This repository contains scripts, processed data, statistical analyses, and publication-ready figures associated with the metagenomic characterization of antimicrobial resistance genes (ARGs) in oral microbiomes from individuals with periodontitis and healthy controls.
This study investigated the oral resistome profile using publicly available metagenomic datasets obtained from the NCBI Sequence Read Archive (SRA). Comparative analyses were performed between periodontitis-associated samples and periodontal healthy samples to identify differences in ARG richness, abundance, and co-occurrence patterns.
| Sample ID | Group |
|---|---|
| SRR1044006 | Periodontitis |
| SRR1795229 | Periodontitis |
| SRR10903401 | Healthy |
| SRR10903402 | Healthy |
The computational workflow included:
- Quality control using FastQC and fastp
- Metagenomic assembly using MEGAHIT
- Gene prediction using Prodigal
- ARG detection using ABRicate with the CARD database
- Statistical analysis and visualization in R
scripts/ R scripts used to generate publication-ready figures
figures/ Final figures used in the manuscript
results/ Processed ARG tables and statistical outputs
data/ Metadata and sample information
- Periodontitis-associated metagenomes exhibited higher ARG richness and abundance.
- Tetracycline resistance genes were predominant in diseased samples.
- Healthy samples showed limited or absent ARG detection.
- Co-occurrence analysis suggested potential ecological associations among ARGs in periodontitis-associated microbiomes.
To reproduce the final figures:
Rscript scripts/refazer_figuras_publicaveis_4amostras.RAll sequencing datasets analyzed in this study are publicly available from the NCBI SRA database under their respective accession numbers.
If you use this repository, please cite the associated manuscript and repository DOI (Zenodo).
Lobo et al.