Associations among rearing environment and the infant gut microbiome with early-life neurodevelopment and cognitive development in a nonhuman primate model (<i>Macaca mulatta</i>)

Early gut microbiome development may impact brain and behavioral development. Using a nonhuman primate model (<i>Macaca mulatta</i>), we investigated the association between social environments and the gut microbiome on infant neurodevelopment and cognitive function. Infant rhesus monkeys (<i>n</i> = 33) were either mother-peer-reared (MPR) or nursery-reared (NR). Neurodevelopmental outcomes, namely emotional responsivity, visual orientation, and motor maturity, were assessed with the Primate Neonatal Neurobehavioral Assessment (PNNA) at 14-30 days. Cognitive development was assessed through tasks evaluating infant reward association, cognitive flexibility, and impulsivity at 6-8 months. The fecal microbiome was quantified from rectal swabs via 16S rRNA sequencing. Factor analysis was used to identify "co-abundance factors" describing patterns of microbial composition. We used multiple linear regressions with AIC Model Selection and differential abundance analysis (<i>MaAsLin2</i>) to evaluate relationships between co-abundance factors, microbiome diversity, and neuro-/cognitive development outcomes. At 30 days of age, a gut microbiome co-abundance factor, or pattern, with high <i>Prevotella</i> and <i>Lactobacillus</i> (<i>β</i> = -0.88, <i>p</i> = 0.04, AIC Weight = 68%) and gut microbiome alpha diversity as measured by Shannon diversity (<i>β</i> = -1.33, <i>p</i> = 0.02, AIC Weight = 80%) were both negatively associated with infant emotional responsivity. At 30 days of age, being NR was also associated with lower emotional responsivity (Factor 1 model: <i>β</i> = -3.13, <i>p</i> < 0.01; Shannon diversity model: <i>β</i> = -3.77, <i>p</i> < 0.01). The infant gut microbiome, along with early-rearing environments, may shape domains of neuro-/cognitive development related to temperament.