The human digestive tract, which includes the mouth, esophagus, stomach, intestines, anus, and rectum, contains a highly diverse and complex community of microorganisms, known collectively as the gut microbiome. The gut microbiome forms during birth and rapidly evolves throughout infancy. This phase of development is absolutely crucial for the health of the immune system, metabolism, and long-term health outcomes, as it plays a large role in reducing the risk of allergies, diabetes, and many bowel and cardiovascular diseases (Borrego-Ruiz and Borrego, 2025). While it may be tempting to think that the sharing of microbes among infants is a bad thing, this is largely not the case. The microbes that are transmitted in a nursery and other similar environments are mainly non-pathogenic, meaning that they do not cause disease. Many of these microbes are actually beneficial for health, aiding in digestion, immune system development, and more. Typically, the development of the gut microbiome has been thought to be through vertical transmission, where microbes are passed from the mother or other close, immediate family contact, to infants. However, a recent study from Ricci et al. (2026) published in Nature suggests that gut microbiome development through simple vertical transmission serves as an incomplete model. Instead, they suggest that another key process is at play: horizontal transmission. This kind of transmission is the sharing of microbes between unrelated people. In infants, this often occurs in communal environments like nurseries.
Researchers Ricci and colleagues sought to investigate if infants obtained microbes just from their families, or if they acquired them from their peers, especially in a daycare setting. In the study, Ricci et al. analyzed how social interactions influence the human gut microbiome in infants by studying 43 infants in the UK between the ages of four and fifteen months, as well as their parents, siblings, caregivers, and even household pets. These authors analyzed DNA sequences obtained from samples of the stool of these infants over time to gather data about which microbes were present in their gut microbiomes. They analyzed several timepoints, including before and after nursery attendance began. This study design allowed the researchers to effectively track the transmission of microbes between individuals. The DNA sequencing approach taken by this group offered the advantages of more accurate, strain-level identification of microbes and allowed tracking of where certain microbes originated, because they analyzed entire DNA sequences. The alternative to this approach is culturing stool samples, which offers opportunity for additional testing but a severe limitation in that most microbes can not be cultured in a lab (Ricci et al., 2026).
Looking specifically in a daycare setting, the researchers discovered that infants experienced a significant increase in sharing of microbes, indicating that a nursery setting can play an important role in shaping the gut microbiome. This increase in transmission was seen at a much higher rate compared to settings within family-only units, where sharing was relatively stable. These findings indicate that horizontal transmission can be just as important as vertical transmission when it comes to developing and increasing biodiversity of the infant gut microbiome.
But how are microbes transmitted between infants in a nursery environment? It all comes down to proximity and activities. Researchers found increased microbial transmission between infants who spent more time together or had frequent physical contact compared to those that didn’t. Additionally, activities such as playing with the same toys and touching the same surfaces further facilitated microbe exchange. These findings show that exchange of microbes between infants in a nursery is not random, but rather a process that follows a pattern of behavior exhibited by the infants.
On top of understanding that microbial transmission occurs, the study highlighted the individual differences between infants and how they were affected by the conditions in the nursery. The researchers found that infants with siblings had more diverse microbiomes from the start of the study compared to those without, likely due to more microbe exposure at home from siblings. In turn, these infants acquired less new microbe strains, suggesting that previous microbe exposure can influence later development of the microbiome. This highlights the importance of being exposed to a diverse range of microbes as an infant, tying into the hygiene hypothesis, which states that without an early, diverse exposure to microbes, children are more likely to develop allergies and autoimmune diseases (Sironi and Clerici, 2010). Infants who had previously taken antibiotics, and therefore had a lack of diversity in their gut microbiome, experienced a recovery from being in a nursery environment. While the infants did recover fully, they recovered with a different composition of microbes. Through exposure to new strains around them, infants regained microbial diversity, highlighting the adaptability of the infant gut microbiome in the face of disruption. The findings of the study illustrate how the social environments of infants can be crucial in developing a gut microbiome that supports a healthy body.
This study also has its limitations. The number of nurseries was quite small, three to be exact, and researchers did not address the long-term presence of these microbes and their impact on health in the future. As such, because the infants were from a similar region, these findings may not be applicable to other populations who have different environmental and socioeconomic differences. Additionally, possible confounding variables such as diet and broader environmental conditions were not studied. Future research is needed to account for these limitations and progress the body of knowledge on infant horizontal transmission, as well as the microbial composition of infants who do not get placed in daycare or other social settings.
Overall, Ricci et al. (2026) challenge our current understanding of how the human gut microbiome develops. By looking beyond the process of vertical transmission, we learn that the microbiome is also influenced by social interaction, behaviors, and shared environments. Specifically, nursery settings are centers of important microbial exchanges, where infants are constantly exposed to new microbes. The results of this study emphasize that infant social interactions can biologically shape long-term health through development of the gut microbiome.
Works Cited
Borrego-Ruiz A, Borrego JJ. 2025. Early-life gut microbiome development and its potential long-term impact on health outcomes. Microbiome Res Rep. 4(2). doi:10.20517/mrr.2024.78. [accessed 2026 May 3]. https://www.oaepublish.com/articles/mrr.2024.78.
Ricci L, Heidrich V, Punčochář M, Armanini F, Ciciani M, Nabinejad A, Fazaeli F, Piperni E, Servais C, Pinto F, et al. 2026. Baby-to-baby strain transmission shapes the developing gut microbiome. Nature. 651(8104):191–200. doi:10.1038/s41586-025-09983-z. [accessed 2026 May 3]. https://www.nature.com/articles/s41586-025-09983-z.
Sironi M, Clerici M. 2010. The hygiene hypothesis: an evolutionary perspective. Microbes and Infection. 12(6):421–427. doi:10.1016/j.micinf.2010.02.002. [accessed 2026 May 3]. https://linkinghub.elsevier.com/retrieve/pii/S128645791000050X.