A Healthy Gut Microbiome is Fundamental for Optimal Health

What we eat is inextricably linked to human health.  Decades of scientific evidence tells us that diets low in unprocessed plant-based foods are the cause of more diet-related deaths from cardiovascular disease, cancers and type-2 diabetes than from any other risk factor (1).  We also have plenty of data linking specific tiny inhabitants of the gut microbiome to health, both good and bad.  Plant-sourced foods are fermented by “good” gut microbes to produce short-chain fatty acids (SCFAs) which not only promote a healthy gut barrier and lower inflammation but also enhance the health of many other body systems.  Conversely, animal-sourced foods foster different types of microbes which ferment protein, a process which is associated with escalating inflammation both in the gut and in chronic low-level inflammation throughout the body.   These microbes are also linked to increased risks of chronic diseases such as cardiovascular disease and colorectal cancer.  But how do we get those “good” gut microbes into our microbiomes?  (2,3)

A new investigation (4), published January 6, 2025, examined data from over 21,000 individuals from 5 different multinational cohorts (including people from the United States, the United Kingdom, and Italy) to discover how differences in the foods that they are eating are reflected within gut microbiomes. The cohorts consisted of 656 vegans, 1,088 vegetarians, and 19,817 omnivores. Each participant reported their nutritional habits as omnivorous (including meat, dairy and vegetables), vegetarian (excluding meat) or vegan (excluding meat, dairy and other animal products).  The participants also donated stool samples for genetic sequencing to ascertain the species of microorganisms making up their individual gut microbiomes.  Data on the consumption of specific foods was obtained from validated food frequency questionnaires and partially confirmed by DNA-based detection of food types in the stool microbiome.

Study results reveal that the types of foods consumed (the dietary pattern) strongly influences the population of microbes in each person’s gut microbiome. The dietary pattern supports microbes necessary to process the foods being eaten and allows unnecessary microbes to recede into the background or disappear completely.  Dietary patterns are such a strong influence on the microbiome that the species of microbes present in a certain microbiome profile can reliably predict the foods being consumed by that person.

 

This study also linked gut microbiome composition to cardiometabolic health.

Note (5):  Cardiometabolic health means health of the cardiovascular system (heart, blood and blood vessels) and the risk factors that affect it.  These include;

• Body mass index and waist circumference in ideal ranges
• Normal blood sugar levels (without the help of medication)
• Ideal cholesterol levels (without the help of medication)
• Normal blood pressure (without the help of medication)
• No evidence of prior heart disease such as a heart attack or stroke

 

This analysis found that red meat consumption creates “omnivore” microbiomes that are correlated with poor cardiometabolic health.  Such microbiomes have an increased presence of bacteria implicated in inflammatory diseases such as inflammatory bowel disease, colorectal cancer and a decrease in health-giving SCFAs.

On the other hand, diets high in unprocessed plant-sourced foods and lacking in animal-sourced foods create “vegan” microbiomes that are correlated with favourable cardiometabolic health. These microbiomes are rich in bacteria involved in the fermentation of fiber and the production of health-giving SCFAs such as butyrate.  Such microbes are associated with beneficial effects on the health of the gut itself as well as reduced whole-body inflammation, an enhanced immune system, and lowered risks of developing obesity, diabetes, cancer, cardiovascular disease and liver disease.

This study also noted that diversity in the microbiomes of vegans and vegetarians was lower than in omnivores.  However, diversity does not take into account the quality and functionality of the bacteria present.  The researchers observed that the impact of eating plant-sourced foods has a very positive effect on the microbiome.  Simply avoiding meat or dairy products will not be beneficial for health unless the person is consuming a variety of plant-sourced products as well.  In fact, whether they are vegans, vegetarians or omnivores, people who eat healthier dietary patterns that include lots of different plant-sourced foods will have a microbiome made up of healthier microbes.  What makes our microbiomes thrive is a wide assortment of foods from naturally fiber-rich plants.

 

To Sum Up (4)…

• Dietary choices are directly related to the composition of the microbiome.
• Emphasizing plant-sourced foods results in a healthy microbiome and, in turn, favourable cardiometabolic health.
• Emphasizing animal-soured foods results in an unhealthy microbiome and poor cardiometabolic health.
• Increasing the intake of plant-sourced foods in any dietary pattern can improve gut health and overall cardiometabolic health.

 

SOURCES:

1  Afshin, A. et al. Health effects of dietary risks in 195 countries, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2019; 393:1958–1972.

2  Valles-Colomer, M. et al. Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. 2023.  Nat. Med.; 29:551–561.

3  Xiong, R.G., Zhou, D.D., Wu, S.X., Huang, S.Y., Saimaiti, A., Yang, Z.J., Shang, A., Zhao, C.N., Gan, R.Y., Li, H.B. Health Benefits and Side Effects of Short-Chain Fatty Acids. Foods. 2022 Sep 15;11(18):2863. Doi: 10.3390/foods11182863. PMID: 36140990; PMCID: PMC9498509.

4  Fackelmann. G., Manghi, P., Carlino, N., Heidrich, V., Piccinno, G., Ricci, L., et al.  Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. Nat Microbiol. 2025 Jan;10(1):41-52. Doi: 10.1038/s41564-024-01870-z. Epub 2025 Jan 6. PMID: 39762435.

5  https://www.health.harvard.edu/blog/how-good-is-your-cardiometabolic-health-and-what-is-that-anyway-202208182803