Eggs: Are They On The Menu For Your Gut Microbiome?

“They couldn’t even boil an egg!” might be how you describe someone who couldn’t cook to save their life. But if cooking an egg is considered so simple, then why are scientists making such a meal to work out whether eggs are good or bad for health?

It has now been over 50 years since the American Heart Association first suggested we should be limiting egg intake to help protect us from heart disease. In that time, research has helped us further understand the links between egg consumption and heart health but confusion persists as to whether eggs are a ‘healthy’ food or not.

Much of the reason for this confusion is that the link between diet and health is not simple. Nutrition experts will often tell you there are no ‘good’ or ‘bad’ foods. The health of a diet is not determined by the intake of any one nutrient or food but rather by how the balance of these matches the personal requirements of the individual.

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Eggs and heart disease

The main reason behind the American Heart Foundation’s recommendation to limit egg intake is due to the link between the cholesterol found in egg yolks and the risk of heart disease. Cholesterol is a type of fat, which at high levels in the blood is a well-studied risk factor for heart disease.

However, what has been less clear is whether the amount of cholesterol in your diet is important in determining the amount of cholesterol in your blood. The current understanding is that although the amount of cholesterol in your diet does have a small impact on your blood cholesterol levels, the intake of foods that are rich in saturated or trans fat is much more important1. Sources of saturated fat include butter, lard, palm oil and coconut oil, as well as products made from these, such as biscuits, cakes and ice cream.

What is perhaps more important is considering whether eating eggs is associated with an increased risk of heart disease.

Although the research is still ongoing, the current consensus is that eggs have a neutral relationship with heart health, meaning they neither increase nor decrease the risk of heart disease.

The only exception to this is in people with type 2 Diabetes Mellitus, where research has shown that consuming more than 7 eggs per week is associated with 69% more heart attacks or strokes1. For this reason, the National Heart Foundation of Australia recommends that people with type 2 diabetes limit their egg intake to a maximum of 7 eggs per week.

Eggs and the microbiome

An emerging area of science is exploring the link between egg consumption and the microbes living within our gut. Some nutrients we eat are digested and absorbed in the small intestine, while others are delivered to the colon, where microbes convert them into compounds that impact human health.

An emerging risk factor for heart disease is a compound called trimethylamine-n-oxide or TMAO. Studies have shown that people with the highest blood levels of TMAO have a 62% increased risk of heart attack or stroke compared to those with the lowest levels of TMAO2.

Image caption: Fig 1. Trimethylamine is produced by gut microbes before it is transported to the liver and converted to trimethylamine-n-oxide (TMAO).

TMAO in the blood originates from the microbiome. Some microbes can convert choline and carnitine into a compound called TMA or trimethylamine. This is then absorbed and converted in the liver to TMAO (Fig 1.).

Eggs are the richest dietary source of choline, so until recently, if someone’s microbiome contained lots of microbes with the capacity to produce TMA they were advised to limit their consumption of eggs. However, in recent years numerous research studies have confirmed that egg consumption does not lead to increased blood levels of TMAO3.

The reason for this is that eggs contain a lipid-soluble form of choline which is very well absorbed in the small intestine so does not reach the microbes in the colon and therefore does not lead to the microbial production of TMA4. As such, if someone has a high potential to make TMA in their microbiome we no longer recommend limiting egg intake and instead suggest they focus on the reduction of dietary carnitine, mostly found in red meat.

The link between red meat intake and heart disease is well established, with the National Heart Foundation of Australia recommending that heart-healthy dietary patterns should include a maximum of 350g (cooked weight) of unprocessed red meat per week. We now understand that this recommendation is of particular importance for those with a high capacity to produce TMA in their microbiomes.

Although we no longer recommend reducing the intake of choline-rich foods (such as eggs), if someone has a high potential to make TMA in their microbiome, it may still be warranted to avoid choline supplements. Most choline supplements contain water-soluble choline, which does reach the microbiome and can lead to increased blood TMAO levels4.

Unfortunately, this does not mean that eggs are totally out of the spotlight when it comes to personalising diet to the microbiome. Some microbes are able to convert the sulphur-containing amino acids, cysteine and methionine, into hydrogen sulphide gas5. Elevated levels of hydrogen sulphide can be toxic to the gut barrier, leading to gut inflammation in susceptible individuals. If a person has a high potential to make hydrogen sulphide in their gut microbiome, they may wish to limit their intake of sulphur-containing amino acids, which are found in high amounts in eggs, poultry and fish.


The role of eggs in a healthy diet has been debated for many decades. The reason for the confusion is that whether a person should be increasing or decreasing their egg intake depends on many individual factors, including their current diet, nutritional needs, medical history and the composition of their microbiome.

The good news is that for most of us, the latest research says that consuming eggs as part of a healthy dietary pattern is not linked to an increased risk of heart disease and does not lead to an increase in microbial TMA production.

Including eggs as part of a healthy diet can be an important source of nutrients, including protein, vitamin B12, iron, and vitamin D.

Testing your microbiome can help to identify a high potential to produce trimethylamine (TMA) and hydrogen sulphide. Those with a high potential to produce hydrogen sulphide may benefit from avoiding excessive egg consumption.

For those with type 2 diabetes, the National Heart Foundation of Australia recommends limiting egg intake to a maximum of 7 eggs per week. Others may avoid eggs completely due to egg allergies or a vegan or lacto-vegetarian diet.

We always recommend testing the gut microbiome with a certified Co-Biome Practitioner who has received training on interpreting the Co-Biome report and is uniquely placed to develop personalised dietary plans to meet individual health needs and goals.

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Heart Foundation. Eggs and cardiovascular health. Summary of Evidence NHFA: Melbourne (2019). Doi:
Heianza Y, Ma W, Manson JE, Rexrode KM, Qi L. Gut Microbiota Metabolites and Risk of Major Adverse Cardiovascular Disease Events and Death: A Systematic Review and Meta-Analysis of Prospective Studies. J Am Heart Assoc, 6(7):e004947 (2017). Doi: 10.1161/JAHA.116.004947
Zhu C, Sawrey-Kubicek L, Bardagjy AS, Houts H, Tang X, Sacchi R, Randolph JM, Steinberg FM, Zivkovic AM. Whole egg consumption increases plasma choline and betaine without affecting TMAO levels or gut microbiome in overweight postmenopausal women. Nutr Res, 78:36-41 (2020). Doi: 10.1016/j.nutres.2020.04.002. Epub 2020 Apr 22. PMID: 32464420
Cho CE, Aardema NDJ, Bunnell ML, Larson DP, Aguilar SS, Bergeson JR, Malysheva OV, Caudill MA, Lefevre M. Effect of Choline Forms and Gut Microbiota Composition on Trimethylamine-N-Oxide Response in Healthy Men. Nutrients,12(8):2220 (2020). Doi: 10.3390/nu12082220. PMID: 32722424; PMCID: PMC7468900
Yao CK, Rotbart A, Ou JZ, Kalantar-Zadeh K, Muir JG, Gibson PR. Modulation of colonic hydrogen sulfide production by diet and mesalazine utilizing a novel gas-profiling technology. Gut Microbes, 9(6):510-522 (2018). Doi: 10.1080/19490976.2018.1451280. Epub 2018 May 9. PMID: 29561196; PMCID: PMC6287689.
Missimer A, Fernandez ML, DiMarco DM, Norris GH, Blesso CN, Murillo AG, Vergara-Jimenez M, Lemos BS, Medina-Vera I, Malysheva OV, Caudill MA. Compared to an Oatmeal Breakfast, Two Eggs/Day Increased Plasma Carotenoids and Choline without Increasing Trimethyl Amine N-Oxide Concentrations. J Am Coll Nutr, 37(2):140-148 (2018). Doi: 10.1080/07315724.2017.1365026. Epub 2018 Jan 9. PMID: 29313753.
Lemos BS, Medina-Vera I, Malysheva OV, Caudill MA, Fernandez ML. Effects of Egg Consumption and Choline Supplementation on Plasma Choline and Trimethylamine-N-Oxide in a Young Population. J Am Coll Nutr, 37(8):716-723 (2018). Doi: 10.1080/07315724.2018.1466213. Epub 2018 May 15. PMID: 29764315.