Unique and enriched microbes and their potential “allies and foes” in the human gut microbiomes of ASD patients

Studies with animal models and humans show that alternations in the composition and activity of the gut microbiome can contribute to the etiopathogenesis of core symptoms in the ASD (autism spectrum disorder) patients. The role has been investigated by extending classic brain-gut axis to brain-gut-microbiome (BGM) axis. Nevertheless, there is not yet a consensus regarding the compositional changes associated with ASD. Here we fill a gap by computationally detecting and compiling the lists of US (unique species) and ES (enriched species) associated with ASD from big datasets on ASD-microbiome studies. The gap is that different existing studies generated conflicting evidence regarding the ES/US status, and the existing ES/US lists often lack rigorous statistical quantifications, which is likely responsible for the inconsistencies. To fill the gap, we apply and extend a recent computational advance for virome comparison (VC) that statistical rigorously determines the US/ES status and their holistic differences between the diseased treatments and healthy controls. We further extend the VC approach by building the first-order (nearest neighbor) network (FON) of US/ES taxa to deepen our understanding of the microbes associated with ASD, including their allies and foes. We obtained the US/ES lists from 8 individual datasets separately and their pooled datasets with statistical rigor and computed their union/intersection sets to make recommendations for practical applications of US/ES catalogues. We also built the FON and revealed possibly general species occurrence patterns of US/ES in ASD patients, analyzed the extreme complexity in gut microbiome alternations associated with ASD.