The Olive Wellness Institute is a science repository on the nutrition,
health and wellness benefits of olives and olive products, which is
all subject to extensive peer review.

The Mediterranean Diet and the Microbiome

The Mediterranean Diet and the Microbiome


The human microbiome is a complex environment and we are just beginning to touch the tip of the iceberg in our understanding of how this symbiotic relationship affects our health. This article aims to briefly touch on what we do know about the symbiotic relationship between humans and our microbiota, and ways in which we can support its proper health by following a Mediterranean Diet.     




The human microbiome is a complex and diverse habitat of over 1000 different species of bacteria that can contribute to a mass of over 2 kg in the average human gut.1 There are many hypothesized relationships occurring between the food you eat, the health and diversity of your gut microbiota and your overall health.2,3,4 Could the Mediterranean diet provide an ideal combination of foods and lifestyle for the human microbiome?



The Mediterranean diet: Great for heart health, metabolic health, brain health… And gut health?

The abundance of scientific evidence of the benefits of the Mediterranean Diet on cardiovascular and metabolic systemic disease is staggering. Suffice to say that it’s relationship in helping manage, and in some cases even eliminate, these major diseases has been well established. From keeping our cholesterol balanced and in check by raising the beneficial high-density lipoproteins which in turn lower low-density lipoproteins (LDL)5, to helping with chronic inflammation6, to the high number of antioxidants and their various health benefits7, to its protective nature to many neurodegenerative diseases8 we have safely established that the Mediterranean diet is a healthy way to eat and live. However, with new popular interest in the human microbiome and its role in human health we had to ask the question: What is the role of the Mediterranean Diet on the human gut microbiome and, could this be where many of the health benefits of the Med Diet stem from?



A brief overview of the role the microbiome plays in digestion:

Our microbiota, the community of bacteria that live in our gut, thrive when there is a well-balanced diversity of bacteria inhabiting it.9 This diversity is unique to each different person and it has been tailor made by factors such as the circumstances of our birth, our genealogy and the foods that we have been eating our whole lives.10 The saying “you are what you eat” takes on a very literal meaning when talking about the microbiome, because everything you ingest will either add or detract from the microbiota living inside you. And here is where the role of diet and health come into play, because issues such as irritable bowel syndrome (IBS), chronic kidney disease (CKD) coeliac disease, functional dyspepsia, antibiotic associated diarrhoea and many more, occur when an imbalance, called dysbiosis, occurs in the bacterial community.11

The microbiota contributes to digestion mainly through 2 catabolic pathways: saccharolytic, which uses fermentation, and proteolytic, which uses putrefaction. To separate this into food groups, the saccharolytic pathway is the breaking down of fibres, carbohydrates and starches (i.e. plant-based foods), and proteolytic is the breakdown of proteins.11 While both processes need to occur and are natural and healthy, it is generally agreed that a healthy well-balanced colonic microbiota will be predominantly saccharolytic.11 This is mainly because during saccharolytic fermentation, beneficial short chain fatty acids are produced that have been shown to have a protective effect on the microbiome.4,12

The risk with the proteolytic pathway is that during the fermentation of certain animal proteins, such as red meats and processed meats, dangerous cancer-causing by-products can be produced.4,13 While consuming small amounts of animal protein has not been found excessively harmful, the danger lies in the risk of eating too much and not getting enough fibre to keep food moving through your bowels, amongst other issues.14 The addition of more fibre not only aids in promoting the favorable saccharolytic pathway, but it also aids in transporting the undigested food out of your colon before it can sit and begin to putrefy. And because of the Med diets focus on high amounts of fibre and healthy fats and lower amounts of animal proteins such as red meats, processed meats and dairy products, the Med diet favors the less risky saccharolytic pathway.4



How can the Mediterranean diet help shape your microbiome?

 A large issue that plagues many people that abide a mostly Westernized diet is a lack of fibre in their diet and an excess of animal products, encouraging the potentially risky proteolytic pathway.4 This imbalance can have dangerous repercussions, ranging from the discomfort of constipation to life threatening risks like colorectal cancer.4 In contrast, and as mentioned above, with the Mediterranean diets emphasis on plant-based foods, healthy fats, and active lifestyle, it is the ideal candidate to keep your microbiome happy and diverse.11 With the new health movement taking over social media and encouraging people to eat a more balanced diet, there has been an increase in the demand for research into the actual benefits of more plant-based diets rather than the more typical meat and dairy focused one.15 And what more and more studies are finding is that what we are eating is having large impact on the types of bacteria living in our microbiome.14

Studies show that individuals scoring higher Med diet scores have different, more beneficial, bacteria living in their microbiome compared to individuals with a lower Med diet score who eat more junk food and animal products.2,3. Individuals who score higher Med Diet scores have lower E. coli counts, a better overall balance between E. coli and bifidobacteria species, increased levels of fecal SCFA, and more frequent defecation.2,3 The balance between bifidobacteria and E. coli is significant because bifidobacteria are relatively delicate and very important bacteria in the saccharolytic pathway, and unfortunately they are easily taken over by bacteria that is more efficient to propagate, such as pathogenic E. coli.16 This is a risk because if this balance remains unchecked it can lead to dysbiosis, which is especially problematic seeing as bifidobacteria along with other bacteria species such as bacteroides, parabacteroides, clostridium, lactobacillus and faecalibacterium prausnitzii are all the main producers of the beneficial SCFA, and any loss to their numbers can have severe impacts on the overall healthy functioning of the microbiome.17 It should also be noted that commensal E. coli is thought to be one of the original colonizers of the human microbiome and is essential for a healthy gut. And it is the pathogenic E. coli that can pose the greatest risk to struggling gut bacteria because of its ability to take over, thereby causing dysbiosis.18



So, what does this all mean?

What the evidence seems to unanimously point to is that to have a healthy microbiome, it needs to favor the saccharolytic catabolic pathway, which produces more beneficial SCFA. It is generally agreed that a diet rich in whole natural plant foods leads to a more diverse microbiome and that eating an excess of animal protein can cause dysbiosis and can lead to increased risks of colon cancer, IBS, CKD, and countless inflammatory related gut issues. Therefore, if you eat a well-balanced diet with lots of fresh veggies, fruit, grains, legumes and plant fats and keep your intake of animal proteins and fats at a moderate to low level, you have a greater chance of promoting a healthy environment for your microbiota. And a healthy microbiota is a healthy human.

View article references


MetaHIT Consortium, Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010 Mar;464(7285):59–65.


Mitsou EK, Kakali A, Antonopoulou S, Mountzouris KC, Yannakoulia M, Panagiotakos DB, et al. Adherence to the Mediterranean diet is associated with the gut microbiota pattern and gastrointestinal characteristics in an adult population. British Journal of Nutrition. 2017 Jun;117(12):1645–55.


De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016 Nov;65(11):1812–21.


Yang J, Yu J. The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get. Protein & Cell. 2018 May;9(5):474–87.


Farràs M, Castañer O, Martín-Peláez S, Hernáez Á, Schröder H, Subirana I, et al. Complementary phenol-enriched olive oil improves HDL characteristics in hypercholesterolemic subjects. A randomized, double-blind, crossover, controlled trial. The VOHF study. Molecular Nutrition & Food Research. 2015 Sep;59(9):1758–70.


Souza P, Marcadenti A, Portal V. Effects of Olive Oil Phenolic Compounds on Inflammation in the Prevention and Treatment of Coronary Artery Disease. Nutrients. 2017 Sep 30;9(10):1087.



Konstantinidou V, Covas M-I, Muñοz-Aguayo D, Khymenets O, de la Torre R, Saez G, et al. In vivo nutrigenomic effects of virgin olive oil polyphenols within the frame of the Mediterranean diet: a randomized controlled trial. The FASEB Journal. 2010 Jul;24(7):2546–57.


Anastasiou CA, Yannakoulia M, Kosmidis MH, Dardiotis E, Hadjigeorgiou GM, Sakka P, et al. Mediterranean diet and cognitive health: Initial results from the Hellenic Longitudinal Investigation of Ageing and Diet. Feart C, editor. PLOS ONE. 2017 Aug 1;12(8):e0182048.

Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012 Sep;489(7415):220–30.



Forbes JD, Van Domselaar G, Bernstein CN. The Gut Microbiota in Immune-Mediated Inflammatory Diseases. Frontiers in Microbiology [Internet]. 2016 Jul 11 [cited 2018 Jul 25];7. Available from:


Montemurno E, Cosola C, Dalfino G, Daidone G, De Angelis M, Gobbetti M, et al. What Would You Like to Eat, Mr CKD Microbiota? A Mediterranean Diet, please! Kidney and Blood Pressure Research. 2014;39(2–3):114–23.


Morrison DJ, Preston T. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes. 2016 May 3;7(3):189–200.


Birkett A, Muir J, Phillips J, Jones G, O’Dea K. Resistant starch lowers fecal concentrations of ammonia and phenols in humans. The American Journal of Clinical Nutrition. 1996 May 1;63(5):766–72.


Zimmer J, Lange B, Frick J-S, Sauer H, Zimmermann K, Schwiertz A, et al. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European Journal of Clinical Nutrition. 2012 Jan;66(1):53–60.


Glick-Bauer M, Yeh M-C. The Health Advantage of a Vegan Diet: Exploring the Gut Microbiota Connection. Nutrients. 2014 Oct 31;6(11):4822–38.



O’Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Frontiers in Microbiology [Internet]. 2016 Jun 15 [cited 2018 Jul 26];7. Available from:


Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Medicine [Internet]. 2016 Dec [cited 2018 Jul 26];8(1). Available from:


Conway T, Cohen PS. Commensal and Pathogenic Escherichia coli Metabolism in the Gut. Microbiol Spectr. 2015 Jun;3(3).