Microbes May Secretly Rewire the Human Brain Before Birth

Microbes may secretly help build the brain, starting in the womb and continuing at birth. Michigan State University researchers discovered t...

Microbes may secretly help build the brain, starting in the womb and continuing at birth.

Michigan State University researchers discovered that microbes begin shaping the brain while still in the womb, influencing neurons in a region critical for stress and social behavior. Microbes, or microorganisms, are all around us and play an important role in bodily functions. New research from Michigan State University suggests they also help sculpt the brain before and during birth. Their findings, published in Hormones and Behavior, highlight how maternal microbes influence brain structure in the womb and continue shaping development as newborns encounter microbes during delivery.

Modern obstetric practices like peripartum antibiotic use and Cesarean delivery can disrupt maternal and neonatal microbiomes. In the United States alone, about 40% of women receive antibiotics around childbirth and one-third of all births occur via Cesarean section. This makes the findings especially relevant for healthcare policy and neonatal care.

“At birth, a newborn body is colonized by microbes as it travels through the birth canal. Birth also coincides with important developmental events that shape the brain. We wanted to further explore how the arrival of these microbes may affect brain development,” said Alexandra Castillo Ruiz, assistant professor in MSU’s Department of Psychology.

The team focused on the paraventricular nucleus of the hypothalamus (PVN), a region essential for regulating stress responses, blood pressure, water balance, and social behavior. Previous work had shown that germ-free mice — raised without microbes — exhibited increased neuronal death in this region. The new study set out to determine whether those early changes persisted into adulthood and whether they originated before or after birth.

Using a cross-fostering experiment, researchers compared germ-free newborns with those exposed to microbes after birth. Strikingly, mice gestated by germ-free mothers had fewer PVN neurons regardless of microbial exposure after birth. Even in adulthood, germ-free mice showed reduced neuron counts, pointing to prenatal signals from maternal microbes as a critical influence.

The findings suggest that the presence or absence of maternal microbes during pregnancy has long-term consequences for brain development. This raises important questions about how medical interventions that alter the microbiome might inadvertently affect neurological outcomes later in life.

“Our study shows that microbes play an important role in sculpting a brain region that is paramount for body functions and social behavior. In addition, our study indicates that microbial effects start in the womb via signaling from maternal microbes,” said Castillo Ruiz.

Looking ahead, researchers plan to investigate the molecular mechanisms behind this microbe–brain communication. Do microbial metabolites cross the placenta? Are maternal immune signals relaying information to the fetus? Answering these questions could open the door to new strategies that protect brain development during pregnancy. Rather than shunning microbes, the researchers emphasize viewing them as partners in early life. “They’re helping build our brains from the very beginning,” Castillo Ruiz explained.

This research has potential implications for prenatal care, neonatal health, and even mental health policy. Conditions like anxiety, autism spectrum disorders, and stress dysregulation all involve brain regions linked to the hypothalamus. If microbes influence these systems early on, clinical practices that safeguard healthy microbiome development may reduce risks of certain conditions later in life.

Healthcare providers may need to consider alternative practices that preserve microbial diversity — such as limiting unnecessary antibiotic use, encouraging breastfeeding, or even developing targeted probiotics that support maternal and infant health. Public health messaging may eventually include microbiome-friendly prenatal guidelines.

The growing body of evidence on the microbiome suggests that human health is deeply interconnected with microbial communities. This study adds to the idea that humans and microbes co-evolved not just for digestion and immunity, but also for brain and behavioral development. Protecting microbial diversity could be as essential as ensuring access to proper nutrition during pregnancy.

Moreover, societal trends — from rising C-section rates to the use of antiseptics in everyday life — may need to be re-evaluated in light of their long-term impact on brain development. Balancing safety with microbial exposure may become one of the defining challenges of modern obstetrics.

Ultimately, this research reminds us that health begins long before birth. The microbes that colonize us may not just be passengers, but architects of our brains, influencing how we respond to stress, how we connect socially, and how our bodies maintain balance throughout life.