Regulation of Gut Microecology in Ischemic Stroke Fecal Microbiota Transplantation Mice by Buyang Huanwu Decoction and Soy Isoflavones
Description
This study established a fecal microbiota transplantation (FMT) mouse model using samples from ischemic stroke patients to investigate stroke-specific gut dysbiosis and its functional implications. Mice pretreated with antibiotics received FMT to mimic clinical microbial disruption.
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Steps to reproduce
Primers 341F (CCTACGGGGNGGCWGCAG) and 806R (GGACTACHVGGGGTATCTAAT) were used for PCR amplification of the V3-V4 region of the 16S rRNA gene, followed by Illumina sequencing and library construction. The sequencing data were processed for quality control using the Qiime2 method to obtain OTU representative sequences and their abundance information; meanwhile, the data were processed for de-weighting, correction, noise reduction and de-chimerisation using the DADA2 method to obtain ASV sequences and their abundance information. All OTU/ASV sequences were annotated by SILVA database (version 138.1). In the analysis process, Chao1, Shannon, Simpson, Good's coverage, observed_species and PD-whole tree indices were used for Alpha diversity analysis to compare the species richness within the samples, in which comparisons between two groups were made using Welch 's t-test for comparison between two groups and Kruskal-Wallis H-test for comparison between multiple groups.For Beta diversity analysis, four distance indices, namely Bray_curtis, Jaccard, weighted_unifrac and unweighted_Unifrac, were used to assess the differences in the colony structure between the groups. Difference analyses were performed by LEFse software, firstly, Kruskal-Wallis rank sum test was performed on all group samples, and the screened difference species were then compared two-by-two by Wilcoxon rank sum test, and finally, the differences were ranked using LDA (Linear Discriminant Analysis), and the results were mapped to the taxonomic tree to generate the evolutionary branching diagrams. In addition, bacterial KEGG metabolic pathways were analysed using Tax4Fun, which constructs a species-gene network based on the complete genome, and outputs the relative abundance of KOid and pathway functions in each sample after selecting the reference species by combining the absolute abundance table of OTU/ASV in the SILVA species annotations of the samples.
Institutions
- Chongqing University of Posts and Telecommunications