Phylogenetic Association Study

This repository contains the scripts used for the study "Global human gut microbiome species genetic diversity is related to geographic location and host health." The study employs phylogenetic reconstructions of dominant gut microbial strains to investigate geographical stratification and strain-level associations with disease.

Code Includes:

• Scripts for tree building
• Scripts for geographic associations and factors related to geographical stratification
• Scripts for tree-phenotype associations
• Downstream analysis scripts

Sample Selection

We included 90 publicly available studies from curatedMetagenomicDataCuration. Additionally, three Dutch publicly available studies and a Tanzanian study were added:

• KurilshikovA_2019 (300 Obesity, 300OB) DOI: 10.1161/CIRCRESAHA.118.314642
• GacesaR_2022 (Dutch Microbiome Project, DMP) DOI: 10.1038/s41586-022-04567-7
• ZhernakovaA_2016 (Lifelines Deep, LLD) DOI: 10.1126/science.aad3369
• StražarM_2021 (300 Tanzanian, 300TZN) DOI: 10.1038/s41467-021-25213-2

Biobakery4 Run

MetaPhlAn4 and StrainPhlAn4 were executed using the mpa_vJan21_CHOCOPhlAnSGB_202103.pkl database.
The specific StrainPhlAn4 command:

strainphlan -o {OUTPUT} -n {CPU} --sample_with_n_markers 50 --secondary_sample_with_n_markers 50 --sample_with_n_markers_after_filt 33 --marker_in_n_samples 50 --samples {PRIMARY} --secondary_samples {SECONDARY} -c {SGB} -d /shares/CIBIO-Storage/CM/scratch/databases/metaphlansgb_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.pkl --treeshrink --debug

The specific python script preparing jobs for an HPC batch run is avaialble in: scripts_phylogeny/

Associations

Geography vs Phylogeny

Mantel test script between genetic and geographical distances can be found in: scripts_geography/Geography_vs_phylopgenyMantel.R

Strain sharing

Scripts for computing strain sharing, and its association to mantel's rho value can be bound in scripts_geography/Strain_sharing/

Bacterial characteristics vs Geographical effect

Scripts for associating mantel's rho value and microbial features can be found in scripts_geography/Bacterial_Features

Anpan associations

Scripts using for phenotype-phylogeny assocaitions (using anpan) are available in: scripts_phenotype/

Data Access

To be updated!