Library preparation and amplicon sequencing

We employed a two-step PCR amplification approach for microbial 16S library preparation. The V3-V4-regions of the bacterial 16S rRNA gene were amplified by PCR using the primers 341F (5′-CCTAYGGGRBGCASCAG-3) and 806R (5′-GGACTACNNGGGTATCTAAT-3) [42]. A subsequent PCR amplification was performed with the Nextera™ XT index primers (Illumina Inc., San Diego, US) in order to attach Illumina MiSeq™ sequence adapters and barcodes to each DNA extract. Full details of 16S library preparation and sequencing are listed in Additional file 1. In the following, the term microbiome refers to the data obtained from the 16S-based libraries.