By Deborah Burwitz
People are not only people, but also microbes, which is a big summation of the choices they make: their social interactions, the food they eat, the medications they take, their activity level, and their daily habits. Sometimes microbes that pass from one person to another are beneficial, but their odds of causing harm are a little better, according to computational biologist Nicola Segata, Ph.D., professor and principal investigator in the CIBIO Department of the University of Trento and principal investigator at the university’s European Institute of Oncology in Milan.
The microbial portion of the human body (about 39 trillion cells) is built over the course of a lifetime and is “the most we can change to influence the course of our health,” Segata says. A better understanding of these microbes and their role in health and disease is key to supporting healthy aging efforts as well as medical practices such as fecal microbiota transplantation (FMT).
As Segata and his colleagues recently discovered, people who coexist with each other share a greater number of oral and gut microbes than other people in their communities (Click on the cell in blue, doi: 10.1016/j.cpblue.2026.100034). The researchers also found a link between more transmissible microbes and some risk for certain diseases, which may help design more targeted treatments to improve people’s microbiome.
When estimating the transmissibility of different microbes, they found that among the most transmissible bacteria in the gut were associated with biomarkers of type 2 diabetes and poor cardio-metabolic health, and in the oral microbiome, there were, in particular, two microbes associated with colorectal cancer and several opportunistic pathogens. The difficult task ahead is to figure out how to change this internal ecosystem in a predictable way.
It’s not that people can be categorized by microbiome type and prescribed “the same recipe” to improve their health, Segata says. “Every person has a unique microbiome…more unique than the human genome.”
Recurrent bacteria
As addressed in previous research, “microbes rarely come directly from the environment or food,” Segata says. “In 99% of cases, these viruses come from other people, because gut microbes are very well adapted to living in the human gut.”
He says that individuals who have no social and physical interaction share about 15% of the strains after living together for two to three years. Even on the first day of life, 50% of the microbes in the intestines of babies come from the mother, provided that the baby was not delivered by caesarean section. The research team recently reported that one-year-old children in daycare shared an average of 20% to 30% of their microbiome with other children in the same room after just four months (nature, doi: 10.1038/s41586-025-09983-z).
Although proinflammatory microbes are more transmissible, they have different and largely unexplored effects in terms of the relative risk of people developing microbiome-related diseases. Part of the problem, Segata explains, is that bacteria can “encourage” disease rather than directly cause it. This means that microbes that normally live harmlessly in the body facilitate inflammation and chronic disease when the microbiome is out of balance.
He says the frequent bacteria that are higher in diabetics and those who convert to diabetes could be present for many plausible reasons, including a diet that directly works on insulin resistance. “It is difficult to isolate what effect each insect has on increasing the risk of disease… Our body is a very complex system.”
Whether these frequent bacteria are more or less abundant in healthy people is a related question, Segata says. But this association is not evidence that microbes cause diabetes.
An additional difficulty with colorectal cancer, Segata says, is that many microbes found only in the stool of people with the disease are abundant in the oral cavity of all people, whether healthy or not. These specific bacteria colonize the growing tumor microenvironment in the intestine, a mechanism separate from oral to intestinal transmission itself.
Arithmetic feat
Segata’s specialty is metagenomics, the DNA sequencing of microbial communities that generates a huge amount of data that requires advanced computational tools to interpret. “Computational microscopy” is required when it comes to studying transmissibility where the task is to distinguish or match pairs of strains and their genomes to see whether they have been transmitted directly between individuals or may have been acquired independently from a shared environment.
“If we find exactly the same strain, the most logical hypothesis is that it was transmitted,” he says. Coming to this conclusion means piecing together a lot of puzzles, such as reconstructing the genomes of every strain in the microbiome.
For the latest Click on the cell in blue In this study, he and his team analyzed metagenomic data from the oral and gut microbiota of 430 people living in 207 households in Italy, and from a previous study from Fiji. The microbial strains identified in individuals were then compared with strains found among people who lived together to see whether transmission was occurring.
This led to the discovery that cohabiters share significantly more oral and gut lineages than people from the same population who do not live together. On average, cohabiting individuals shared 19% of the gastrointestinal microbiome phylogenies and 26% of the oral microbiome phylogenies, compared with 6% and 0%, respectively, for individuals living in different households. Romantic partners share an average of 44% of their oral microbes with each other, and the logical explanation is that they kiss.
A lifelong story
Segata says his experiences with his children helped fuel his interest in microbiome research. Studies of mother-to-infant transmission of microbes began around the time of the birth of his eldest son, who is now 12 years old. “It is not only the mother, but also the father… who transmits certain strains to the child.”
It adds, and vice versa, to the daily contact required of parenthood. Idea for the latest nature The study arose after he spent a semester chronically ill from the constant barrage of infections brought home from a day care center.
But with the bad comes some good. In a separate paper published in nature Late last year, Segata and his team analyzed more than 34,000 microbiomes to identify 50 gut bacteria strongly associated with better health (doi: 10.1038/s41586-025-09854-7). They also discovered two nutritional interventions that increased the abundance and spread of preferred species while reducing unpreferred species.
One somewhat provocative message is that a healthy diet and lifestyle “not only helps you, but it also helps the people around you,” Segata says. The joke is that microbiome testing can be used to prove compatibility between cohabiting couples, but that’s just a marketing gimmick and not hard science.
But at the population level, this is a legitimate area of investigation, Segata continues. His previous work has identified a “completely different” gut microbiome in Western and non-Western populations, which mirrors the microbes found in ancient mummies 5,000 to 6,000 years old.
“The story here is that if an entire population ate fast food every day for every meal and forgot to eat fiber, those microbes that eat, live, and grow on fiber would disappear from the population,” Segata says. “And if they disappear from the population, even if you are the healthiest person in the world, you will have no sources of these bacteria to colonize your gut… (and) it will be very difficult to get them back.”
Clinical effects
At the population level, a good first step is to cultivate, store and maintain beneficial gut bacteria, whose numbers are declining in Western populations, Segata says. There is also a lot of interest in both health and medical fields about how to change the microbiome in a simple and reproducible way, for example, through next-generation probiotics and prebiotics as well as FMT – “the most radical way to use cross-infection in a medical setting.”
There’s no disputing that it’s a “drastic procedure, but it’s effective,” says Segata, at least in treating recurrent cases Clostridium difficile Infections in people with weak immunity. The FMT has changed dramatically C. difference From a fatal and often chronically relapsing condition to a highly treatable condition, it is likely that clinical practice will soon be established for many other diseases.
In order to make FMT “less invasive,” he adds, efforts are being made to grow individual microbes in isolation, then pool them to mimic coexisting microbial communities. But this treatment lacks the predictable, universally applicable standard success rates required for widespread adoption as a treatment for many diseases.
“It’s a matter of identification “The trade-off is between benefits and potential problems, because there may be diseases that are only 10% associated with the microbiome,” says Segata. The question is whether cases go beyond that C. difference The benefits are worth the risks given Lack of long-term safety data and the potential for severe adverse reactions if patients are not medically supervised.
