Microbial Profiling of Environmental Samples

Genomic DNA of fecal and effluent samples was extracted using the FastDNA Spin kit for soil (MP Biomedicals, Illkirch, France) according to the manufacturer’s instructions. The V4 region of the 16S rRNA gene was amplified with the primers 806R (5′-GGACTACHVGGGTWTCTAAT-3′) and 515F (5′-GTGCCAGCMGCCGCGGTAA-3′). Amplicons were barcoded PCR based. Library preparation and sequencing (Illumina, CA, USA) using an Illumina MiSeq flow cell with a V2 reagent kit for 2 × 250-bp paired-end Nextera chemistry supplemented with 10% PhiX were performed in collaboration with the Genetic Diversity Center (GDC; ETH Zürich, Switzerland).
Raw data obtained from 16S rRNA sequencing were processed using Cutadapt (57 (link)) and DADA2 pipeline (58 (link)) to obtain amplicon sequence variants. Taxonomy was assigned using the SILVA database (v.132) (59 (link)) (full method described in Text S1).