Mouse pellet from mouse 4 CON.2 D8
16S sequencing was performed for murine studies in which known bacterial strains that were previously whole genome sequenced were given to ex-germ-free mice. V4-V5 region within 16S rRNA gene was amplified using universal bacterial primers  563F (5-nnnnnnnn-NNNNNNNNNNNN-AYTGGGYDTAAA- GNG-3) and 926R (5-nnnnnnnn-NNNNNNNNNNNN-CCGTCAATTYHT-TTRAGT-3), where N represents the barcodes, n are additional nucleotides added to offset primer sequencing. Approximately ~412bp region amplicons were then purified using a spin column-based method (Minelute,Qiagen), quantified, and pooled at equimolar concentrations. Illumina sequencing-compatible Unique Dual Index (UDI) adapters were ligated onto the pools using the QIAseq 1-step amplicon library kit (Qiagen). Library QC was performed using Qubit and Tapestation and sequenced on Illumina MiSeq platform to generate 2x250bp reads.