lydiakirsche/urban-ethiopian-children-microbiome

Reproducible R Markdown pipelines for 16S rRNA and shotgun metagenomic analysis of fecal microbiome data from urban Ethiopian children, supporting a study on westernized lifestyle effects and traditional dietary influences on gut microbiota composition. # Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children This repository contains R Markdown analysis pipelines supporting the manuscript: **“Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children” (Communications Biology)** The repository includes two independent workflows for: 1. 16S rRNA gene sequencing data processing and analysis using QIIME2 2. Shotgun metagenomic data processing, taxonomic profiling, and functional pathway analysis These pipelines were developed to analyse fecal microbiome data from 207 urban Ethiopian children aged 2–5 years living in Adama, Ethiopia, and to enable transparent, reproducible microbiome research. --- ## Repository structure - `Kirsche_et_al_16S_pipeline.rmd` R Markdown workflow for QIIME2-based 16S rRNA gene sequencing analysis, including diversity analyses and downstream visualisation. - `Kirsche_et_al_shotgun_metagenomics.rmd` R Markdown workflow for shotgun metagenomic data processing, taxonomic profiling, and functional pathway analysis. --- ## Scientific context The study investigates how an urban, westernized lifestyle in a developing country shapes the gut microbiome of young children, and how traditional dietary components such as fermented teff products may mitigate these effects. The pipelines were used to generate the microbiome results reported in the associated manuscript. --- ## Requirements - R ≥ 4.2 - RStudio (recommended) - QIIME2 (for 16S processing pipeline) - Conda or mamba environment recommended for QIIME2 - R packages listed at the end of each `.Rmd` file --- ## Usage 1. Clone the repository: ```bash git clone github.com ``` 2. Open the desired `.Rmd` file in RStudio. 3. Adjust file paths and parameters in the configuration sections. 4. Execute the document to reproduce the analyses. --- ## Cite If you use the data, or find this work useful, please cite: ### G …