4.3.2. Functional and Pathway Analysis of DEGs

Differential expression analysis of B. bifidum biofilm and planktonic cells was performed using the DESeq2 [52]. Specified pairwise transcriptome comparisons (22 h B vs. 22 h P; 32 h B vs. 32 h P; 32 h B vs. 22 h B; 32 h P vs. 22 h P) were performed to identify the main DEGs with an absolute value of log2 FC > 1.0 [24,53]. Venn diagram was used to show the comparison and overlap between DEGs in different biofilm formation stages [54]. KEGG pathway and GO analyses were conducted using clusterprofiler (R package) [55] for DEGs obtained from different stages.