You may already know that a more diverse gut microbiota is linked to better general health. And when you think of what you can eat to boost microbial diversity, you might be thinking about fruit, veggies, and whole grain foods. If so, you are completely correct: these are all excellent choices for taking good care of your gut microbial community.

What you might not expect is that adding to your diet other foods, like coffee, tea, dark chocolate or even red wine, might also help boost your gut microbiota diversity.

This is one of the main findings of two studies published recently in the journal Science: one study from Belgium and the other from its neighbour, the Netherlands. These gut microbiota studies include the largest number of healthy people examined to date. And both studies concluded a person’s diet, lifestyle and medication intake have profound effects on the gut microbiota, which in turn could impact significantly on general health.

To arrive at that conclusion, researchers examined each individual’s stool samples. In fact, they looked at the stools of more than 4,000 people and analysed them to better understand how microbes interact with lifestyle factors. They mapped out the species of bacteria living inside the guts of the volunteers and were able to link the presence and abundance of some of those bacteria to the people’s measurements and reported activities.

The first study, led by researcher Jeroen Raes, from the Flanders Institute of Biotechnology, was based on the ‘Flemish Gut Flora Project’.Started in 2012, this project is one of the largest population-wide studies on gut microbiota variation among healthy volunteers. Raes and colleagues analysed more than 1000 human samples and cross-checked their results with a Dutch health monitoring program called LifeLines.

The researchers identified 69 factors associated with gut microbiota composition, and most of those factors were linked to diet. For instance, they observed that a diet rich in sugar is linked with the presence of bacteria that process simple carbohydrates but prevent other microbial species from growing. They also saw that the more fiber in the diets of volunteers, from fruits, vegetables, legumes, and whole grain bread, the more diverse the gut microbiota was.

The researchers also saw a correlation between gut microbiota diversity and beer consumption, for reasons not yet clear. This was also true for dark chocolate, but not milk chocolate. The authors of the study think this is probably due to some cocoa compounds more abundant in dark chocolate.

“Our research has given us a tremendous amount of new insight into the microbiota composition of normal people like you and me…The majority of previous studies focused on specific diseases… However, analysing the ‘average’ gut microbiota is essential for developing gut bacteria-based diagnostics and drugs. You need to understand what’s normal before you can understand and treat disease”, states Raes in a press release.

The study also found drugs have a strong influence on gut microbiota: not only antibiotics, as expected, but also laxatives, antihistamines, hormones and anti-inflammatory drugs.

In the second study, led by geneticist Cisca Wijmenga, from Groningen University (The Netherlands), the researchers analysed 1135 stool samples and similarly identified some beneficial food for gut microbiota diversity: in addition to fruits and vegetables, they found nuts, coffee, tea, and red wine favoured the diversity of bacteria.

“In total we found 60 dietary factors that influence the diversity. There is a good correlation between diversity and health: greater diversity is better”, says researcher Alexandra Zhernakova from the University of Groningen.

These results, though, don’t mean you should scarf down chocolate and give up your medication in the name of a better gut. “For now, these are really just associations. We don’t really know the cause or consequence of them”, cautions Raes.




  1. Zhernakova, A. Kurilshikov, M. J. Bonder et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversityScience, 2016; 352 (6285): 565 DOI:10.1126/science.aad3369

G. Falony, M. Joossens, S. Vieira-Silva, et al. Population-level analysis of gut microbiome variationScience, 2016; 352 (6285): 560 DOI: 10.1126/science.aad3503