- Fecal microbiota changes associated with the standardized AIN-93Mdiet
Whole-microbiome significance testing using Anosim showed significant differences after AIN-93M intervention (R=1, P=0.003, CA vs CB) (Fig. 2A). The alpha diversity test using the Shannon index with the Wilcoxon signed-rank test showed that the AIN-93M intervention significantly decreased the microbial diversity of the fecal microbiota (P=0.0082, CA vs CB) (Fig. 2B).
The MetaStat analysis results showed no significant differences in the abundances of Firmicutes and Bacteroidetes, which were the most abundant phyla (abundance>0.1) (Fig. 2C 2E). At the genus level, Bacteroides, Parabacteroides, Alistipes and Odoribacter were the most abundant genera (Abundance>0.01). AIN-93M significantly increased the abundances of Bacteroides, Parabacteroides and decreased that of Odoribacter (Fig. 2D).
- Fecal microbiota changes associated with the fish oil-intensive diet
Whole-microbiome significance testing results showed no significant difference between the fish oil and control groups before intervention (R=0.1426, P=0.081, FB vs CB). The fish oil-intensive diet had a significant influence on the microbiota (R=0.9185, P=0.001, FA vs FB), and there was a significant difference in the whole microbiome between these two groups after intervention (R=0.8926, P=0.002, FA vs CA) (Fig. 2A). No difference in microbial diversity was observed between the fish oil and control groups before intervention (P=0.1989, FB vs CB). Interestingly, the fish oil-intensive diet significantly increased the microbial diversity (P=0.7024, FA vs FB) (Fig. 2B).
At the phylum level, the fish oil-intensive diet intervention significantly reduced the abundance of Bacteroidetes and increased that of Firmicutes (Fig. 2C 2E). At the genus level, the fish oil-intensive diet intervention increased the abundance of Parabacteroides and decrease that of Odoribacter but had no influence on the abundance of Bacteroides (Fig. 2D).
- Fecal microbiota changes associated with VSL#3 intervention
There was a significant difference in the fecal microbiota between the VSL#3 and control groups before intervention (R=0.2148, P=0.034, VB vs CB). However, no significant difference was observed after intervention (R=0.1315, P=0.083, VA vs CA). The intervention had significant influence on the fecal microbiota (R=0.8778, P=0.002, VA vs VB). There was no significant difference between the VSL#3 and control groups on microbial diversity (P=0.0729, VB vs CB, P=0.7296, VA vs CA). Similar to the AIN-93M intervention, the AIN-93M plus VSL#3 intervention significantly reduced the diversity of the fecal microbiota (P=0, VA vs VB) (Fig. 2B).
At the phylum level, Firmicutes, Bacteroidetes and Proteobacteria were the most abundant phyla (abundance>0.1). The AIN-93M and VSL#3 intervention significantly reduced the abundance of Firmicutes and increased that of Proteobacteria but had no influence on Bacteroidetes. (Fig. 2C 2E) At the genus level, Bacteroides, Parabacteroides, Alistipes, Bilophila, Odoribacter, Parasutterella and Muribaculum were the most abundant genera influenced in all the groups (Abundance>0.1). The AIN-93M and AIN-93M plus VSL#3 interventions showed a similar influence over the fecal microbiota at the genus level, exhibiting increased abundances of Bacteroides, Parabacteroides, Bilophila and Parasutterella and decreased abundances of Alistipes, Odoribacter and Muribaculum (Fig. 2D).