R scripts and analysis workflow for quantitative microbiome profiling of Three Gorges Dam sediments

This repository contains the R scripts, analysis workflow, and code for generating figures associated with the research article: "Quantitative profiling of bacterial community restructuring and functional potential variation across upstream and downstream sediments of the Three Gorges Dam" (submitted to Environmental Technology & Innovation) Contents: R scripts for quantitative microbiome data processing and statistical analysis Code for alpha and beta diversity analysis Scripts for differential abundance analysis Functional potential prediction and visualization code Figure generation scripts Study Overview: This study employed quantitative microbiome profiling (QMP) to evaluate bacterial community structure and functional potential in sediments collected from upstream (GDK, XXH, MH) and downstream (HLM, NJG) sites of the Three Gorges Dam, 21 years after dam operation commenced. The analysis revealed significant reductions in bacterial abundance, alpha diversity, and functional genes associated with carbon, nitrogen, sulfur, and phosphorus cycling in downstream sediments. Usage: These scripts are provided to ensure the reproducibility and transparency of our analyses. Users can adapt the code for similar quantitative microbiome studies. Citation: If you use these scripts, please cite both this repository and the associated publication.