Proteomic and N-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes in vitro

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dc.authorid0000-0003-4056-1673
dc.authorid0000-0002-8542-6531
dc.authorid0009-0006-6708-5784
dc.authorid0000-0002-8017-3280
dc.authorid0000-0003-2053-5830
dc.authorid0000-0001-7748-1402
dc.contributor.authorBolino, Matthew
dc.contributor.authorDuman, Hatice
dc.contributor.authorAvci, Izzet
dc.contributor.authorKayili, Haci Mehmet
dc.contributor.authorPetereit, Juli
dc.contributor.authorZundel, Chandler
dc.contributor.authorSalih, Bekir
dc.date.accessioned2026-02-03T12:00:42Z
dc.date.available2026-02-03T12:00:42Z
dc.date.issued2025
dc.departmentÇanakkale Onsekiz Mart Üniversitesi
dc.description.abstractAdvances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. Here, we have characterized the protein composition and N-glycome of a yeast-synthesized and commercially available whey protein ingredient and compared this novel ingredient to whey protein isolate powder derived from bovine milk. Despite strong similarities in protein composition, we found that the N-glycome significantly differs between the two protein sources, reflecting the biosynthetic machinery of the production systems. Furthermore, the diversity of proteins found in yeast-synthesized whey protein were lower relative to bovine whey protein, despite both being predominantly beta-lactoglobulin. Finally, to understand whether these differences in N-glycome profiles may affect the human gut microbiome, we compared these proteins in an in vitro fecal fermentation model. The two whey protein sources generated significant differences among three representative gut microbiomes in vitro, most likely due to differences in N-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of synthesized proteins and how these differences impact the human gut microbiome.IMPORTANCERecent advances in food technology have led to the production of animal-free products from yeast that are traditionally derived from animals, such as milk proteins. These new processes raise important questions about the use of synthetic proteins as a replacement for traditionally sourced protein, especially in the context of the gut microbiome. Importantly, yeast produce N-glycans comprised primarily of mannose, while animals synthesize structurally and compositionally complex N-glycan structures. Given these differences, we characterized a new, yeast-derived whey protein ingredient and compared it to bovine whey protein. We found that yeast-derived whey protein differs in its impact on human gut microbiomes because of differences in N-glycan structures, despite similarity in protein composition. These findings raise important questions as to whether these differences in synthetic proteins lead to significant changes to the gut microbiome in vivo, and whether this may impact the utility of these novel ingredients.
dc.description.sponsorshipNational Institute of Food and Agriculture [RRID:SCR_017761, SCR_017802, RRID:SCR_012598]
dc.description.sponsorshipWe thank the Mitch Hitchcock, Ph.D., Nevada Proteomics Center (RRID:SCR_017761) and the Nevada Bioinformatics Center (RRID:SCR_017802) for their technical support, as well as the Molecular Research Core Facility at Idaho State University (RRID:SCR_012598). We also thank Dr. David C. Dallas (Oregon State University; http://www.dallaslab.org) for providing the bovine milk-specific protein database used in the proteomic analysis.
dc.identifier.doi10.1128/spectrum.00200-25
dc.identifier.issn2165-0497
dc.identifier.issue8
dc.identifier.pmid40569063
dc.identifier.scopus2-s2.0-105012747918
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1128/spectrum.00200-25
dc.identifier.urihttps://hdl.handle.net/20.500.12428/34672
dc.identifier.volume13
dc.identifier.wosWOS:001516965500001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherAmer Soc Microbiology
dc.relation.ispartofMicrobiology Spectrum
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_WOS_20260130
dc.subjectgut microbiome
dc.subjectfiber
dc.subjectN-glycan
dc.subjectwhey
dc.subjectprotein glycosylation
dc.titleProteomic and N-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes in vitro
dc.typeArticle

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