Fig. 2

The composition, alpha diversity, beta diversity, and indicator of gut microbiota. A The composition and relative abundance of the top 10 phyla. The bars with different colours represent different phyla. B The composition and relative abundance of the top 10 genera. The bars with different colours represent different genera. C The three groups' diversity indices (Shannon, Simpson, Chao1, and ACE). The outliers were calculated by Tukey's test. The horizontal lines of the boxplot, from top to bottom, represent the maximum value except for outliers, upper quartile, median, lower quartile, and minimum value except for outliers, respectively. D Every point in the plot represents a sample. NMDS plot shows a clear separation of every two groups. ANOSIM demonstrates that culture systems significantly impacted the gut bacterial community composition (R > 0 indicates that the difference between groups is greater than within groups, and FDR < 0.05 indicates that the difference is significant). E, F LEfSe analysis: The log LDA score of gut microbiota at the phylum and genus levels (log LDA score > 2.0). The bars with different colours represent the significant phyla or genera of the corresponding group. G The heatmap of the top 20 significant pathways predicted by PICRUSt2 (FDR < 0.05). The boxes with purpler colours represent higher expression levels, and yellower colours represent lower expression levels