CD patients have also previously been shown to have an altered gut microbiota with higher levels of (48). a lower diversity of T-cell repertoire and expression level of IgE, as well as a reduced large quantity of inflammation-related genes in the gut microbiota were potentially associated with a control group with long-term vegetarians. Therefore, the composition and period of the diet may have an impact on the balance of pro-/anti-inflammatory factors in the gut microbiota and immune system. with and multiplying with JAKL 100, where was acquired by 10,000 permutations. Reporter Score for Pathways/Modules Gene practical analysis was performed based on KO profile. Significant Kaempferide modules and pathways (the KEGG Class Level 3) were identified using a reporter feature algorithm (36) based on the pathway-KO and module-KO analyses. One-tail Wilcox rank-sum test was first performed on all the KOs and modified for multiple-test using FDR controlling. Then, the reporter score for each pathway/module was computed using based on the module-KO or pathway-KO relations as: =?denotes the number of KO involved in the pathway. Third, the background distribution of and dividing by the standard deviation (Cscores of 1 1,000 units of KO chosen randomly from the whole metabolic KO network by: (Number S2B in Supplementary Material). No significant relationship between enterotype and diet pattern was, however, recognized. PCA was furthermore performed based on gene profile and demonstrating that samples from different organizations clustered collectively (Number ?(Figure22A). Open in a separate window Number 2 The effect of diet pattern on general composition, richness, and diversity of the gut microbiota. (A) Principal component analysis based on the gut bacterial gene profile. (B) Violin plots Kaempferide showing the richness in the gene level for each subgroup. (C,D) Violin plots showing the alpha- and beta-diversity in the genus level, for each subgroup. We next investigated the richness and evenness of the gut microbiota in all samples in the genus, varieties, and gene levels. No significant difference was observed in gene count or alpha diversity (Shannon index) whatsoever levels between the two time points Kaempferide in any organizations (Numbers ?(Numbers2B,C2B,C and data not shown). The beta diversity, however, accessed by using JensenCShannon divergence, showed a tendency for reduction after changing to the short-vegetarian diet, and reached significance in the genus and varieties level (A vs. B subgroup, Number ?Number2D;2D; Number S3 and Table S3 in Supplementary Material). Therefore, the general composition of gut microbiota did not seem to be associated with the diet pattern, but there might be specific alterations associated with the switch to the short-term vegetarian diet, especially within the genus and varieties levels. We next directly compared the bacterial profiles from before- (A subgroup) and after- (B subgroup) samples to search for biomarkers that might be associated with the alteration of diet pattern. In the phylum level, no significant switch was observed between the A and B subgroups. However, seven genera were significantly associated with switch to Kaempferide the short-term vegetarian diet (Table S4 in Supplementary Material). Specifically, were decreased after the short-term vegetarian diet (Number ?(Number3B;3B; Table S5 in Supplementary Material). In addition, the large quantity of Kaempferide nine varieties was significantly associated with the switch in diet. For example, the large quantity of (was improved and reduced, respectively, in the B subgroup samples (Table S5 in Supplementary Material). Open in a separate window Number 3 Metagenomic biomarkers associated with short-term vegetarian diet. The relative large quantity (log) of selected genera (A) and varieties (B) that were significantly different between A and B subgroups were plotted for each subgroup. Wilcoxon signed-rank test was used for the statistical calculation. The complete dataset is definitely offered in Furniture S4 and S5 in Supplementary Material. To search for biomarkers that might be associated with a long-term vegetarian diet, we compared the gut bacterial profiles among settings and observed a list of genera (is found to be enriched in the control group 1, the omnivores. This varieties belongs to a group of bacteria that grow in the presence of bile (38) and has been reported to be associated with colon cancer (39). Varieties enriched in the long-term vegetarians included the butyrate-producing and (40), the H2-utilizing acetogen (formally known as (and chain,.