The billions of microscopic bacteria that reside in our intestines play a major role in our health
THOM LEACH/SCIENTIFIC PHOTO LIBRARY
We often hear that things are good for our microbiome and, therefore, our health. But it wasn’t entirely clear what a healthy gut microbiome consisted of. Now, a study of more than 34,000 people has given us a better understanding of the mixes of microbes that reliably signal that we have low inflammation, good immunity, and healthy cholesterol levels.
Your gut microbiome can influence your immune system, your rate of aging and your risk of poor mental health. Despite a wealth of at-home tests promising to reveal the makeup of your gut community, their usefulness has been debated because it’s difficult to pin down what a “good” microbial mix is.
Previous measures mainly focused on species diversity, with greater numbers of bacteria being better. But it’s difficult to identify particular communities of interacting organisms involved in a specific aspect of our health, because microbiomes vary so much from person to person.
“There is a very complex relationship between the food we eat, the composition of our gut microbiome and the effects of this on our health. The only way to try to map these links is to have large enough samples,” explains Nicola Segata of the University of Trento in Italy.
To create such a map, Segata and colleagues assessed a dataset from more than 34,500 people who participated in the PREDICT program in the UK and US, run by microbiome testing company Zoe, and validated the results against data from 25 other cohorts from Western countries.
Among the thousands of species residing in the human gut, researchers focused on 661 bacterial species found in more than 20% of Zoe participants. They used this data to determine the 50 bacteria most associated with markers of good health – assessed via markers such as body mass index and blood sugar – and the 50 most linked to poor health.
The 50 species of “good bugs” – 22 of which are new to science – appear to influence four key areas: cholesterol levels; inflammation and immune health; body fat distribution; and blood sugar control.
Participants rated healthy, because they had no known health problems, had about 3.6 more than people with the condition, while people with a healthy weight had about 5.2 more than those with obesity.
Researchers suggest that good or bad health outcomes could arise due to the vital role the gut microbiome plays in releasing chemicals involved in cholesterol transport, reducing inflammation, fat metabolism and insulin sensitivity.
When it comes to the specific species present, most of the microbes in the “good” and “bad” rankings belong to the class Clostridia. Within this class, species of the family Lachnospiraceae appeared 40 times, with 13 apparently having favorable effects and 27 unfavorable ones.
“The study highlights bacterial groups that could be subject to further study regarding their potential positive or negative impact. [on] health problems, such as high blood sugar or obesity,” says Ines Moura of the University of Leeds, UK.
The link between these microbes and diet was assessed via dietary questionnaires and data recorded on the Zoe app, where users are advised to consume at least 30 different plants per week and at least three servings per day of fermented foods, with an emphasis on fiber and not too many ultra-processed options.
The researchers found that most microbes corresponded to either a generally healthy diet and better health, or a poorer diet and poorer health. But 65 of the 661 microbes were not suitable.
“These 65 bacteria are testament to the fact that the picture is even more complex than what we saw,” says Segata, who also works as a consultant for Zoe. “The effects may depend on other microbes present, the specific strain of bacteria, or the specific diet.”
This sorting of “good” and “bad” bacteria allowed researchers to create a 0 to 1,000 ranking scale for the overall health of a person’s gut microbiota, which is already used in Zoe’s gut health tests.
“Think of a healthy gut microbiome as a community of chemical factories. We want a large number of species, we want the good ones to outnumber the bad ones, and when you get that, you produce really healthy chemicals, which have impacts throughout the body,” says team member Tim Spector from King’s College London, co-founder of Zoe.
This does not mean, however, that the ideal healthy gut microbiome has been defined. “Defining a healthy microbiome is a difficult task, because the composition of the gut microbiome is influenced by diet, but it can also change depending on environmental factors, age and health conditions that require long-term medication,” says Moura.
“We really need to think of our body and our microbiome as two complex systems that together form an even more complex system,” says Segata. “When you change one thing, everything is changed a little bit as a result. Understanding what cause and effect is in many cases can be very complex.”
Larger studies are needed to untangle these links and cover a larger portion of the world’s population, Segata says. However, once we’ve established the foundation of your health and microbiome, it should become possible to recommend specific foods to change your gut bacteria, he says.
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