New research suggests that the types and variety of bacteria in a baby’s gut shortly after birth may shape how they react emotionally as toddlers. In a longitudinal study published in Development and Psychopathology, researchers found that greater microbial diversity in the gut at just two weeks of age was associated with higher levels of negative affect—such as irritability and fearfulness—when the children were two and a half years old. Interestingly, this association was not seen when gut diversity was measured later in infancy, highlighting how timing may play a key role in how early gut development relates to emotional traits.
The gut microbiome, made up of trillions of microbes living in the digestive tract, has become a growing focus of developmental science. These microorganisms not only influence digestion and immunity, but are also thought to interact with the brain through what’s known as the gut-brain axis. While this area of research is still emerging, there is mounting evidence that early differences in gut microbial communities may be linked to a child’s temperament and later risk for emotional or behavioral problems.
In adults, altered gut microbiome profiles have been associated with mood and anxiety disorders. In children, some studies have shown links between specific microbes and traits like fear, fussiness, and emotional reactivity. But results have varied widely, in part due to differences in when the microbiome was measured and how emotional outcomes were assessed. The current study aimed to fill this gap by tracking the gut microbiome at two time points during infancy and examining how it related to negative affect measured more than two years later.
“I was driven to explore how the gut microbiome in infancy predicts negative affect as a way to better characterize how the gut microbiome shapes cognitive and emotional development,” said study author Sarah C. Vogel of Boston University. “There is growing interest in the role of the gut microbiome in temperament and later risk for psychopathology, and I wanted to contribute to a growing body of literature helping us better understand those associations.”
The study was part of a broader longitudinal project involving 203 pregnant women in the southeastern United States. Of those, 96 children provided stool samples during infancy and completed a behavioral assessment at 30 months old. Stool samples were collected from diapers when the infants were two weeks and again at 18 months. These samples were analyzed using whole genome sequencing to assess the diversity and relative abundance of bacterial species.
At 30 months, each toddler participated in a virtual home visit with a researcher over Zoom. During the session, trained raters used a standardized behavioral coding system to evaluate how each child responded to new situations and how often they appeared unhappy or irritable. These ratings were combined into a composite score of negative affect.
The researchers also collected information about a variety of factors that could influence gut microbiome development or emotional behavior. These included the child’s sex, race, family income and education, method of birth (vaginal or cesarean), and breastfeeding history. These variables were accounted for in the statistical models.
The clearest finding from the study was that infants with higher gut microbiome diversity at two weeks old tended to show more negative affect at 30 months. This was true across two commonly used measures of microbial diversity. However, this link was not present for microbiome diversity at 18 months, suggesting that the first few weeks of life may be a particularly sensitive window for microbiome-related influences on emotional development.
The researchers did not find evidence that overall differences between infants’ microbiomes—known as beta diversity—were related to later emotional behavior. But when they looked at specific types of bacteria, they found some associations. Higher levels of certain bacteria at two weeks of age, including Lactobacillus, Streptococcus, and Veillonella, were weakly linked to more negative affect in toddlerhood. Another bacterium, Ruthenibacterium, showed a similar pattern when measured at 18 months.
However, none of these specific associations remained statistically significant after adjusting for multiple comparisons. This means they could be due to chance and should be interpreted with caution. Even so, these bacteria have been flagged in previous research as potentially relevant to emotional development, and the authors note that they deserve further investigation.
“Infants with more diverse gut microbiomes very early in infancy tended to be less happy, more fearful, and more irritable in their temperament as toddlers,” Vogel told PsyPost. “These findings suggest that having a more diverse microbiome in infancy may not confer the same benefits to health and development that a diverse gut microbiome does later in life. Our findings also highlight our growing scientific understanding of the role of the gut microbiome in child development.”
These findings raise important questions about how the early gut microbiome might shape emotional tendencies. One possibility is that greater microbial diversity in the first weeks of life reflects a more “adult-like” gut environment that emerges too soon, potentially disrupting the natural course of immune or nervous system development. In fact, past studies have linked higher microbial diversity in infancy with exposure to early adversity and with differences in brain development.
Another explanation is that certain bacteria may influence how babies react to stress through pathways involving the vagus nerve or stress hormone systems. Animal studies have shown that gut bacteria can affect emotional behavior through these routes, but human research is still catching up.
Interestingly, the study found that diversity scores from two weeks and 18 months were not correlated with each other. This suggests that the gut microbiome changes in significant ways over time and that early measures may reflect very different processes than those taken later in infancy.
While the study offers important insights, it also comes with limitations. The sample size was relatively small, and participants were mostly from a specific geographic region, which may limit how widely the findings apply. The researchers also did not collect data on antibiotic use in the first weeks of life—a factor known to strongly influence the gut microbiome. And while they looked at a range of possible bacterial influences, none of the individual genera showed strong enough effects to rule out the role of chance.
Future research with larger and more diverse samples could help clarify whether these early associations hold up. It would also be helpful to collect data on emotional behavior earlier in development to see how gut-related patterns emerge over time. Including more precise measures of biological pathways—like stress hormones, immune responses, or brain imaging—could help pinpoint how exactly the gut microbiome might influence emotional traits.
The study, “Longitudinal associations between the infant gut microbiome and negative affect in toddlerhood,” was authored by Sarah C. Vogel, Nicolas Murgueitio, Nicole Huth, Kathy Sem, Rebecca C. Knickmeyer, Sarah J. Short, Roger Mills-Koonce, Cathi Propper, and Nicholas J. Wagner.
