# Causal Effects of Yogurt Intake on Gut Microbiota: A European Mendelian Randomization Study

**Authors:** Mengqi Yang, Liping Wang, Peng Zhou, Jiazeng Xia

PMC · DOI: 10.1155/ijog/2921181 · International Journal of Genomics · 2026-03-03

## TL;DR

This study investigates how yogurt consumption affects gut bacteria using genetic data from European populations.

## Contribution

The study provides causal evidence linking yogurt intake to specific gut microbiota changes using Mendelian randomization.

## Key findings

- Yogurt intake is linked to increased abundance of Haemophilus and Clostridium sensu stricto_1.
- Low-fat yogurt is associated with increased Eubacterium ruminantium and Methanobacteriaceae.
- Yogurt consumption decreases the abundance of Ruminococcaceae UCG-011 and Betaproteobacteria.

## Abstract

Yogurt is reported to maintain the balance of gut microbiota and prevent disease, but the causal relationship remains unclear.

We selected data from UK Biobank and MiBioGen to perform Mendelian randomization analysis. MR Egger, inverse variance weighted, and so forth were employed to assess the causality between yogurt intake, low‐fat and full‐fat yogurt, and 196 taxa of gut microbiota. Parallelly, low‐fat and full‐fat yogurt were integrated to perform multivariable Mendelian randomization. Then, we summarized preliminary results according to microbiotic taxonomy.

Statistics hinted at the implicit associations between yogurt intake and Haemophilus (OR = 2.08), Clostridium sensu stricto_1 (OR = 1.84), Peptostreptococcaceae (OR = 1.53), Betaproteobacteria (OR = 0.70), Bilophila (OR = 0.58), and Ruminococcaceae UCG-011 (OR = 0.40), along with the associations between low‐fat yogurt and Eubacterium ruminantium (OR = 2.48), Methanobacteriaceae (OR = 3.06). The findings were causal and consistent, albeit with some false positive rates.

Yogurt intake suggestively increased the abundance of Haemophilus, Clostridium sensu stricto_1, and Peptostreptococcaceae and decreased the abundance of Ruminococcaceae UCG-011, Betaproteobacteria and Bilophila; low‐fat yogurt suggestively increased the abundance of Eubacterium ruminantium and Methanobacteriaceae.

## Linked entities

- **Species:** Haemophilus (taxon 724), Peptostreptococcaceae (taxon 186804), Betaproteobacteria (taxon 28216), Bilophila (taxon 35832), Eubacterium ruminantium (taxon 42322), Methanobacteriaceae (taxon 2159)

## Full-text entities

- **Genes:** TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}
- **Diseases:** appendicitis (MESH:D001064), inflammation (MESH:D007249), epilepsy (MESH:D004827), autism spectrum disorder (MESH:D000067877), death (MESH:D003643), Parkinson's disease (MESH:D010300), narcolepsy Type 1 (MESH:C563534), neuropsychiatric disorders (MESH:D001523), dilated cardiomyopathy (MESH:D002311), pregestational diabetes (MESH:D003920), immunologic disorder (MESH:D007154), attention deficit hyperactivity disorder (MESH:D001289), knee osteoarthritis (MESH:D020370), MVMR (MESH:C562757), age-related macular degeneration (MESH:D008268), urinary urolithiasis (MESH:D052878), proinflammatory cytokine (MESH:D000080424), irritable bowel syndrome (MESH:D043183), Type 2 diabetes (MESH:D003924), autoimmune diseases (MESH:D001327), obesity (MESH:D009765), inflammatory bowel disease (MESH:D015212), bipolar disorder (MESH:D001714), primary biliary cholangitis (MESH:D008105), atopic dermatitis (MESH:D003876), cognition impairment (MESH:D003072), non-small-cell lung cancer (MESH:D002289), myasthenia gravis (MESH:D009157)
- **Chemicals:** LPSN (-), lipid (MESH:D008055), glucose (MESH:D005947), SCFA (MESH:D005232), calcium (MESH:D002118)
- **Species:** Eubacterium ruminantium (species) [taxon 42322], Methanobacteriaceae (family) [taxon 2159], Methanobacteriota (euryarchaeotes, phylum) [taxon 28890], Bilophila (genus) [taxon 35832], Clostridium (genus) [taxon 1485], Haemophilus (genus) [taxon 724], Lactobacillus (genus) [taxon 1578], Bifidobacterium (genus) [taxon 1678], Homo sapiens (human, species) [taxon 9606], Desulfovibrionales (order) [taxon 213115], Betaproteobacteria (b-proteobacteria, class) [taxon 28216], Clostridiaceae (family) [taxon 31979], Methanobacteria (class) [taxon 183925], Methanobacteriales (order) [taxon 2158], Eubacteriales (order) [taxon 186802]
- **Mutations:** rs6888979, rs149870452, rs9604488, rs317656, rs2517506

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12957542/full.md

## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12957542/full.md

## References

58 references — full list in the complete paper: https://tomesphere.com/paper/PMC12957542/full.md

---
Source: https://tomesphere.com/paper/PMC12957542