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Multi-omics profiling finds synbio milk differs nutritionally from bovine milk and contains 93 uncharacterized fungal metabolites and 236 fungal proteins
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  • Published: 03 April 2026

Multi-omics profiling finds synbio milk differs nutritionally from bovine milk and contains 93 uncharacterized fungal metabolites and 236 fungal proteins

  • Ravikishore Velamuri1,2,
  • Thejaswi Yertha2 &
  • John Fagan1,2 

Scientific Reports , Article number:  (2026) Cite this article

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

  • Biotechnology
  • Expression systems
  • Metabolic engineering

Abstract

Synbio milk, containing recombinant bovine β-lactoglobulin (β-LG), produced in the fungus Trichoderma reesei, was deficient nutritionally compared to bovine milk. It also contained both fungal proteins and fungal metabolites never verified safe for human consumption. By three independent methods synbio milk was found to contain predominantly fungal protein, not the 90–99% β-LG, claimed by the product developer. By (1) shotgun proteomics, (2) ELISA and classical protein analysis, and (3) simulated mixing experiments, measuring percent deviation of the amino acid composition of synbio milk from that of bovine milk, fungal protein content was found to be 75.1%, 86.5% and 90–95%, respectively. Additionally, high sensitivity untargeted mass spectrometry revealed substantial levels of 69 nutrients in bovine milk, of which only 7 were present in small amounts in synbio milk. This analysis also revealed 93 compounds in synbio milk, byproducts/waste products of fungal fermentation, whose chemical identities could not be established searching large mass spectral databases, suggesting they are novel compounds. Neither these nor the fungal proteins found in the synbio milk have been tested for safety or allergenicity at exposure levels relevant for synbio milk consumption. Therefore, comprehensive toxicity and allergenicity testing are needed to assess the safety of synbio milk for human consumption.

Data availability

All data used in this research are freely available and can be obtained on reasonable request from the corresponding author. Proteomic mass spectrometry data and search results are available from the Massive data repository (massive.ucsd.edu) and Proteome exchange (www.proteomexchange.org) using the repository numbers MSV000099870 and PXD070657 respectively. For questions, contact ccms@proteomics.ucsd.edu.

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Acknowledgements

This study was supported by grants from the Organic and Natural Health Association, the Non-GMO Project, Abby Rockefeller, the Foundation for Agricultural Integrity, as well as in kind support from Health Research Institute. We thank Churchtown Dairy and Radiance Dairy for providing milk samples. We thank Dr. Gabriela Grigorean for performing the shotgun proteomic analysis, including sample prep, the proteomic LC-MS/MS analysis and data analysis and draft writeup of the proteomics method, working in the Proteomics Core Facility of the Genome Center, University of California, Davis. The Bruker timsTOF HT LC/MS system was supported by the Howard Hughes Medical Institute, Investigator Award for Dr. Neal Hunter, UC Davis.

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Authors and Affiliations

  1. Health Research Institute, 505 Dimick Drive, Suite 111, Fairfield, IA, 52556, USA

    Ravikishore Velamuri & John Fagan

  2. Maharishi International University, 1000 North 4th Street, Fairfield, IA, 52556, USA

    Ravikishore Velamuri, Thejaswi Yertha & John Fagan

Authors
  1. Ravikishore Velamuri
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  2. Thejaswi Yertha
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Contributions

All authors contributed to design of the research. R.V. and T.Y. carried out analytical procedures. R.V. conducted UPLC-QTOF data analysis and compound identification. All authors analyzed results. J.F. wrote the first draft, except for Methods, which were written by R.V. All authors reviewed and revised the manuscript. J.F. conceived of, planned and supervised the research.

Corresponding author

Correspondence to John Fagan.

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Competing interests

T.Y. declares no competing interests. J.F. is Chief Science Officer and CEO, and K.V. is Laboratory Director at the Health Research Institute, which provides authenticity, nutritional and residue testing to companies within the food, agriculture and nutritional supplements sectors including organic companies. None of the authors hold patents or have financial investments related to the content of this manuscript. JF has collaborated with Rodale Institute on research regarding organic agriculture. Maharishi International University has a department that specializes in regenerative organic agriculture. The funders of this project did not have input into the design, execution or interpretation of the research, nor did they have input into the writing and publication of the article.

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Velamuri, R., Yertha, T. & Fagan, J. Multi-omics profiling finds synbio milk differs nutritionally from bovine milk and contains 93 uncharacterized fungal metabolites and 236 fungal proteins. Sci Rep (2026). https://doi.org/10.1038/s41598-026-38994-7

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  • Received: 07 January 2025

  • Accepted: 02 February 2026

  • Published: 03 April 2026

  • DOI: https://doi.org/10.1038/s41598-026-38994-7

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Keywords

  • Synthetic biology
  • Synbio
  • Milk
  • β-lactoglobulin
  • Liquid chromatography-untargeted mass spectrometry
  • Trichoderma reesei
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