We know that the brain and gut microbiome influence mental health through the microbiome-gut-brain axis. But, there hasn’t been a lot of work focused on understanding how the axis works during childhood, a time when the brain and gut microbiome are both developing tremendously and many mental health issues initially emerge. Studying the brain and gut microbiome together is challenging since both are very complex and high-dimensional. One possible solution is to use multivariate machine learning techniques, such as sparse partial least squares regression (sPLS), to identify combinations of variables that maximize covariance with an outcome of interest. Using sPLS, we found one microbial profile, mostly comprised of microbes from the Clostridiales order and Lachnospiraceae family, was linked with depression/anxiety symptoms at school age via a brain signature characterized by connectivity within emotion-related brain networks. Results suggest one way the early life gut microbiome may contribute to mental health is through shaping functional brain development. It also gives some clues about which brain networks and microbes may be most involved in developmental psychopathology.

The COVID-19 pandemic and resulting public health directives led to many changes in families’ social and material environments. Prior research suggests that these changes are likely to impact composition of the gut microbiome, particularly during early childhood when the gut microbiome is developing most rapidly. Importantly, disruption to the gut microbiome during this sensitive period can have potentially long-lasting impacts on health and development. In the current study, we compare gut microbiome composition among a socioeconomically and racially diverse group of 12-month old infants living in New York City who provided stool samples before the pandemic (N = 34) to a group who provided samples during the first 9-months of the pandemic (March–December 2020; N = 20).

This study draws on a large longitudinal cohort to demonstrate that adversity experienced prenatally or during early childhood, as well as adversity experienced by the mother during her childhood, impacts the gut microbiome of second-generation children at 2 y old. Notably, some of the microbiome profiles linked to these types of adversity, especially at higher taxonomic levels, were similar to those associated with the child’s current and future socioemotional functioning. Additionally, microbes uniquely associated with adversity exposures or socioemotional functioning have similar immune-related functions within the gut, highlighting the need for further research into how generational adversity affects the gut microbiome’s functional potential.