tmichael@salk.edu.

PMID: 40930091
DOI: 10.1016/j.cell.2025.08.020

Abstract

The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.

Keywords: Oxford Nanopore Technologies; Pacbio HiFi; childhood undernutrition; human gut microbiome; linear growth faltering; long-read sequencing; metagenomics; microbial GWAS; microbial pangenome; stunting.

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Conflict of interest statement

Declaration of interests 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.

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Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition

Affiliations

Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition

Authors

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Abstract

Conflict of interest statement

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Research Materials