Yoghurt and the gut microbiome: Effects on microbial composition

Yoghurt is a widely popular fermented milk product that is commonly consumed in Europe. Yoghurt is made through a fermentation process, in which bacterial cultures are added to milk, causing it to ferment and thicken. (1) The two strains commonly added to milk to create yoghurt are Streptococcus thermophilus and Lactobacillus delbrueckii subsp bulgaricus, but often additional bacterial strains are added, such as those from the Lactobacillus and Bifidobacterium genera.

Yoghurt can be an additional source of protein as the milk protein is highly digestible and bioavailable (1), but it is also often marketed as a digestive aid. We often see yoghurt ads that highlight the probiotic benefits of yoghurt, and many yoghurts we find in the supermarket will have some form of "live culture" or "bacterial strain" label on them. But what does that mean, and can the bacteria in yoghurt truly benefit our microbiome?

What does the evidence say?

The dynamics of the microbiome are still an emerging area of research, but several studies have looked at the impact of yoghurt consumption on microbial composition.

• One study from 2022 found an increase in microbial strains S. thermophilus and B. animalis subsp. lactis in the yoghurt consumption group. (2) However, the researchers noted that the presence of the bacteria was transient (i.e. temporary and not sustained over time). Additionally, the authors concluded that yoghurt consumption is often associated with overall healthier dietary patterns, which may act as a confounding factor when interpreting its effects on the microbiome. (2)

• Another crossover trial compared plain yoghurt consumption with yoghurt combined with rolled oats, suggesting that the addition of fibre from the rolled oats may enhance changes in microbial diversity. (3) An increase in yoghurt containing bacterial strains such as Streptococcus thermophilus and Lactobacillus delbrueckii was observed in the plain yoghurt group, however, researchers reported similar findings overall: a transient increase in yoghurt-derived bacterial strains with no significant long-term changes in microbial diversity. The addition of rolled oats contributed to increased microbial evenness (a more balanced distribution of bacterial strains) but again showed no evidence of lasting structural changes to the microbiome. (3)

• One cross-sectional study also reported a higher abundance of the bacterial subgroup Lactobacillus gasseri in yoghurt consumers. (4) Interestingly, researchers observed a higher increase in Lactobacillus casei subgroups in female participants compared to male subjects. These findings support the idea that microbiome responses are highly individual and may differ based on host factors.

  
  

What does that mean in practice?

• The bacterial strains present in yoghurt may provide temporary benefits as they transit through the digestive tract, as there is some evidence of increased detection of these strains following yoghurt consumption.

• However, the current consensus suggests that live cultures consumed through yoghurt rarely colonise the gut or lead to long-term changes in microbial composition. Instead, any potential benefits are likely due to their metabolic activity during transit rather than permanent integration into the gut microbiome. (5)

• A healthy, balanced diet rich in dietary fibre will likely play a far more significant role in supporting resident microbial populations. (6)

  
  

Key takeaway

Yoghurt can be a great source of additional protein in our diet, and the live cultures it contains may exert short-term functional benefits as they transit through the gut. However, we should not assume that these live cultures colonise the microbiome or lead to a sustained increase in beneficial bacteria.

References:

1. Sumi K, Tagawa R, Yamazaki K, Nakayama K, Ichimura T, Sanbongi C, Nakazato K. Nutritional value of yogurt as a protein source: digestibility/absorbability and effects on skeletal muscle. Nutrients. 2023 Oct 14;15(20):4366. doi:10.3390/nu15204366.

2. Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Falchi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD. Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome. BMC Microbiol. 2022 Feb 3;22(1):39. doi:10.1186/s12866-021-02364-2.

3. Thriene K, Stanislas V, Huang KD, Strowig T, Michels KB. Impact of yogurt and rolled oats consumption on the gut microbiome: a randomized crossover study displaying individual responses and general resilience. J Nutr. 2026 Apr;156(4):101408. doi:10.1016/j.tjnut.2026.101408.

4. Suzuki Y, Ikeda K, Sakuma K, Kawai S, Sawaki K, Asahara T, Takahashi T, Tsuji H, Nomoto K, Nagpal R, Wang C, Nagata S, Yamashiro Y. Association between yogurt consumption and intestinal microbiota in healthy young adults differs by host gender. Front Microbiol. 2017;8:847. doi:10.3389/fmicb.2017.00847.

5. Zaccaria E, Klaassen T, Alleleyn AME, et al. Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial. Microbiome. 2023;11:43. doi:10.1186/s40168-023-01491-4.

6. Fu J, Zheng Y, Gao Y, Xu W. Dietary fiber intake and gut microbiota in human health. Microorganisms. 2022 Dec 18;10(12):2507. doi:10.3390/microorganisms10122507.

Disclaimer: This article is for educational purposes only and does not replace medical advice. Individual needs vary, and personalised guidance from a qualified healthcare professional is recommended for tailored support.