Noma Metagenomics

This repository includes the code used to run the analysis in a study published in PLOS Neglected Tropical Diseases:

Shotgun metagenomic analysis of the oral microbiomes of children with noma reveals a novel disease-associated organism

Michael Olaleye, Angus M O’Ferrall, Richard N. Goodman, Deogracia W Kabila, Miriam Peters, Gregoire Falq, Joseph Samuel, Donal Doyle, Diana Gomez, Gbemisola Oloruntuyi, Shafiu Isah, Adeniyi S Adetunji, Elise N. Farley, Nicholas J Evans, Mark Sherlock, Adam P. Roberts, Mohana Amirtharajah, Stuart Ainsworth

PLOS Neglected Tropical Diseases 20(3): e0014118, https://doi.org/10.1371/journal.pntd.0014118

The code used in the analysis is linked below for the taxonomic based metagenomic analysis of noma samples and healthy dataset (Table 1, Figures 1-3 and Supplementary Figures S1-S4), the recovery and analysis of Treponema MAGs from noma samples (Figure 4) and AMR profiling of noma metagenomes (Figure 5).

Part 1 - Taxonomic based metagenomic analysis

Part 1.1 - R markdown - Within noma dataset analysis (Table 1B, Figure 1A, Figure S1)

Part 1.2 - R markdown - Within healthy dataset analysis

Part 1.3 - R markdown - Noma vs healthy dataset analysis (Table 1A, Figures 1B, 2 and 3, Figures S2-S4)

Part 2 - Treponema MAGs from noma samples

Part 2.1 - R script - Descriptive plot of Treponema MAGs (Figure 4A)

Part 2.2 - R script - Tree of high-quality Treponema MAGs in context of previously characterised Treponema RefSeq genomes (Figure 4B)

Part 2.3 - Python script - Average nucleotide identity (ANI) matrices for novel Treponema MAGs (Figure 4C)

Part 3 - Antimicrobial resistance (AMR) profiling

Part 3.1 - R script - AMR plots (Figure 5)