Myricetin and M10 reshaped gut microbiome taxonomic diversity in mice
All pharmacological effects of Myricetin and M10 in mice were confirmed and issued in these UC mice [19]. To characterize the composition of gut microbiome in these UC mice, we randomly selected and analyzed eight stool samples of each group. Each stool sample was subjected to 16S rDNA Amplicon sequencing, which was followed by profiling of microbial community taxonomic composition and potential function. 16S rDNA Amplicon sequencing retrieved an overall number of 1423136 clean reads, which were clustered in 10360 operational taxonomic units (OTUs) according to strict criteria. Goods coverage of all samples was greater than 99.9% (Table 1), indicating that this sequencing reflects the true nature of intestinal flora. Over 99% of sampled sequences belonged to 6 phyla: Firmicutes (38.80 ± 7.83%), Verrucomicrobia (31.20 ± 18.84%), Bacteroidetes (23.19 ± 15.25%), Proteobacteria (4.07 ± 3.71%), Actinobacteria (2.49 ± 0.83%), and Candidatus Saccharibacteria (0.21 ± 0.11%) (Fig. 1A).
Table 1
The index of richness and diversity of gut microbiota in every group
Alpha diversity | Healthy control | UC model | Mesalazine | M10 | Myricetin |
Chao1 | 312.76 ± 14.67 | 284.99 ± 11.46 | 283.61 ± 27.87 | 257.63 ± 19.77 | 263.05 ± 22.19 |
Observed species | 280.5 ± 9.87 | 247 ± 15.02 | 242.37 ± 17.68 | 221.25 ± 24.41 | 228.25 ± 24.35 |
PD whole tree | 18.22 ± 0.57 | 16.71 ± 0.73 | 16.66 ± 0.75 | 15.18 ± 1.31 | 15.58 ± 1.00 |
Shannon | 5.98 ± 0.19 | 4.54 ± 0.33 | 4.68 ± 0.49 | 3.7 ± 0.47 | 3.88 ± 0.53 |
Simpson | 0.96 ± 0.00 | 0.86 ± 0.05 | 0.87 ± 0.04 | 0.73 ± 0.08 | 0.75 ± 0.08 |
Goods coverage | 0.99 ± 0.0003 | 0.99 ± 0.0002 | 0.99 ± 0.0004 | 0.99 ± 0.0002 | 0.99 ± 0.0003 |
Data show as mean ± SD. N = 8. |
In order to clarify the detailed differences of intestinal flora between different groups, we drew scatter diagrams of Top 6 flora content and then compared their differences. The compositions of Firmicutes, Verrucomicrobia and Actinobacteria in UC model mice are significantly increased as compared with healthy mice, whereas Bacteroidetes and Proteobacteria are significantly reduced (Fig. 1B). Although there were slight differences in intestinal flora content (Table 2), the trends of microbiome in Mesalazine-treated mice and UC model mice were completely consistent, indicating that control drug Mesalazine didn’t show significant modification on gut microbiome community. In contrast, M10 and Myricetin modified the composition of gut microbiota in UC mice. The proportions of Verrucomicrobia and Actinobacteria were significantly increased in the M10-treated mice and Myricetin-treated mice as compared with healthy mice, whereas the proportions of Bacteroidetes and Proteobacteria are significantly reduced. We have noticed that the proportions of Firmicutes showed no difference in the M10-treated mice and the Myricetin-treated mice when compared with healthy mice, whereas there are decreased as compared to UC model mice.
Table 2
The contents of gut microbiome community after drugs treatment at phylum level
Group | Firmicutes | Verrucomicrobia | Bacteroidetes | Proteobacteria | Actinobacteria | Candidatus Saccharibacteria |
Healthy control | 34.57 ± 7.19 | 3.87 ± 5.32 | 49.35 ± 6.17 | 10.67 ± 3.50 | 1.05 ± 0.59 | 0.40 ± 0.19 |
UC model | 47.41 ± 13.20 | 31.34 ± 10.67 | 15.29 ± 3.29 | 2.94 ± 0.62 | 2.87 ± 0.87 | 0.13 ± 0.07 |
Mesalazine | 47.15 ± 15.87 | 23.52 ± 14.68 | 24.00 ± 15.93 | 2.04 ± 0.82 | 3.11 ± 2.98 | 0.12 ± 0.09 |
M10 | 31.26 ± 10.09 | 50.10 ± 8.48 | 13.63 ± 5.05 | 2.29 ± 1.25 | 2.50 ± 2.44 | 0.19 ± 0.30 |
Myricetin | 33.62 ± 10.33 | 47.19 ± 9.50 | 13.67 ± 3.67 | 2.41 ± 0.96 | 2.91 ± 1.92 | 0.19 ± 0.21 |
Data show as mean ± SD. N = 8. |
M10 and Myricetin normalize alpha diversity of gut microbiota in mice
We further investigated the richness and evenness of gut microbiome among five groups of mice. Alpha diversity (α diversity) revealed a significant change in drug-treatment groups as compared with healthy control mice. All parameters represented alpha diversity in drug-treatment groups were lower than healthy group, indicating that community richness was decreased in all experimental groups. Moreover, M10-treated mice and Myricetin-treated mice demonstrated significant difference as compared to UC model mice (Fig. 2). The detailed results are shown in Table 1.
M10 and Myricetin normalize Beta diversity in intestinal microbiota of UC mice
To examine the weighted UniFrac distance, all groups were separated on PCoA plot (P = 0.001), Adonis plot (P = 0.001) and NMDS plot (Fig. 3). It shows that the samples of Mesalazine-treated group have the largest intra-group difference, while other groups have small intra-group difference. At PCoA1 (57.24%; P < 0.001), healthy mice is significantly different with other four groups of mice. However, at PCoA2 (23.25%; P = 0.045), chronic UC model mice and Mesalazine-treated mice are different with healthy control mice, while M10-treated mice and Myricetin-treated mice are similar with healthy control mice (Fig. 3A). In Adonis analysis, we found that at PCoA1 (57.24%), healthy control group is significantly different with other four groups. However, at PCoA2 (23.25%), M10-treated mice and Myricetin-treated mice are very similar with healthy control mice (Fig. 3B). The results of NMDS analysis (Fig. 3C) are consistent with PCoA and Adonis analysis, indicating that M10 and Myricetin could normalize the gut microenvironment in mice with UC.
M10 and Myricetin treatment resulted in changes of proportions of probiotics and pathogens to relieve UC symptoms
As regards to the analysis of bacteria differential abundance, relative abundance of intestinal flora at genuss level in top 20 differential species was displayed in Fig. 4. We found numerous changes of gut microbiota, as follows: 1) the proportions of Akkermansia, Clostridium XlVa, Olsenella, Clostridium IV, Ruminococcus, Parvibacter and Romboutsia were more abundant in UC model group than that of healthy mice (P < 0.05), and the proportions of Desulfovibrio, Parasutterella, Acetatifactor, Oscillibacter, Barnesiella, Parabacteroides, Flavonifractor, Alistipes, Lactobacillus, Prevotella, Odoribacter and Saccharibacteria_genera_incertae_sedis were significantly decreased (P < 0.05); 2) The proportions of Akkermansia, Bacteroides, Olsenella, Clostridium IV, Ruminococcus, Parvibacter and Romboutsia were more abundant in Mesalazine-treated group than that of healthy control group (P < 0.05), and the proportions of Desulfovibrio, Parasutterella, Acetatifactor, Oscillibacter, Barnesiella, Parabacteroides, Flavonifractor, Lactobacillus, Odoribacter, Prevotella and Saccharibacteria_genera_incertae_sedis were decreased (P < 0.05); 3) The proportions of Akkermansia and Ruminococcus were more abundant in M10-treated group than that of healthy control group (P < 0.05), and the proportions of Desulfovibrio, Parasutterella, Acetatifactor, Oscillibacter, Barnesiella, Parabacteroides, Flavonifractor, Alistipes, Lactobacillus, Prevotella, Odoribacter and Saccharibacteria_genera_incertae_sedis were decreased (P < 0.05); 4) The proportions of Akkermansia and Ruminococcus were more abundant in the Myricetin-treated mice than that of healthy control mice (P < 0.05), and the proportions of Desulfovibrio, Parasutterella, Acetatifactor, Oscillibacter, Barnesiella, Parabacteroides, Flavonifractor, Alistipes, Lactobacillus, Prevotella, Odoribacter and Saccharibacteria_genera_incertae_sedis were significantly decreased (P < 0.05). As comparing to UC model mice, we found some changes as follows: 1) The proportions of Oscillibacter, Ruminococcus, Clostridium IV, Desulfovibrio, Parabacteroides, Parvibacter and Olsenella were significantly decreased in M10-treated group (P < 0.05); 2) The proportions of Desulfovibrio, Parabacteroides, Clostridium IV, Parasutterella, Ruminococcus, Parasutterella and Romboutsia were significantly decreased in Myricetin-treated group (P < 0.05). All above results confirm that after treatment with M10 and Myricetin, the composition of intestinal flora of UC mice is closer to that of normal mice. In addition, the results of heatmap for all horizontally differentiated species are consistent with this conclusion (Supplementary Fig. 1).
Identification of signature bacteria as mediators to accelerate the reshape of inflammed colon
In the UC mice, oral M10 and Myricetin reshaped gut microbiota. To confirm both statistical and biological taxonomic differences between gut microbiota and define biomarker among five groups mice, the LEfSe algorithm with a logarithmic LDA score cutoff ≥ 2.0 (LDA ≥ 2, P < 0.05) was performed, and a total of 110 biomarkers were found. In order to identify the signature bacteria as mediators which accelerate the repairing of inflammed colon, we adopted stricter screening criteria (LDA ≥ 4) than others. As expected in healthy control mice, species such as Bacteroidetes, Proteobacteria, Erysipelotrichaceae_incertae_sedis, Porphyromonadaceae, Enterobacteriaceae, Deltaproteobacteria, Escherichia_Shigella, Desulfovibrionales, Anaerotruncus, Betaproteobacteria, Sutterellaceae, Parasutterella, Acetatifactor, Streptococcus, Streptococcaceae and Barnesiella exhibited elevated proportions, whereas in M10-treated mice, the abundance of Akkermansia, Verrucomicrobiae, Gemmiger and Clostridium XlVa are significantly increased. Mesalazine-treated mice demonstrated increased abundance of Ruminococcaceae. However, UC mice are characterized by increased abundance of Enterobacter, Clostridium, Ruminococcus and Parvibacte (Fig. 5).
M10 and Myricetin changed the metabolic function of gut microbiota
The PICRUSt algorithm (phylogenetic investigation of communities by reconstruction of unobserved states) was used to evaluate functional differences of bacteria in different groups. The differential pathways analysis was performed against KEGG, and analyzed and plotted (Fig. 6). By this way we can estimate the degree of influence of each component's metabolic pathway (KEGG pathway) on different effects, and find metabolic pathway that has a significant difference in sample division (the default screening condition is LDA > 2, The figure takes on third level). The analysis indicated that DSS-induced disruption in colon epithelium was reverted by M10 and Myricetin, which demonstrated similar histopathologic features to healthy control mice. The alteration of abundance of gut microbiota in M10-treated mice was strongly increased both in biosynthesis and degradation activities to improve gut microenvironment, such as sulfur metabolism, pyruvate metabolism, steroid biosynthesis and unsaturated fatty acid biosynthesis. Moreover, Myricetin-treated mice demonstrated significant increased of Ascorbate and aldarate metabolism and lipid metabolism.