How your family and friends shape your microbiome

Because some bacteria cause serious diseases, scientists have long been fascinated by how these microbes pass from one individual to another.

Understanding how transmission works can help reduce the risk of infection.

Of course, not all bacteria cause disease. Some — like many of the bugs in your gut and mouth — are considered “friendly” because they work to protect you against the “bad” bugs.

Plus, having a diverse community of bacteria in your body is linked to better health outcomes.

Researchers have spent much less time studying how “good” bacteria move from person to person and what this transmission might mean for your health. 

But a recent study published in Nature has started to fill in this gap.

The scientists confirm that our mothers play vital roles in shaping our microbiomes, but so do other family members and our friends.

The research — led by Dr. Mireia Valles-Colomer and Prof. Nicola Segata at the University of Trento, in Italy — provides some fascinating insights. 

Prof. Tim Spector, one of the paper’s authors and ZOE’s scientific co-founder, writes, “This study shows the uniqueness of our gut microbes and the importance of family transmission.”

What did they do?

Scientists have known for some time that a large proportion of your gut microbiome comes from your mother

But your bacterial population changes as you age, and new species arrive on the scene. This recent study investigated where these new bacteria come from.

In particular, the scientists focused on two types of transmission:

  • vertical transmission: microbes passing from one generation to the next

  • horizontal transmission: microbes passing between people in close contact, including friends and family

To get answers, they analyzed 7,646 stool and 2,069 saliva samples from 20 countries on five continents.

What did they find?

This huge dataset allowed them to investigate how different relationships influence our microbiomes.

Their analysis included mother-infant pairs, members of shared households, twins, residents of villages, and larger populations.

Let’s take a look at some of the findings.

Mother-child relationships

First, the researchers confirmed that mothers provide most of their children’s gut microbiomes. For example, mothers living with their kids aged 3 years or younger shared 34% of their gut bacteria strains.

This is higher than the percentage of strains shared between identical twins.

This handed-down gut microbiome does last into adulthood, but as we grow, our microbiomes differentiate. By the age of 18, the percentage of shared strains drops to 19%. By the time we hit 30, it’s 15%. 

Impressively, though, the scientists could still identify mothers' influence on participants’ microbiomes in people aged 50–85.

Still, as we age, new species enter the frame — where do they come from?

A shared life

The scientists found that the people in your life help shape your gut and oral microbiomes. 

Family members, friends, housemates, pets, and partners — if you live with someone, they play a role.

In most households, people’s gut microbiomes more closely matched those of the people they lived with than those of other people in the same region.

Using data from twins, the scientists also showed that the longer people live apart, the fewer shared species they have in their gut microbiomes.

From further afield

Even people you don’t live with can influence the population of bacteria within you — but to a lesser degree. 

The researchers found that people living in the same village — but not the same home — had more shared microbes than people living in the same part of the world but in different villages.

Although people in the same village shared significantly fewer species than people who lived together, it shows that even relatively distant contacts can influence your inner world in some small way.

Mouth to mouth

When the researchers investigated the oral microbiome, they found that transmission from mother to child was much less important. Rather, everyone you live with plays a part. 

This makes sense — bacteria can spread through droplets of saliva with relative ease, as infectious disease experts have known for a long time. 

So, while you’re at home, chatting, sneezing, coughing, and singing, microbes may be distributed throughout your apartment.

We saw earlier that as children age, their gut microbiomes slowly diverge from their mothers'. 

With the oral microbiome, it’s the reverse — it becomes more similar to your mother’s as you get older. The researchers found that you share an average of 49 species in your first year, but an average of 85 species at age 18. 

The longer you live with someone, the more similar your oral microbiome becomes. 

The scientists also found that couples tended to share more species than parents or siblings. This, they hypothesize, might be due to, ahem, “intimacy.”

Conclusions and the future

The authors conclude that the sharing of bacteria between people who live together is “a major driver in shaping the personal genetic makeup of the microbiome.” 

This could also have health implications, as Nicola explains:

“Some noncommunicable diseases (such as cardiovascular diseases, diabetes, or cancer) are partly linked to an altered composition of the microbiome.” 

So, demonstrating that “the human microbiome is transmissible could suggest that some of these diseases currently considered noncommunicable could, at least to a certain extent, be communicable.”

He hopes that future research will “explore the possibility of reducing the risk with therapies that act on the microbiome or its transmissible components.”

It’s also interesting that these patterns of transmission were similar across such a diverse range of lifestyles. 

Whether among subsistence farmers, people in crowded developing cities, or individuals in medium-sized affluent cities, the rates of microbe exchange were “remarkably similar.” 

But there's still a host of questions to answer. “Certain bacteria, especially those that survive better outside our bodies, are transmitted much more often than others,” Mireia explains

Interestingly, these species include some “good” and “bad” bacteria.

Many of these, Mireia says, are new to science and haven’t even been named yet. This includes 10% of your gut bacteria and 17% of your oral bacteria. 

She hopes that the findings will inspire scientists to get to know these microbes better. Studying these species might help us understand how bacterial transmission between people works.

What does it mean for you?

This area of research is still young, so it's relatively unclear what exactly the results mean for you. We asked Nicola to comment on two real-life scenarios to help make these findings relatable.

The ‘good’ with the ‘bad’

Imagine that someone with a healthy microbiome moved in with someone who had a less healthy microbiome. They lived together for many years, and neither changed their diet. 

As they shared microbes, would the risk of disease slowly increase for the person with the healthy microbiome and slowly decrease for the person with the unhealthy microbiome?

Or would the healthier microbiome be more stable?

Nicola responded, “My hypothesis would be that the exchange of microbes would not be connected to whether they are ‘good’ or ‘bad’ microbes.”

This, he explains, is because “good” and “bad” bugs were equally likely to be shared in the study. 

However, he noted that this “would need to be verified” with further research.

A variety of microbiomes

Many people live in shared homes for years, perhaps with more than 10 different housemates in that time. We asked Nicola whether this would be positive or negative for health. 

In other words, is it best to be exposed to as many diverse microbiomes as possible? Or is it the quality of the microbiome that matters, in terms of transmission?

Nicola answered: “In principle, I would say that the more different microbiomes you get in touch with, the better! Of course, everything is relative because you would also have a higher chance of picking up a pathogen and then need antibiotics.”

He also mentioned that we still don’t know how long you have to live with someone to share a significant amount of microbes.

And we don’t know “the main transmission routes — direct or indirect touching, shared surfaces, or oral droplets.”

“So, everything considered,” Nicola continued, “it's a difficult question to be answered with the available data, but again, the principle would be that the more diversity of microbes we encounter, the better we can acquire diversity and pick ‘our strains’ from that diversity.”

There’s clearly a lot left to unravel. And this recent study unearths as many questions as it puts to bed. It’s certainly an exciting time for microbiome research. Watch this space.


How do human body–associated microbes spread? The transmission landscape of human microbiomes. (2023). 

Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host & Microbe. (2018). 

The person-to-person transmission landscape of the gut and oral microbiomes. Nature. (2023).