Who You Choose To Live With—and Kiss—Affects Your Gut Microbiome

People who live together have more similar oral and gut microbiomes than people from the same population who do not live together, according to research published in the journal Cell Press Blue.

Oral and gut samples from 207 households revealed that, on average, cohabiting individuals shared 19% of their gut microbial strains and 26% of their oral microbial strains, compared to 6% and 0%, respectively, for individuals living in different households. Cohabiting romantic partners shared even more oral microbes (44%), potentially due to kissing.

Among the most transmissible gut microbes were those associated with poor cardiometabolic health and type 2 diabetes. Understanding the mechanisms by which these microbes spread could lead to more targeted therapies for promoting a healthy microbiome.

Studying cohabitations' influence on the gut microbiome

During and shortly after birth, maternal microbes play a key role in forming the infant microbiome. There is now acknowledgment that microbiome transmission among individuals is also likely to shape the microbiome throughout a person’s life.  

“Previous work from our group and others showed we indeed exchange microbes with cohabitants, but in this particular study we wanted to understand more in-depth what is happening not only in the gut but also in the oral microbiome, how the oral and gut microbiome transmission differs, and, being them connected communities, what was happening at the interface between the oral cavity and the gut,” Dr. Vitor Heidrich, postdoctoral researcher at the University of Trento and first author of the study, told Technology Networks.

To study how microbiomes are transmitted between cohabiting individuals, the researchers analyzed metagenomic data from 430 individuals living in Italy and Fiji.

“By analyzing this data with computational approaches, we can not only identify the microbial species that are present but also look into their genetic variants, allowing us to detect the presence of specifically which strain of those species is present,” explained Heidrich.

“This kind of analysis is showing us that each human essentially carries a unique microbiome fingerprint at the strain level, so whenever we see the same strain in two individuals, the most likely explanation is that they transmitted this strain to each other,” he continued.

The analysis confirmed previous suspicions that a person's microbiome can be shaped by who they live with. In the study, the researchers showed that cohabiting individuals share more oral and gut microbial strains and that romantic partners show heightened oral microbiome transmissibility. This finding suggests that a person’s kissing habits could be a key factor in shaping their oral microbiome.

The researchers found little overlap between oral and gut microbiomes from the same individual (4%); however, among the few cases of commonly present species, the same strain was present at both sites in ~75% of cases. Analysis of species prevalence and strain abundance at both sites suggests that this can be explained by translocation of the microbes via saliva from the mouth to the gut.

“These are likely cases of oral microbes that were so abundant in saliva that after being swallowed they could still be detected in stool. However, this also means that in 25% of cases a different strain of the same species was present in the mouth and the gut, possibly reflecting that the same microbiome species can acquire specific adaptations allowing them to thrive in each of our body sites,” stated Heidrich.

This observation is especially relevant to the study of the oral-gut microbiome axis, which has gained traction in recent years. Oral dysbiosis is increasingly recognized as a contributing factor and potential diagnostic marker for gastrointestinal diseases such as colorectal cancer. Understanding the bidirectional crosstalk between the oral and gut microbiome could therefore help better manage and treat these diseases.

Implications for future microbiome-based therapies

When estimating the transmissibility of the microbes, the researchers found that the most transmissible strains were those associated with poorer cardiometabolic health and with biomarkers of type 2 diabetes. The researchers believe this could reflect an overlap in the traits that enable a microbe to both “survive” transmission and thrive in disease conditions.

“Successful transmission usually requires surviving outside the host, resisting our natural barriers (like the acidic pH of the stomach in the case of transmission of gut microbiome strains) and establishing itself upon arrival in a new environment,” Heidrich said. “Some of these same stress-tolerance mechanisms may also be what allows these species to flourish in the gut environment associated with cardiometabolic disease.”

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Through understanding microbiome transmission and finding what traits make a microbe more transmissible than others, it may be possible to design more targeted and effective microbiome therapies. “For instance, knowing that the most transmissible species tend to be disease-associated raises the question of whether beneficial species face inherent disadvantages in colonization, which is something any effective probiotic strategy will need to account for,” explained Heidrich.

“Overall, we think understanding these mechanisms is a fundamental step to really deliver the promise of microbiome-based precision medicine,” he concluded.

Reference: Heidrich V, Fackelmann G, Ricci L, et al. Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. Cell Press Blue. 2026;1(3). doi: 10.1016/j.cpblue.2026.100034

About the interviewee:

Credit: ©UniTrento - Ph. Federico Nardelli.

Dr. Vitor Heidrich is a postdoctoral researcher in the Computational Metagenomics Lab (led by Prof. Nicola Segata) at the CIBIO department of the University of Trento. His research focuses on the human microbiome, with a particular emphasis on characterizing microbial strain transmission dynamics and mechanisms. His work explores the multiple sources of human microbiome strains, including foods, animals, and other humans, as well as the transmission dynamics following microbiome interventions, such as fecal microbiota transplantation.