The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism

Abstract

Background: Gut microbiota has the capacity to impact the regular function of the brain, which can in turn affect the composition of microbiota. Autism spectrum disorder (ASD) patients suffer from gastrointestinal problems and experience changes in gut microbiota; however, it is not yet clear whether the change in the microbiota associated with ASD is a cause or a consequence of the disease.

Methods: We have investigated the species richness and microbial composition in a valproic acid (VPA)-induced rat model autism. Fecal samples from the rectum were collected at necropsy, microbial total DNA was extracted, 16 rRNA genes sequenced using Illumina, and the global microbial co-occurrence network was constructed using a random matrix theory-based pipeline. Collected rat microbiome data were compared to available data derived from cases of autism.

Results: We found that VPA administration during pregnancy reduced fecal microbial richness, changed the gut microbial composition, and altered the metabolite potential of the fecal microbial community in a pattern similar to that seen in patients with ASD. However, the global network property and network composition as well as microbial co-occurrence patterns were largely preserved in the offspring of rats exposed to prenatal administration of VPA.

Conclusions: Our data on the microbiota of the VPA rat model of autism indicate that this model, in addition to behaviorally and anatomically mimicking the autistic brain as previously shown, also mimics the microbiome features of autism, making it one of the best-suited rodent models for the study of autism and ASD.

Fig. 1

β-diversity in the gut microbial community of rats with or without prenatal valproic acid (VPA) exposure. a Clustering analysis based on Bray-Curtis similarity. Bray-Curtis similarity matrix based on square-root-transformed abundance at an OTU level. b Principal component analysis (PCA) based on Bray-Curtis similarity generated using the Vegan package in the R program. Control: rats without prenatal VPA exposure (N = 11). VPA: rats with VAP exposure (N = 10)

Fig. 2

Microbial taxa displaying significant differences in relative abundance between rats with and without VPA exposure. a The Class Alpha-Proteobacteria. b The family Eubacteriaceae. c The family Enterobacteriaceae. Straight line, group mean abundance; dotted line, median. Control: rats without prenatal VPA exposure (N = 11). VPA, rats with VPA exposure (N = 10)

Fig. 3

Select microbial genera and species with significant differences in relative abundance between rats with and without prenatal VPA exposure. a Anaerotrunus. b Staphylococcus. c OTU assigned to Ruminococcus flavefaciens (GreenGene ID# 1110988). d An OTU belonging to the family Lachnospiraceae (GreenGene ID# 272080). Straight line; group mean abundance; dotted line, median. Control: rats without prenatal VPA exposure (N = 11). VPA: rats with VPA exposure (N = 10)

Fig. 4

Graphical representation of the taxa with significantly different abundance in the gut microbial community of rats induced by prenatal VPA exposure. a Male rats with prenatal VPA exposure (VPA) comparing to male rats without prenatal VPA exposure (Control). b Female rats with prenatal VPA exposure (VPA) comparing to female rats without prenatal VPA exposure (Control). The statistical significance cutoff: absolute linear discriminant analysis (LDA) score log₁₀ ≥ 2.0

Fig. 5

Visualization of microbial co-occurrence networks identified using the fast greedy modularity optimization method in the rats with and without prenatal VPA exposure. a The rats with prenatal VPA exposure (VPA). b Control rats without prenatal VPA exposure. Nodes represent an OTU. Edge (links) with solid lines, positive connection; dashed lines, negative connection. The color of the nodes indicates the phylum to which the OTU belong

Fig. 6

The scatter plot showing the distribution of OTU based on their topological roles in the network in the gut microbial community of rats with and without prenatal VPA exposure. a Control. b VPA. Each dot represents an OTU. Z, within-module connectivity. P, Among-module connectivity