Fig. 4: Maternal antibiotic exposure downregulates IFN1 signaling in neonatal ILC2s.

a–c Lung ILC2s were sorted from neonates born to Abx or PBS dams, and transcriptional profiling was evaluated by SMART-seq. a Volcano plots presenting the differences between two groups. The negative binomial distribution was employed for the identification of differentially expressed genes through the use of DESeq2. The Benjamini-Hochberg method was applied for multiple testing correction. b Top 10 pathways enriched in KEGG analysis. The hypergeometric test was employed to assess the impact of differentially expressed genes on a pathway. The Benjamini-Hochberg method was applied for multiple testing correction. c Gene set enrichment analysis (GSEA) showing the downregulation of interferon β (IFNβ) signaling in Abx group. The one-sided Wilcoxon rank-sum test was employed for the enrichment analysis of the IFNβ signaling pathway within the framework of GSEA. d Amounts of IFNβ in the culture supernatants of lung ILC2s were measured by ELISA (n = 3). e The amounts of IL-5 and IL-13 in the culture supernatants of lung ILC2s in the presence of different dosages of IFNβ were measured by ELISA (n = 4). f–i WT and Ifnar1^-/- pregnant mice were subjected to Abx treatment, pups were intraperitoneally injected with IFNβ (1 × 10⁴ U/mouse) daily for 5 consecutive days. Pups were sacrificed at postnatal day 7 (n = 5). The absolute number of ILC2 (f), the frequency of Ki-67⁺ ILC2s (g), and the frequency of IL-5⁺ IL-13⁺ ILC2s (h) in lungs were analyzed by flow cytometry. i Amounts of IL-5 and IL-13 in BALF were determined by ELISA. In Fig. 4d, 4e and 4i, the data are presented as the mean ± SEM values, by unpaired two-tailed Student’s t test. For box plots, the data are shown as “Min to Max, show all points”. For box plots, the midline represents the median; box represents the interquartile range (IQR) between the first and third quartiles, and whiskers represent the lowest or highest values within 1.5 times IQR from the first or third quartiles (f, g, h). **P < 0.01; ***P < 0.001; ****P < 0.0001 by unpaired two-tailed Student’s t test or one-way ANOVA followed by Tukey-Kramer multiple-comparisons test. Data are presentative of 2-3 independent experiments (d–i). Statistical source data are provided in Source Data.