Bacterial microbiomes of lungs of male C57BL/6J mice optionally treated with high-fat diet to induce obesity

Briefly, male, 2-3-month old, C57BL/6J mice were treated with high-fat diet for 16 weeks to induce obesity. Age/sex-matched control mice were fed normal diet. DNA was isolated from lungs after sacrificing mice using Qiagen® DNeasy PowerSoil Kit. 16S PCR and library preparation were as per Illumina® Metagenomics Guide, using the guide's suggested V3-V4 primers; Kapa Biosystems® KAPA HiFi ReadyMix for PCR, with 35 cycles and 25 ng DNA input (when available; otherwise entire DNA sample). Indexing was with Nextera® XT v2 combinatorial dual index kit, 8 cycles of PCR. Negative controls used were for DNA extraction (three) and 16S PCR (no template; two). One positive control was ZymoBIOMICS™ Microbial Community DNA Standard, Zymo® cat. #6305). All libraries were sequenced together, at ~8 pM each, with 10% PhiX library spike-in, on Illumina® MiSeq with v3 reagents, to obtain 300 b paired-end reads.