Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium

Abstract

Background: Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors.

Methods: Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects.

Results: Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use.

Limitations: The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD.

Conclusions: Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories.

Keywords: Autism; Gene set enrichment analysis; Gut metagenome; Microbiome; Social behavior.

Fig. 1

Diagram of Study Methods. Fecal samples were collected from RESONANCE participants between six weeks and two years postpartum and from New Hampshire Birth Cohort Study (NHBCS) participants at six weeks and/or one year. In both cohorts, DNA was extracted from stools and underwent shotgun metagenomic sequencing. In both cohorts, assessment of autism-spectrum disorder behaviors with the Social Responsiveness Scale, 2nd edition, was completed after age 3 years. Additionally, a subset of NHBCS fecal samples underwent nuclear magnetic resonance spectroscopy to quantify small molecules. These data were integrated with sociodemographic data into statistical models

Fig. 2

Associations Between Bacterial Species Relative Abundance and Social Responsiveness Scale, 2nd Edition (SRS-2), Scores. A Complete cases in the New Hampshire Birth Cohort Study (NHBCS). B Subjects with missing covariate data imputed in the NHBCS. C Among RESONANCE participants. Models adjusted for gestational age, child’s sex, peripartum antibiotic exposure, delivery mode, exclusive breastfeeding at the time of stool sample collection, maternal smoking during pregnancy, maternal and paternal age, maternal marital status, parity, maternal education, and the child’s age at SRS-2 completion. Each point reflects the association between a bacterial species and SRS-2 scores. Points are colored by phylum. Dashed gray lines indicate p = .05 and the Bonferroni corrected p-value for each analysis

Fig. 3

Associations of Microbial Functions and Social Responsiveness Scale, 2nd Edition (SRS-2) Scores. Feature Set Enrichment Analysis of A Raw SRS-2 scores and B regression model residuals with microbial gene sets. C Distribution of correlations between microbial gene families and SRS-2 scores (SCORE), and regression model residuals (RESID). D Association (point estimate and 95% confidence interval) between concentrations of fecal short-chain fatty acids and SRS-2 Scores in the Unadjusted and Fully Adjusted Models. Fully adjusted models include gestational age, child’s sex, peripartum antibiotic exposure, delivery mode, exclusive breastfeeding at the time of stool sample collection, maternal smoking during pregnancy, maternal and paternal age, maternal marital status, parity, maternal education, and the child’s age at SRS-2 completion