16S rRNA sequencing from ASD and TD individuals (resequencing)
Qualified genomic DNA samples were processed for 16S rRNA library preparation and next-generation sequencing at the Microbiome Analysis Laboratory in the Biodesign Swette Center for Environmental Biotechnology (http://krajmalnik.environmentalbiotechnology.org/microbiome-lab.html). The Earth Microbiome Project standard protocols (http://www.earthmicrobiome.org/emp-standard-protocols/) were employed with the barcoded primer set 515F-806R (515F:GTGCCAGCMGCCGCGGTAA, 806R:GGACTACHVGGGTWTCTAAT) that targets the V4 region of the bacterial (and archeal) 16S rRNA gene (Caporaso et al., 2012). Paired-end, 2x150bp, next-generation sequencing was performed using MiSeq Illumina platform (MiSeq Reagent Kit v2; Illumina Inc.; San Diego, CA, USA) and microbiome sequencing data were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME2) software package (Bolyen et al., 2018; Caporaso et al., 2010).