Longitudinal study of stool-associated microbial taxa in sibling pairs with and without autism spectrum disorder

Christine Tataru,Erica Rutherford,Roberta L Hannibal,Michelle Lin,Kaitlyn Dunlap,Marie Peras,Wiputra Hartono,Maude M David,Kayleen Sabino,Alexandra Phillips,Grace E Deitzler,Xiaochen Yin,Shoko Iwai,Austin Martin,Todd Z Desantis,Dennis P Wall,Edward Raack,Yonggan Wu,Brianna S Chrisman

doi:10.1038/s43705-021-00080-6

Abstract

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder influenced by both genetic and environmental factors. Recently, gut dysbiosis has emerged as a powerful contributor to ASD symptoms. In this study, we recruited over 100 age-matched sibling pairs (between 2 and 8 years old) where one had an Autism ASD diagnosis and the other was developing typically (TD) (432 samples total). We collected stool samples over four weeks, tracked over 100 lifestyle and dietary variables, and surveyed behavior measures related to ASD symptoms. We identified 117 amplicon sequencing variants (ASVs) that were significantly different in abundance between sibling pairs across all three timepoints, 11 of which were supported by at least two contrast methods. We additionally identified dietary and lifestyle variables that differ significantly between cohorts, and further linked those variables to the ASVs they statistically relate to. Overall, dietary and lifestyle features were explanatory of ASD phenotype using logistic regression, however, global compositional microbiome features were not. Leveraging our longitudinal behavior questionnaires, we additionally identified 11 ASVs associated with changes in reported anxiety over time within and across all individuals. Lastly, we find that overall microbiome composition (beta-diversity) is associated with specific ASD-related behavioral characteristics.

Highlights

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder that occurs in 1 out of every 54 children in the United States [1]
Eleven amplicon sequencing variants (ASVs) are significantly associated with the ASD phenotype, as determined by the union of at least two differential analysis methods Out of 834 total ASVs (Amplicon Sequence Variants, assigned using DADA2), 117 were identified to be significantly different between the ASD and typically developing (TD) cohorts (Supplementary File 1) by at least one of the contrast analysis methods used after normalization and filtration (DESeq2, MetagenomeSeq, and ANCOM, see methods)
Oscillospiraceae and Bacteroidaceae were the second most represented families with 10 ASVs belonging to each of these families. 93 of the 117 ASVs were detected as significant by DESEQ2, 28 by MetagenomeSeq, and 4 by ANCOM. 45 ASVs were not associated with any lifestyle or dietary variables extracted from the questionnaires

Summary

Introduction

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder that occurs in 1 out of every 54 children in the United States [1]. ASD is characterized by a set of social and cognitive impairments and can be influenced by a growing number of both genetic and environmental factors [2, 3]. Environmental factors such as maternal prenatal medication use, maternal health factors, and prenatal infection have been associated with ASD development [4]. ASD is associated with increased prevalence of gastrointestinal (GI) issues [5, 6] These GI issues can include symptoms such as chronic constipation, diarrhea, abdominal pain, and potential signs of GI inflammation such as vomiting and bloody stools [7]. Growing evidence suggests that ASD is associated with gut dysbiosis. Reductions of core-ASD symptoms with probiotic usage have been observed [14]

Methods

Results

Discussion

Conclusion