Metagenomics revealed a correlation of gut phageome with autism spectrum disorder

Abstract

The human gut bacteriome is believed to have pivotal influences on human health and disease while the particular roles associated with the gut phageome have not been fully characterized yet with few exceptions. It is argued that gut microbiota can have a potential role in autism spectrum disorders (ASD). The public microbiota database of ASD and typically developing (TD) Chinese individuals were analyzed for phage protein-coding units (pPCU) to find any link between the phageome and ASD. The gut phageome of ASD individuals showed a wider diversity and higher abundance compared to TD individuals. The ASD phageome was associated with a significant expansion of Caudoviricetes bacteriophages. Phages infecting Bacteroidaceae and prophages encoded within Faecalibacterium were more frequent in ASD than in TD individuals. The expansion and diversification of ASD phageome can influence the bacterial homeostasis by imposing pressure on the bacterial communities. In conclusion, the differences of phages community in in ASD and TD can be used as potential diagnosis biomarkers of ASD. Further investigations are needed to verify the role of gut phage communities in the pathogenesis of ASD.

Keywords: Autism spectrum disorders; Gut phageome; Metagenomics; crAssphage.

Fig. 1

Schematic workflow for metagenomic analysis and phage taxonomic classification in ASD and TD individuals

Fig. 2

Taxonomic distribution of gut phageome in ASD and TD. A The differential abundance of phage genera detected in ASD and TD. B The differential abundance of different phage species identified in ASD and TD. * P < 0.05, ** P < 0.01, *** P < 0.001 and **** P < 0.0001 showed a significant difference of the particular phage in ASD with TD. Please refer to Additional File 2 for the detail of differential abundance of the phages

Fig. 3

Changes in the gut phageome in ASD and TD individuals. A Chao1 richness and B Shannon’s diversity for the gut phageome of ASD and TD at the contig level. Kruskal–Wallis test, followed by Wilcoxon’s rank-sum test with Bonferroni’s correction were done for alpha diversity between the two test groups. C Principal coordinates analysis (PCoA) was performed based on the Bray–Curtis distance between individual viral groups. D Chao1 richness and E Shannon’s diversity of the gut phageome for TD and ASD according to age from 2 to 11