The importance of a healthy gut microbiota for overall well-being and health is well known. And when that community of bacteria is unbalanced, we also know that it is linked to a broad range of diseases, from allergies, obesity and cardiovascular illness to IBS and even lupus, and that it also plays a role in mental health. We are therefore advised to take good care of our gut microbiota—in general, through diet.

Paradoxically, even though doctors have repeated the mantra over the last decade about how necessary a rich, resilient, and balanced gut bacterial community is to keep disorders at bay, the truth is we still do not know what a healthy gut microbiota looks like.

The guts of different healthy individuals can have different microbial compositions. Indeed, although all human beings share more than 99.8% of their DNA, only 30% of the gut microbiome is the same for everyone. The rest is therefore variable and unique to each individual. So, how can we know which combination or combinations of microorganisms are associated with health?

That is the question a new study by researchers at the University of Groningen in the Netherlands has tried to answer. Its results, published in Nature, shed light on the signature of a healthy and unhealthy microbiome in health and disease and may open the door to the future development of microbiota-targeted therapies.

Scientists profiled the gut bacterial composition of 8,208 Dutch individuals from a three-generational cohort, called the Dutch Microbiome Project, comprising nearly 3,000 families. They analyzed the extent to which the gut microbiota is driven by factors such as genetics or modifiable environmental factors, such as diet, lifestyle or even pollution. Then, they related host and environmental factors to bacterial composition.

What they have found was that there are nine core species in our guts, which we all share. Moreover, five have key roles in the microbial ecosystem. One such example is F. prausnitzii, a major producer of butyrate, a beneficial short fatty acid that shows an important coabundance with Bacteroidetes and Bifidobacterium species, which are known to be highly beneficial.

Even though it has long been suspected that most of the microbiome was shaped by the ‘bugs’ inherited from mothers during birth and genetics, the Dutch researchers identified that the microbiome is shaped primarily by the environment and cohabitation. In fact, they observed that only around 6.6% of taxa are heritable, whereas almost 50% are significantly explained by cohabitation. So, the gut microbiota of people living in the same house is more similar than those of people living separately, regardless of the relatedness of the participants. In other words, you may have more microbes in common with your flatmate than you do with your own family.

The researchers identified nearly 3,000 associations between the microbiome and health and concluded that seemingly unrelated diseases share a common microbiome signature.

For instance, they observed associations between the presence of some microbiota features and diet, socioeconomic status, early life, and environment. The first two or three years of life are crucial for microbiota development and the researchers noted that childhood living environment—having pets, living in a rural/urban area, access to green areas, having parents who smoke, pollution—significantly shaped what the adult microbiota would be like.


Conclusions and takeaway

As expected, the results of the study show that lifestyle factors that are generally considered to be healthy, such as following a healthy diet, not smoking, and living in a green and unpolluted area, are linked to microbiota patterns associated with general health.

“We observed that healthier diet, childhood and current exposures to rural environment and pets, exposure to green space and higher income share signals with healthy microbiome patterns,” state the authors in the paper.

They also highlight how such observations support the microbiome diversity hypothesis (also called the hygiene hypothesis), which suggests that reduced exposure to environmental microbiota contributes to an increase in the frequency of autoimmune and allergic diseases.

“Whereas the classic hygiene hypothesis focuses on pathogens and early-life exposures,” they conclude, “our results suggest that adult exposures also contribute to healthy or unhealthy microbiome patterns and that the environment shapes the microbiome throughout life, meaning that microbiome-targeted therapies could be effective throughout an individual’s life.




Gacesa, R., Kurilshikov, A., Vich Vila, A. et al. Environmental factors shaping the gut microbiome in a Dutch populationNature 604, 732–739 (2022).