Pyrosequencing study of fecal microflora of autistic and control children Original paper

What was studied?

This study examined autism fecal microflora using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) to characterize gut microbial composition in autistic children compared with controls. Drawing on extensive sequencing data, the authors evaluated microbial diversity, richness, and taxonomic patterns, emphasizing how altered microbiota profiles correlate with autism severity and gastrointestinal symptoms. According to the detailed phylum-level charts and diversity tables, the work provides one of the earliest next-generation sequencing–based portraits of microbial differences in autism.

Who was studied?

The research analyzed fecal samples from 33 children with autism spectrum disorder (ASD), all of whom exhibited gastrointestinal symptoms; 7 non-autistic siblings; and 8 unrelated non-autistic controls, all aged 2–13 years. Severity was assessed clinically, allowing comparison of mildly versus severely affected individuals. Samples were collected at home, transported under controlled conditions, and processed using standardized DNA extraction and sequencing protocols. Antibiotic and probiotic exposure was restricted for at least one month before sampling, although diet varied. The control cluster, as illustrated by the PCA plots on pages 4–5, showed distinct microbial separation from autistic and sibling groups.

Most important findings

Autistic children demonstrated significantly higher microbial diversity and richness than controls across OTU-based estimators. Phylum-level differences were especially striking: Bacteroidetes dominated ASD samples, averaging just over 50% of total flora, whereas Firmicutes predominated in controls at roughly 63%. Several microbial signatures emerged as characteristic of autism. Desulfovibrio species—including D. piger, D. desulfuricans, and D. intestinalis—were significantly elevated in severe autism, consistent with their production of hydrogen sulfide and LPS, both biologically disruptive metabolites. Bacteroides vulgatus was also substantially increased and has prior associations with colitis and proinflammatory activity. Correspondingly, protective or beneficial genera—including Bifidobacterium longum and Collinsella—were depleted in autistic subjects, with reductions seen both in prevalence and relative abundance. Genus-level clustering revealed that mildly and severely autistic samples grouped, while unrelated controls formed distinct clusters, reinforcing the consistency of the ASD-associated microbial pattern. The sibling group often resembled autistic subjects more closely than controls, suggesting potential household transmission or shared environmental factors.

Key implications

This work supports a distinct microbial signature in autism characterized by Bacteroidetes enrichment, Firmicutes depletion, and elevated sulfate-reducing and LPS-producing taxa. These findings highlight the importance of microbial metabolites—such as propionic acid and hydrogen sulfide—in gut-brain interactions. While causality cannot be inferred, the altered microbiome may contribute to symptom severity and gastrointestinal pathology. The overlap between autistic and sibling profiles underscores a potential environmental or transmissible microbial component, suggesting new avenues for diagnostics and targeted microbiome-modulating therapies. The study further motivates controlled interventional trials, including antibiotic, probiotic, and microbiota-transplant-based–based strategies.

Citation

Finegold SM, Dowd SE, Gontcharova V, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe. 2010;16(4):444-453. finegold2010