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Human milk and infant formula influence lactobacilli metabolism in a species-specific manner
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  • Published: 02 April 2026

Human milk and infant formula influence lactobacilli metabolism in a species-specific manner

  • Alyssa Gutierrez1,
  • Katherine E. Chetta2,3,
  • Brenton Puckett1,
  • Sigmund J. Haidacher4,5,
  • Thomas D. Horvath4,5,6 &
  • …
  • Melinda A. Engevik1,7 

npj Science of Food , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Applied microbiology
  • Microbiology

Abstract

The neonatal gut is colonized by commensal bacteria, including lactobacilli, that play a critical role in promoting host health. While lactobacilli are known for producing bioactive metabolites, species-specific responses to neonatal diets remain unclear. We hypothesized that human milk and infant formula would differentially influence lactobacilli metabolite production. Six species (Lactobacillus acidophilus, Levilactobacillus brevis, Lactobacillus johnsonii, Lacticaseibacillus paracasei, Limosilactobacillus reuteri, Lacticaseibacillus rhamnosus) were cultured in defined media with human milk, formula, or water, and supernatants were analyzed via untargeted LC-MS/MS metabolomics. Principal coordinates analyses showed distinct metabolomic profiles among lactobacilli species and across dietary treatments. Human milk enhanced the production of several metabolites, including hydroxyphenyllactic acid, tyrosine, indoles, vaccenic acid, and di-peptides. Interestingly, several unique metabolites were upregulated in the presence of infant formula, including isonicotinic acid. These results highlight the differential effects of human milk and infant formula on the metabolomic profiles of lactobacilli species, emphasizing significant species-specific variation and pronounced production of potentially beneficial compounds in response to human milk. This work underscores the importance of understanding diet-microbe interactions to optimize neonatal gut health.

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Data availability

The raw data supporting the conclusions of this manuscript are openly available in the NIH Common Fund's National Metabolomics Data Repository (NMDR).

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Acknowledgements

We would like to express our deepest appreciation to the families that participated in this study. The Texas Children’s Research Institute provides salary support to staff members who work in the Virginia and L.E. Simmons Family Foundation Mass Spectrometry Laboratory and purchased all of the reagents, consumables and durable supplies described.

Funding

This study was supported by T32DK124191-01A1 (AG), NATS NIH KL2TR001452 (KEC), Darby Pediatrics pilot grant (KEC), UL1TR001450 (KEC), 3P20 P20 GM130457 (COBRE in Digestive & Liver Disease, MUSC; GM130457-04S1 supplement), P30 DK123704 (Digestive Disease Research Center, MUSC). The Virginia and L.E. Simmons Family Foundation Mass Spectrometry Laboratory housed within the Texas Children’s Research Institute - Microbiome Center is supported by an NIH S10 Shared Instrumentation Grant 1S10ODO36416-01 (TDH), and by a NIH P30DK056338 (TDH).

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Authors and Affiliations

  1. Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina (MUSC), Charleston, SC, USA

    Alyssa Gutierrez, Brenton Puckett & Melinda A. Engevik

  2. Department of Pediatrics, C.P. Darby Children’s Research Institute, MUSC, Charleston, SC, USA

    Katherine E. Chetta

  3. Department of Pediatrics, Division of Neonatal-Perinatal Medicine, MUSC, Shawn Jenkins Children’s Hospital, Charleston, SC, USA

    Katherine E. Chetta

  4. Department of Pathology and Immunology, Baylor College of Medicine (BCM), Houston, TX, USA

    Sigmund J. Haidacher & Thomas D. Horvath

  5. Texas Children’s Research Institute (TCRI) – Microbiome Center, Texas Children’s Hospital, Houston, TX, USA

    Sigmund J. Haidacher & Thomas D. Horvath

  6. Department of Pharmacy Practice & Translational Research, University of Houston (UH), Houston, TX, USA

    Thomas D. Horvath

  7. Department of Microbiology & Immunology, MUSC, Charleston, SC, USA

    Melinda A. Engevik

Authors
  1. Alyssa Gutierrez
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  2. Katherine E. Chetta
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  3. Brenton Puckett
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  4. Sigmund J. Haidacher
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  5. Thomas D. Horvath
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Contributions

Concept and design (A.G., B.P., M.A.E.); intellectual contribution (K.E.C., T.D.H., M.A.E.); data acquisition and analysis (A.G., B.P.), interpretation (A.G., K.E.C., M.A.E.); drafting manuscript (A.G.), editing manuscript (B.P., K.E.C., T.D.H., M.A.E.); funding (K.E.C., T.D.H., M.A.E.).

Corresponding author

Correspondence to Melinda A. Engevik.

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Competing interests

T.D.H. is an Editorial Board Member and is contracted as an Associate Academic Editor for Cell Press – STAR Protocols. T.D.H. is a voluntary participant in the SCIEX Global Thought Leaders in Mass Spectrometry Program. All other authors have no competing interests to declare.

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Gutierrez, A., Chetta, K.E., Puckett, B. et al. Human milk and infant formula influence lactobacilli metabolism in a species-specific manner. npj Sci Food (2026). https://doi.org/10.1038/s41538-026-00759-x

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  • Received: 14 May 2025

  • Accepted: 05 February 2026

  • Published: 02 April 2026

  • DOI: https://doi.org/10.1038/s41538-026-00759-x

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