Discover What a Healthy Gut Microbiome Looks Like

We frequently hear about the benefits of certain foods for your microbiome and overall health. However, the exact composition of a healthy gut microbiome has not been fully understood until now. A recent study involving over 34,000 individuals has advanced our knowledge of the microbial combinations that indicate low inflammation, robust immunity, and healthy cholesterol levels.

The gut microbiome influences various aspects of health, including the immune system, aging, and mental well-being. While many home testing kits claim to analyze gut composition, their effectiveness remains questionable, as defining a “healthy” microbial balance is complex.

Earlier efforts have mainly concentrated on species diversity, under the assumption that a greater variety of bacteria is beneficial. However, since microbiomes differ significantly between individuals, pinpointing specific microbial communities linked to particular health outcomes is challenging.

“The interplay between our diet, gut microbiome composition, and health is intricate. The only way to unravel these connections is through large sample sizes,” explains Nicola Segata from the University of Trento, Italy.

To develop a comprehensive understanding, Segata and his team analyzed data from over 34,500 participants in the PREDICT program, conducted in the UK and the US by the microbiome testing company Zoe, and cross-referenced the findings with data from 25 additional cohorts in Western nations.

Among the thousands of bacterial species in the human gut, researchers focused on 661 species present in over 20% of Zoe participants. They identified 50 bacteria closely linked to health markers, such as BMI and blood glucose levels, as well as 50 associated with poor health.

The 50 “good” bacterial species (22 of which are newly identified) seem to affect four key areas: inflammation and immune function, body fat distribution, and blood sugar regulation.

Healthy participants, with no known medical issues, carried approximately 3.6 more of these beneficial species than those with health conditions, while individuals at a healthy weight had about 5.2 more species compared to those who were obese.

Researchers propose that the gut microbiome plays a crucial role in releasing chemicals that influence health outcomes, including cholesterol transport, inflammation reduction, fat metabolism, and insulin sensitivity.

Among the species analyzed, most bacteria classified as either “good” or “bad” belong to the genus Clostridium. Within this group, 40 species from the family Lachnospiraceae were highlighted; 13 showed positive impacts while 27 were linked to negative effects.

“This research identifies a subset of bacteria worth further exploring for their potential impacts on health conditions like high blood sugar and obesity,” states Ines Moura from the University of Leeds, UK.

The connection between these microorganisms and diet is analyzed through food questionnaires and data collected via the Zoe app, which suggests aiming for at least 30 different plant types each week and consuming three servings of fermented foods daily, promoting fiber intake and reducing ultra-processed food consumption.

The findings indicate that most microorganisms tend to enhance health with a balanced diet or exacerbate health issues with a poor diet. However, 65 of the 661 microorganisms exhibited an inconsistent relationship.

“These 65 bacteria highlight the complexity of our microbiome,” remarks Segata, who also consults for Zoe. “Their effects might depend on the presence of other microorganisms, specific bacterial strains, or particular dietary factors.”

This classification of “good” and “bad” bacteria enables researchers to assess an individual’s gut health on a scale from 0 to 1000, which is already being applied in Zoe’s gut health assessments.

“Think of a healthy gut microbiome as a network of chemical factories. We need a diverse range of species and a predominance of beneficial bacteria to generate health-promoting chemicals that benefit the entire body,” says Tim Spector, PhD from King’s College London and co-founder of Zoe.

Nonetheless, establishing a definitive model of a healthy gut microbiome is challenging. “Defining a healthy microbiome is not straightforward, as gut composition is impacted by diet and can shift due to environmental factors, age, and health conditions requiring long-term treatment,” adds Moura.

“We need to view our bodies and microbiomes as two intricate systems that combine to create an even more complex system,” says Segata. “A change in one element can subtly affect everything else. Understanding the causative relationships is often quite complicated.”

Segata advocates for larger studies to further clarify these links and represent a wider global population. However, once a health and microbiome baseline is set, he believes it should be feasible to recommend specific foods to optimize gut bacteria.