Effect of antibiotic-mediated gut microbiota perturbation on postnatal mice ileum transcriptomics

The postnatal period is one of the important windows for developing the gastrointestinal tract's structure-function and associated mucosal immunity. Recent studies suggest a promising contribution of gut microbiota in maintaining host health, immunity, and gut development. However, the function of postnatal gut microbiota dynamics concerning intestinal mucosal development needs to be better understood. To decipher the causal role of gut microbiota on barrier integrity and intestinal epithelium development, we executed an antibiotic-mediated perturbation and tracked the kinetics in postnatal mice. We observed a postnatal age-related impact of antibiotic-mediated gut microbiota perturbation with a substantial decrease in total bacterial load on P14D and also in the barrier integrity and IECs marker. To enhance our knowledge of the mechanisms behind this, we employed a global transcriptomics approach to see the alterations in the mucosal innate immunity and other relevant pathways. Postnatal mice were orally gavaged with AVNM (Ampicillin, Vancomycin, Neomycin and Metronidazole) cocktail once daily from P3D to P14D along with a set of vehicle control (PBS). Mice were sacrificed at P14D from the two groups (control and AVNM) and collected from different littermates' separate cages to minimize the effect. After sacrifice, the ileum was dissected out, washed with cold PBS, cut into small pieces, and stored in the RNAlater. High-quality RNA was extracted using Direct- zol RNA miniprep (Zymo Research), and quality and quantity were determined using Nanodrop, Gel electrophoresis, Qubit and Tapestation.