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Similarity of Citizen-Science American Gut Project to Published ASD Studies on Gut Microbiota
The gut microbiome has been hypothesized to play a role in gastrointestinal and behavioral symptoms in autism spectrum disorder (ASD). Existing studies have sought to identify differentially methylated taxa between ASD and non-ASD samples, but are limited in sample size. The recently established “American Gut Project” (AGP) is a “citizen science” approach that invites participation from the general public, and includes some individuals with self-reported ASD.
Objectives:
In this study we analyzed publically available microbiota data among participants of the AGP who self-reported ASD, and pursued a descriptive comparison of these profiles to published microbiome profiles from non-crowd sourced ASD-specific studies. This provides important information about the potential utility of AGP for gut studies of ASD.
Methods:
We included 33 AGP participants who completed a fecal sample as well as reported having ASD [diagnosed by a medical professional, by an alternative medicine practitioner, or being self-diagnosed]. Fecal samples were collected at home using a swab. Samples were processed according to the 16s Illumina Amplicon Protocol, targeting the V4 region of the 16s small ribosomal subunits rRNA. Closed-reference OTU picking was used, according to 97% similarity with the Greengenes database. The top 10 phyla, classes, orders, families, genera, and species were summarized across the ASD sample. We descriptively compared AGP taxa to taxa from a sample of 20 children with ASD published by Son et al., PLoS One 2015, and to a sample of 66 children with ASD from the Simons Simplex Community, published by Kang et al., PLoS One 2013.
Results:
All taxa identified in the AGP ASD sample belonged to the Bacteria or Archaea kingdom. The top 10 phyla were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia, Tenericutes, Euryarchaeota, Synergistetes, Cyanobacteria, and Fusobacteria. The top 10 genera were Bacteroides, Prevotella, Faecalibacterium, Ruminococcus, Blautia, Coprococcus, Parabacteroides, Akkermansia, Roseburia, and Dialister. The top 10 species were copri, prausnitzii, muciniphila, fragilis, bromii, distasonis, faecis, adolescentis, oxytoca, and uniformis. These findings are consistent with existing published studies that found that Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia tend to be the top 5 phyla in ASD samples. The top genera were also consistent with published studies, with the exception of genera Subdoligranulum, which has previously been reported as a top 5 genera in ASD, but was not observed in the AGP sample.
Conclusions:
The top phyla and genera from the citizen science-based American Gut Project ASD samples are largely consistent with published rankings based on ASD-specific datasets. This suggests that crowdsourcing may be a useful approach to sampling gut microbiome data that is representative of ASD populations, although larger samples are still needed to confirm this.