Modulation of Distinct Gut Microbiota Signatures in Acute and Chronic DSS-Colitis by Bawei Huangqin Enema in Mice

Description

Ulcerative colitis (UC) is a common inflammatory bowel disease (IBD) with limited current treatments and high recurrence rates. Dysfunction of the intestinal microbiota plays a crucial role in the pathogenesis of UC by promoting immune activation and damaging the intestinal barrier. While the importance of the microbiota is recognized, in-depth comparative studies on its dynamics, especially the distinct characteristics of the microbiota between acute UC (AUC) and chronic UC (CUC), are lacking. This study aimed to evaluate the therapeutic effects of Bawei Huangqin Enema (BHE), a traditional Chinese medicine formula hypothesized to possess immunomodulatory and gut microbiota-modulating properties. We conducted the study using DSS-induced AUC and CUC mouse models and investigated BHE's influence on the gut microbiota and intestinal barrier. By elucidating the distinct characteristics of the gut microbiota in AUC and CUC, this study provides novel insights into UC pathogenesis, highlighting their importance for personalized treatment.

Steps to reproduce

Initially, HiFi readings were assigned barcodes and filtered based on length. Bacterial 16s rRNA sequences that are less than 1000 base pairs or more than 1800 base pairs will be excluded, while fungal ITS sequences that are not in the range of 300 - 900 base pairs will also be discarded. were discarded. OTU representative sequences were classified taxonomically using RDP Classifier version 2.218 with a confidence threshold of 0.7, using 16s rRNA reference databases such as Silva v13818. Alpha diversity (Shannon, Chao indices) was then calculated to assess community richness and diversity. Principal coordinate analysis (PCoA) and non-metric multidimensional scale analysis (NMDS) were used to delineate differences in sample or group structure. In order to statistically assess differences between groups, ANOSIM and Adonis tests were performed. Drawing from the taxonomic annotation, stacked bar charts and heatmaps were generated. Visualizations present the composition of microbial communities at the genus level between different groups, focusing on changes in the composition and relative abundance of key species. Linear discriminant analysis of effect size (LEfSe) was also performed to identify bacterial groups with statistically significant differences in abundance, covering taxonomic levels from phylum to genus. The analyzed community abundance data were processed using reliable statistical techniques, including Kruskar-Wallis rank-sum test, one-way analysis of variance, and Wilcoxon rank-sum test. The purpose of these tests was to perform hypothesis testing on species abundance variations across microbial groups, ascertain the significance of observed differences, and identify species exhibiting significant differential abundance between groups. Finally, metagenomic function prediction was carried out using PICRUSt219, leveraging the OTU representative sequences. PICRUSt2 incorporates several tools for this purpose: HMMER was used to align OTU representative sequences with reference sequences, while EPA-NG and Gappa were used to map these OTU sequences into the reference phylogenetic framework. Castor normalized the copy number of the 16s gene and applied MinPath to infer gene family characteristics and associate them with corresponding metabolic pathways. The entire analysis process is carried out in strict accordance with the standardized procedures specified in PICRUst2.

Institutions

• Beijing University of Chinese Medicine

Categories

Funders

• "Jiebang Guashuai" Project of Beijing University of Chinese Medicine

  Grant ID: 2022-JYB-JBZR-043

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