The last decade in microbiome research has allowed scientists to learn that diet is a major determinant of the composition and function of the human gut microbiota. However, one of the main challenges of human microbiome studies is determining the effects of specific nutrient groups on the microbiome. Although non-digestible carbohydrates are gut microbes’ preferred fuel and have attracted much attention in human dietary intervention trials, scientists have just started focusing on the role played by dietary fats—in terms of both quantity and quality—in human gut microbiome composition.

Numerous mice studies have largely studied how a high-fat diet induces alterations in gut microbiota, with the subsequent development of chronic disease risk. For instance, saturated fat and fish oil have shown dissimilar effects on the gut microbiome (here; here). Furthermore, high-fat diets containing either milk fat, corn oil or olive oil have been shown to alter relative gut microbe concentrations and predicted functions in mice. Together, these findings in mice highlight the importance of considering fat quality in microbiome research.

Exploring the effect of dietary fats on the gut microbial ecosystem in humans is not as easy as in rodent studies, given that each individual gut microbiome profile tends to remain unaltered in response of environmental factors related to diet.

In a recent systematic review, human observational and intervention studies—the latter of which showed the limited effects of fat type on the gut microbiota—have revealed associations between total fat intake—mainly saturated fatty acids—and a reduction in total bacterial number, bacterial richness and diversity in the gut.

For instance, high intake of saturated fatty acids was positively associated with the abundance of Clostridium bolteae and Blautia, which have been related to increased insulin resistance and increased body mass index, respectively. In contrast, a diet rich in polyunsaturated fatty acids seems to be associated with favorable changes in gut microbiota composition, with opposite effects when comparing omega-3 versus omega-6 fats. The effects of monounsaturated fatty acids on microbiome composition were less consistent and deserve further study.

As most of the studies included measured gut microbiota composition according to quantitative polymerase chain reaction and fluorescence in situ hybridization methods, rather than whole genomics sequencing, there is a call for new human intervention studies with next generation sequencing methods when exploring the impact of dietary fats on the gut microbiota. Furthermore, long follow-up periods, close control of participants´ compliance, as well as personnel blinding prior to study evaluation, are needed to lessen the risk of bias, together with a complete reporting of the studies’ outcomes.

Two recent randomized controlled trials (RCTs) have shed light on the impact of dietary omega-3 and omega-6 polyunsaturated fatty acids on gut microbiota composition and bacterial metabolites in healthy adults.

The first one found that a daily intake of 4g of the omega-3 polyunsaturated fatty acids eicosapentaenoic and docosahexaenoic over 8 weeks in middle-aged volunteers (n = 22) may lead to reversible changes at gut family and genus levels, including short-chain fatty acid producers.

More recently, a 6-month RCT with a larger sample of healthy adults (n = 217) has looked at how three dietary patterns differing in carbohydrate and fat proportions affect the gut microbiota, fecal bacterial metabolites and markers of inflammation.

None of the three diet groups changed microbial community richness during the study. However, dietary fat mainly coming from soybean oil, rich in omega-6 polyunsaturated fatty acids, had a selective effect on the human gut bacteria. At the genus level, the higher-fat diet (40% fat from soybean oil and 46% carbohydrate from rice and white flour) led to a decrease in the abundance of butyrate producers Faecalibacterium and Blautia and an increase in the abundance of Alistipes and Bacteroides, which have been related to imbalanced glucose metabolism, compared with the lower-fat diet. Furthermore, Blautia and Bacteroides showed correlations with serum total cholesterol, low-density lipopolysaccharide-cholesterol and high-density lipopolysaccharide-cholesterol.

When compared with the middle- and low-fat groups, the higher-fat diet also led to a decreased fecal concentration of butyrate and total short-chain fatty acids, and increased inflammatory markers including C-reactive protein, thromboxane B2, leukotriene B4 and prostaglandin E2. The observed differences in fecal short-chain fatty acids could be explained by the high content of carbohydrates in the moderate-fat and low-fat diets, with resistant starch from white rice and bread possibly fermented by the gut microbiota.

In contrast, the lower-fat diet increased Faecalibacterium and Blautia abundance and increased butyrate fecal levels.

In conclusion, different levels of scientific evidence based on mouse and human studies support that idea that the role of dietary fat in shaping gut microbiota composition should be considered from now on. Most importantly, the above findings highlight how both fat quantity and the influence of dietary fat types should be studied in future gut microbiome and related fecal metabolomics studies.




Wolters M, Ahrens J, Romaní-Pérez M, et al. Dietary fat, the gut microbiota, and metabolic health – A systematic review conducted within the MyNewGut project. Clin Nutr. 2018. doi: 10.1016/j.clnu.2018.12.024.

Watson H, Mitra S, Croden FC, et al. A randomized trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota. Gut. 2018; 67(11):1974-83. doi: 10.1136/gutjnl-2017-314968.

Wan Y, Wang F, Yuan J, et al. Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial. Gut. 2019; 0:1-13. doi: 10.1136/gutjnl-2018-317609.