Amplicon-based analysis of bacterial communities of rat lung and gut following antibiotic treatment.
Metagenomic DNA was extracted of bronchoalveolar lavage fluid from wild type LEW/Crl rats (Rattus norvegicus) after 7 days of intratracheal or per os treatment with PBS. Three technical replicates were performed.  Subsequently, the V3-V4 region of 16S rRNA genes was amplified. All samples were amplified in triplicate, purified and pooled in equal amounts. Sequences were determined using an Illumina MiSeq sequencer.