Comprehensive Statistical Analysis Pipeline

GraphPad software version 7.0 (GraphPad Software, La Jolla, CA, USA) was used for graph design and statistical analysis. One-way analysis of variance (ANOVA) followed by Tukey’s multiple comparisons test was performed to analyze the log₂ fold-change of gene expression after Q-PCR. For RNA-seq analysis, the read count was adjusted by TMM, then differential expression analysis was performed by using the EdgeR R package. For microbiome analysis, the classification results were filtered through several statistical post-processing steps (K-mer-based classification, artifact filtering, and species-level abundance estimation [25 (link),26 (link)]) to eliminate false-positive results caused by contamination or sequencing artifacts.