Respiratory Microbiome Project

This repository contains all the source code used to conduct the "Respiratory Microbiome Project (RM-TB)".

RM-TB Sample selection criteria

The diagram outlines the participant selection criteria for a study on tuberculosis (TB) and microbiota:

1. Initial Pool: The study starts with 730 participants from the CAGE-TB pool.
2. Inclusion Criteria: Participants must be HIV+ or HIV−, aged 18 or above, and of any gender.
3. Exclusion Criteria:
   • 99 participants with prior anti-TB treatment were excluded.
   • 39 participants with chronic illnesses (e.g., hypertension, asthma, arthritis, cholesterol, e.t.c) were excluded.
4. Final Selection:
   • 631 eligible participants remained.
   • 592 underwent a GeneXpert TB diagnostic test.
   • Based on results: 126 were TB-positive (GeneXpert+), and 466 were TB-negative (GeneXpert−).
5. Randomized Selection: Using a custom script (seed = 42), a subset was chosen:
   • 50 GeneXpert+ (RM-TB+).
   • 100 GeneXpert− (RM-TB−).

This process ensured a well-defined and controlled sample selection that can be replicated for microbiota analysis.

Downstream microbiome analysis

Microbiome data analysis was performed using R. The main script is located in the bin directory. Prior to the R analysis, outputs from sylph were processed using custom scripts located in the Scripts directory