Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

Background Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 1013 bacteria in the human intestines, have been implicated because children with ASD often suffer gastrointestinal (GI) problems that correlate with ASD severity. Several previous studies have reported abnormal gut bacteria in children with ASD. The gut microbiome-ASD connection has been tested in a mouse model of ASD, where the microbiome was mechanistically linked to abnormal metabolites and behavior. Similarly, a study of children with ASD found that oral non-absorbable antibiotic treatment improved GI and ASD symptoms, albeit temporarily. Here, a small open-label clinical trial evaluated the impact of Microbiota Transfer Therapy (MTT) on gut microbiota composition and GI and ASD symptoms of 18 ASD-diagnosed children. Results MTT involved a 2-week antibiotic treatment, a bowel cleanse, and then an extended fecal microbiota transplant (FMT) using a high initial dose followed by daily and lower maintenance doses for 7–8 weeks. The Gastrointestinal Symptom Rating Scale revealed an approximately 80% reduction of GI symptoms at the end of treatment, including significant improvements in symptoms of constipation, diarrhea, indigestion, and abdominal pain. Improvements persisted 8 weeks after treatment. Similarly, clinical assessments showed that behavioral ASD symptoms improved significantly and remained improved 8 weeks after treatment ended. Bacterial and phagedeep sequencing analyses revealed successful partial engraftment of donor microbiota and beneficial changes in the gut environment. Specifically, overall bacterial diversity and the abundance of Bifidobacterium, Prevotella, and Desulfovibrio among other taxa increased following MTT, and these changes persisted after treatment stopped (followed for 8 weeks). Conclusions This exploratory, extended-duration treatment protocol thus appears to be a promising approach to alter the gut microbiome and virome and improve GI and behavioral symptoms of ASD. Improvements in GI symptoms, ASD symptoms, and the microbiome all persisted for at least 8 weeks after treatment ended, suggesting a long-term impact. Trial registration This trial was registered on the ClinicalTrials.gov, with the registration number NCT02504554 Electronic supplementary material The online version of this article (doi:10.1186/s40168-016-0225-7) contains supplementary material, which is available to authorized users.

Additional file 3: Figure S3. Vineland Developmental Age (in years) for individual subscales and for the average of all subscales, measured at baseline and at the end of observation 4 months later. Note that the average chronological age was 10.9 years at the start of treatment (showed in a dotted line). As seen here, at baseline there were delays in all areas, especially in the core autism areas of language and social (interpersonal) ability. Subscales are under either communication domain (receptive, expressive, and written), or daily living skills domain (personal, domestic, and community), or socialization domain (Interpersonal relationships, play and leisure Time, and coping skills). *: p<0.05, **: p<0.01, ***: p<0.001 (two-tailed Wilcoxon signed-rank test).
Additional file 3: Figure S4. Stool microbiota changes in community richness with fecal microbiota transplant. Change in community richness, as measured by Observed OTUs, a non-phylogenetic diversity metric. Additional file 3: Figure S5. Gut phageome taxonomy is still mostly unknown. a Viral populations were assigned to a viral family if >50% of the genes in the viral contig had a blastx bit score >50 to the to the same viral family in the Viral Protein RefSeq database. All viral populations that could be assigned to a viral family were members of the Order Caudovirales, with 2.97% assigned to the family Siphoviridae, 0.73% to Myoviridae, and 0.67% to Podoviridae. Most viral populations (95.64%) could not be assigned a familial level taxonomy. b Viral populations were considered to related to the 23 core gut phages identified in Manrique et al.

Observed
[59] if they had a blastn alignment length > 500bp to one the 23 core gut phage contigs at a percent identify greater than 75%. In total, 4.91% of the gut viral populations identified in our study were related to the core phages.
Additional file 3: Figure S6. Subscores of the PGI-III at end of treatment (week 10). The scale goes from 3 (much better) to 2 (better) to 1(slightly better) to 0 (no change) to minus 3 (much worse). Scores were similar after 8 weeks of no treatment (week 18). The data points represent 18 individual participants, and some data points overlap in the box plot. The bar represents mean values of subscores. Average betweenneurotypical Additional file 3: Figure S9. Engraftment plots with four diversity metrics (Stool samples). A decrease in the distance to donor is an indication that some engraftment has occurred. Additional file 3: Figure S10. Stool microbiota changes with fecal microbiota transplant. a Unweighted UniFrac distances between ASD gut microbiota and major initial donor sample. 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. Following treatment, the MTT recipients were more similar to donors than normal interpersonal variation. *: q<0.05, **: q<0.01, ***: q<0.001 (two-tailed Wilcoxon signedrank test comparing week 3, 10, and 18 to week 0 values) b Distances between ASD gut microbiota and donor sample on a per individual basis. Most individuals became more similar to the donor over the study period.

a b
Unweighted UniFrac to donor