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

Datasets included in this study are publicly available. All datasets, with the exception of GacesaR_2022, ZhernakovaA_2016, KurilshikovA_2019, and StražarM_2021, have been collected previously and are curated in CuratedMetagenomicData. Accessions collected in that study are included in Supplementary Table 1.1. Phenotypes are available as part of CuratedMetagenomicData.

Datasets not included in CuratedMetagenomicData

Lifelines datasets: Metagenomics data can be requested from the European Genome-Phenome Archive (EGA) for GacesaR_2022 (EGAS00001005027) and ZhernakovaA_2016 (EGAD00001001991). Phenotypes can be requested by filling out the application form at https://www.lifelines.nl/researcher/how-to-apply/apply-here.
VichVilaA_2018: Raw metagenomics, host genomics and phenotypic data used in this study are available from the EGA data repository: 1000 Inflammatory bowel disease (IBD) cohort (EGAD00001004194). Metagenomics data can be requested from the EGA (EGAD00001004194).
KurilshikovA_2019: Metagenomics data can be requested from EGA (EGAS00001003508). Phenotype data can be requested via: http://www.humanfunctionalgenomics.org StrazarM_2021: Metagenomics data can be accessed from the European Nucleotide Archive (PRJNA686265). Phenotype data is included in the original publication.

Acess to phylogenies

Phylogenetic trees generated in this work are available in the corresponding Zenodo repository: https://doi.org/10.5281/zenodo.14651412