Effect of gastric fluid aspiration and antibiotic treatment on the lung microbiota of laboratory rats

The pulmonary microbiota is important for both normal homeostasis and the progression of disease, and may be affected by aspiration of gastric fluid and by administration of antibiotics. This dataset includes 16s amplicon sequence data from three related projects which investigated changes in the lung microbiota of laboratory rats induced by aspiration of gastric fluid, administration of antibiotics by different routes, and the interaction of gastric fluid aspiration in rats treated with antibiotics.For the aspiration project rats were either unaspirated, or aspirated with saline, gastric fluid, or sterilized gastric fluid. For the antibiotic project rats were either untreated or administered antibiotics subcutaneously, orally, or by IV. For the interaction project rats aspirated with gastric fluid were either untreated or administered antibiotics subcutaneously. Fpr all projects, animals were sacrificed on the fourth day after the procedure and lungs were harvested for DNA extraction and sequencing of the v4 region of the 16s ribosomal RNA gene.