Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota

Abstract

Many studies have reported abnormal gut microbiota in individuals with Autism Spectrum Disorders (ASD), suggesting a link between gut microbiome and autism-like behaviors. Modifying the gut microbiome is a potential route to improve gastrointestinal (GI) and behavioral symptoms in children with ASD, and fecal microbiota transplant could transform the dysbiotic gut microbiome toward a healthy one by delivering a large number of commensal microbes from a healthy donor. We previously performed an open-label trial of Microbiota Transfer Therapy (MTT) that combined antibiotics, a bowel cleanse, a stomach-acid suppressant, and fecal microbiota transplant, and observed significant improvements in GI symptoms, autism-related symptoms, and gut microbiota. Here, we report on a follow-up with the same 18 participants two years after treatment was completed. Notably, most improvements in GI symptoms were maintained, and autism-related symptoms improved even more after the end of treatment. Important changes in gut microbiota at the end of treatment remained at follow-up, including significant increases in bacterial diversity and relative abundances of Bifidobacteria and Prevotella. Our observations demonstrate the long-term safety and efficacy of MTT as a potential therapy to treat children with ASD who have GI problems, and warrant a double-blind, placebo-controlled trial in the future.

Figure 1

Changes in GI- and ASD-related symptoms of 18 children with ASD at two-year follow-up after treatment stopped. Asterisks (at the top of the box plot) indicate whether individuals (at each time point) have significantly changed since pre-treatment (Week 0 of original Phase 1 trial). Based on two-tailed Wilcoxon signed-rank test, ns indicates not significant, single asterisk indicates p < 0.05, double asterisks indicate p < 0.01, triple asterisks indicate p < 0.001. See also Supplementary Figs S1–S3.

Figure 2

CARS and SRS diagnostic category for ASD at baseline, 8 weeks after treatment, and two-year follow-up after treatment stopped. (a) For CARS, Minimal-to-No Symptoms (15–29.5 for ages less than 13; 15–27.5 for ages 13 or older), Mild-to-Moderate Symptoms (30–36.5 for ages less than 13; 28–34.5 for ages 13 or order), and Sever Symptoms (37 and higher for ages less than 13; 35 and higher for ages 13 or order). (b) For SRS, Normal (0–53), Mild or High Functioning autism (54–86), Clinical diagnosis of autistic disorder, Asperger’s disorder, or more severe cases of Pervasive developmental disorder not otherwise specified (PDD-NOS) (>87). (c–g) Strong and significant correlations between improvements in GI symptoms (GSRS) and behavior symptoms based on % changes in 2 years.

Figure 3

Stool microbiota assessments at two-year follow-up after treatment stopped. (a) Faith’s phylogenetic diversity (PD) in the microbiota of 18 children with ASD as measured from stool samples. Orange lines indicate median PD of the donor samples (dashed line represents initial donor samples (n = 5), and dotted line represents maintenance dose samples (n = 2)), and green line indicates median PD of 20 neurotypical controls at week 0. ns indicates not significant, single asterisk indicates p < 0.05, double asterisks indicate p < 0.01, triple asterisks indicate p < 0.001 (two-tailed Wilcoxon signed-rank test comparing weeks 3, 10, and 18 and two-year to week 0 values). (b) Unweighted UniFrac distances between ASD gut microbiota and most relevant donor sample (initial donor sample at weeks 0 and 3, most recent maintenance dose sample at weeks 10 and 18, and 2 years). Green line indicates the median interpersonal variation between neurotypical controls and illustrates that prior to treatment the difference in gut microbiota composition between MTT recipients and donors was on the order of normal interpersonal variation. Statistics are the same as those used in (a). See also Supplementary Figs S5 and S6.

Figure 4

Changes in relative abundances of Bifidobacterium, Prevotella, and Desulfovibrio. ns indicates not significant, single asterisk indicates p < 0.05 and double asterisks indicate p < 0.01 (two-tailed Wilcoxon signed-rank test comparing weeks 3, 10, and 8 and two-year to week 0 values). Orange lines indicate median of the donor samples (dashed line represents initial donor samples, and dotted line represents maintenance dose samples), and green line indicates median of 20 neurotypical controls at week 0.