Eating Fat and Your Microbiome

The media has been sending out very mixed messages in the last few years regarding the effects of fat in our daily diet. Some headlines announce “Fat is Back!” while serious scientific research that gathers evidence about the very real harms of eating saturated fat are quietly relegated to the background. The scientific community is learning that the microorganisms in our digestive system play a pivotal role in both health and disease, affecting many body processes including the immune system, the cardiovascular system, the brain, control of blood sugar level and body weight. This information is spreading and many people are now aware that a healthy gut microbiome with high species diversity is associated with decreased risks for the development of many common chronic diseases. So let’s look at dietary fat from the point of view of the microscopic residents inhabiting our gut.

The outcomes of a new study from China examining the effects of eating fat on the human microbiome were published in January of 2019 (1). Researchers recruited 217 healthy young adults between the ages of 17 and 35 and fed them one of three diets, all equal in calories, for six months. All food was provided to the participants for the duration of this study.
The three diets were;
1 A lower-fat diet (with fat providing 20% of the energy from the diet along with 66% from carbohydrate and 14% from protein)
2 A moderate-fat diet (with fat providing 30% of the energy from the diet along with 56% from carbohydrate and 14% from protein)
3 A higher-fat diet (with fat providing 40% of the energy from the diet along with 46% from carbohydrate and 14% from protein).
The effects of these three diets on the gut microbiota, the faecal (stool) composition and body inflammation were observed and analyzed.

Here are the results (1);

All three groups lost weight during the intervention.

The lower-fat diet was associated with;
– weight loss and reduction in waist circumference significantly greater than that of the higher-fat group
– reductions in total cholesterol, LDL-cholesterol, HDL-cholesterol and non-HDL cholesterol significantly greater than those in the higher-fat group
– increased diversity in the gut microbiota relative to the higher-fat diet
– alterations in the content of the gut microbiota with increased abundance of species of Faecalibacterium and Blautia
– decreased amounts of p-cresol and indole, two metabolites known to be associated with metabolic disorders
– reduced inflammatory markers in the blood

The higher-fat diet was associated with;
– reduced diversity in the gut microbiota relative to the lower-fat diet
– alterations in the content of the gut microbiota with decreased numbers of Faecalibacterium species and increased numbers of Alistipes and Bacteroides species
– increased arachidonic acid (an inflammatory fatty acid) in the stool
– elevated inflammatory markers in the blood
– significant and potentially detrimental changes in the metabolism of long-chain fatty acids that can trigger inflammation
– compared to the other diet groups, the higher-fat group showed significantly reduced concentration of the short-chain fatty acids produced by beneficial gut microorganisms that are linked to so many of the health advantages stemming from a robust gut microbiome

Soybean oil was added to the diets used in this study where necessary to reach their required levels of fat. In real world diets, fat intake is often skewed more toward saturated fat from animal-based foods and processed foods and such fat intake might show further detrimental effects beyond what was observed in this study. More research is necessary to determine the specific influences of different fat types on the environment and microorganisms of the gut (1).

The researchers involved in this study concluded that nutritional guidelines should advise against increased intakes of dietary fat and that the goal for fat content in the diets of the general healthy population should strive to be under 30% of total energy intake. Changes in microbiome seen during this study were produced without increasing calorie intake or body weight and yet they are similar to those created by obesity and type-2 diabetes. The researchers noted that the consequences of higher fat intake illustrated by this study may help to explain the dramatic increase in cardiovascular disease, type-2 diabetes and obesity that has been observed in recent years in China as the country’s dietary habits evolve from a traditional low-fat high-carbohydrate diet to a more Westernized diet style that is high in fat and reduced in carbohydrate (1).

This study corroborates previous research that has found detrimental effects on gut health from eating fat. A 2016 review examined the relationship between a high-fat diet, the gut microbiota and gastrointestinal diseases, noting that diet in general is an important factor in determining the composition of microorganisms in the gut. Dietary changes can rapidly affect the number of organisms and species types in the intestinal microbiome with significant alterations in its structure and stability occurring in as few as four days. Experiments in both animals and humans have shown that a high-fat diet will decrease beneficial species and increase harmful species in the gut microbiome while a low-fat diet does just the opposite. A diet that is high in fat, especially saturated fat, is closely associated with obesity, metabolic syndrome and gastrointestinal diseases such as colorectal cancer, inflammatory bowel disease (including Crohn’s Disease and ulcerative colitis), irritable bowel syndrome and non-alcoholic and alcoholic fatty liver disease (2) .

A review from 2015 looked at the changes in gut microbe composition caused by high-fat diets and the subsequent development of obesity and other chronic diseases. Emerging literature implicates high-fat-induced increases in Firmicutes species and decreases in Bacteriodetes species as probable drivers of this effect. These gut microbiome alterations may result in increased extraction of energy from foods as well as more efficient storage of that energy resulting in greater obesity risk. Also, higher permeability of the gut and increased inflammation may be linked to increased incidence of chronic diseases such as cardiovascular disease, type-2 diabetes and cancer (3).

It is in our best interests to support a healthy gut microbiome. We are only just beginning to realize the far-reaching effects of the activities of these tiny inhabitants in our gut. High fat diets cause multiple changes in the intestinal microbiota that result in detrimental alterations in the species present as well as the overall diversity of species. If we want to encourage the “good” microorganisms in our intestines, we need to eat diets lower in fat and higher in carbohydrates.



1 Wan, Y., Wang, F., Yuan, J., Li, J., Jiang, D., Zhang, J., Li, H., Wang, R. 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 Microbiota. January 18, 2019.

2 Zhang, M., Yang, X.-J. Effects of a high fat diet on intestinal microbiota and gastrointestinal diseases. World J Gastroenterol. 2016 Oct 28; 22(40): 8905–8909.

3 Murphy, E.A., Velazquez, K.T., Herbert, K.M. Influence of High-Fat-Diet on Gut Microbiota: A Driving Force for Chronic Disease Risk. Curr Opin Clin Nutr Metab Care. 2015 Sep; 18(5): 515–520.

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My name is Debra Harley (BScPhm) and I welcome you to my retirement project, this website. Over the course of a life many lessons are learned, altering deeply-rooted ideas and creating new passions.

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