Yogurt as a modulator of gut and beyond gut: Mechanisms, health effects, and clinical translation

Daiyu Yang; Hongwen Zhao; Kun He; Wangyang Chen; Hemiao Xu; Shuai Li; Qiming Xiao; Jinshui Yang; Dong Wu; Daiyu Yang; Hongwen Zhao; Kun He; Wangyang Chen; Hemiao Xu; Shuai Li; Qiming Xiao; Jinshui Yang; Dong Wu

doi:10.3934/microbiol.2026017

AIMS Microbiology

2026, Volume 12, Issue 2: 393-421. doi: 10.3934/microbiol.2026017

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Review Special Issues

Yogurt as a modulator of gut and beyond gut: Mechanisms, health effects, and clinical translation

1.
State Key Laboratory of Complex Severe and Rare Diseases, Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
2.
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
3.
State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
4.
Department of Gastroenterology, The People's Hospital of Xizang Autonomous Region, Lhasa 850000, China

Received: 01 March 2026 Revised: 08 June 2026 Accepted: 23 June 2026 Published: 26 June 2026

Yogurt, a fermented dairy food, has been increasingly recognized for its potential to modulate gut microbiota and promote host health. Accumulating evidence suggests that yogurt consumption influences gut microbial composition, diversity, and functional activity. In this narrative review, we synthesized the findings on yogurt-related effects on the gut microbiota, intestinal barrier, microbial metabolites, immune responses, and selected extra-intestinal outcomes. We distinguished traditional yogurt, probiotic yogurt, synbiotic yogurt, fortified yogurt, and non-dairy or regional yogurt-like fermented products, and then organized proposed mechanisms into a hierarchical framework that separated direct yogurt-derived inputs, including starter cultures, added probiotic strains, fermentation-derived compounds, and dairy matrix components, from resident microbiota-mediated secondary metabolites and host downstream responses. Importantly, limitations and controversies, such as variability in yogurt formulations, strain-specific effects, and inter-individual responses, were critically evaluated. Finally, we highlighted future research directions that emphasize standardized study designs, defined endpoints, long-term randomized controlled trials, and integrative multi-omics approaches to support the development of personalized dietary strategies. Together, this review provides a structured framework for understanding the complex interactions between yogurt, gut microbiota, and host physiology, while outlining key steps needed to translate evidence into actionable nutritional recommendations.
- yogurt,
- gut microbiota,
- probiotics,
- prebiotics,
- health effects,
- microbiome modulation,
- precision nutrition,
- clinical translation
Citation: Daiyu Yang, Hongwen Zhao, Kun He, Wangyang Chen, Hemiao Xu, Shuai Li, Qiming Xiao, Jinshui Yang, Dong Wu. Yogurt as a modulator of gut and beyond gut: Mechanisms, health effects, and clinical translation[J]. AIMS Microbiology, 2026, 12(2): 393-421. doi: 10.3934/microbiol.2026017

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Abstract

Yogurt, a fermented dairy food, has been increasingly recognized for its potential to modulate gut microbiota and promote host health. Accumulating evidence suggests that yogurt consumption influences gut microbial composition, diversity, and functional activity. In this narrative review, we synthesized the findings on yogurt-related effects on the gut microbiota, intestinal barrier, microbial metabolites, immune responses, and selected extra-intestinal outcomes. We distinguished traditional yogurt, probiotic yogurt, synbiotic yogurt, fortified yogurt, and non-dairy or regional yogurt-like fermented products, and then organized proposed mechanisms into a hierarchical framework that separated direct yogurt-derived inputs, including starter cultures, added probiotic strains, fermentation-derived compounds, and dairy matrix components, from resident microbiota-mediated secondary metabolites and host downstream responses. Importantly, limitations and controversies, such as variability in yogurt formulations, strain-specific effects, and inter-individual responses, were critically evaluated. Finally, we highlighted future research directions that emphasize standardized study designs, defined endpoints, long-term randomized controlled trials, and integrative multi-omics approaches to support the development of personalized dietary strategies. Together, this review provides a structured framework for understanding the complex interactions between yogurt, gut microbiota, and host physiology, while outlining key steps needed to translate evidence into actionable nutritional recommendations.

Terminology

Starter cultures

S. thermophilus and L. bulgaricus only

Added probiotic strains

Strains supplemented beyond starters (e.g., Bifidobacterium spp., L. acidophilus)

Live microorganisms

Generic term encompassing starters and added probiotics when distinction is not needed

Yogurt-associated microorganisms

Used when referring to microbes that originate from yogurt (either starters or added probiotics) without specifying colonization status

Postbiotics

Inactivated microbial cells or their components

Fermentation-derived metabolites

Compounds produced during fermentation (e.g., BCHAs, peptides, EPS, lactic acid)

Microbiota-derived secondary metabolites

Compounds produced by resident gut microbes after yogurt consumption (e.g., SCFAs).

Acknowledgments

All authors have made substantial contributions to this work. The manuscript has not been previously published and that the manuscript is not under consideration elsewhere.
This research received financial support from Beijing Research Ward Excellence Program (BRWEP2024W034010103); Science and Technology Projects of Xizang Autonomous Region, China (XZ202501ZY0072, XZ202501JD0021); Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences (2024-RW320-01); National Key Research and Development Program of China (2024YFA0918500); Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (2022-I2M-1-003); Natural Science Foundation of Beijing Municipality (7232123).

Conflict of interest

The authors declare no conflict of interest.

Author contributions

All authors approved the final version of the manuscript, including the authorship list, and agreed to be accountable for the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. DY, HZ and KH contributed conception and searched the literature; DY, WC, HX, QX and SL prepared the figure and wrote sections of the manuscript; JY and DW reviewed the manuscript.

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