Long-term and trimester-specific effects of prenatal stress on the child gut microbiota

•The effects of prenatal stress on the child gut microbiome at 3–4 years is unclear.•Prenatal distress is associated with increased child gut microbial diversity.•Prenatal cortisol correlates with diversity in a trimester-dependent manner.•Stress associations with taxa and metabolites are measure- and trimester-dependent.•These findings provide novel insights into the biological embedding of stress.