Gut microbes harbour millions of single nucleotide variants (SNVs).
This resource catalogues associations between core-genome common SNVs in the human gut microbiome
and host phenotypes / environmental exposures from a phenome-scale metagenome-wide association study (MWAS).
Across 6 cohorts and 10,781 host individuals, the study genotyped
12,761,497 microbial SNVs in 433 gut species against 244 phenotypes.
Meta-analysis yielded 49,346 study-wide significant associations
(Pmeta < 5.42×10⁻¹¹), linking 39,663 SNVs from 101 species to
69 phenotypes and exposures.
What is in the online catalog?
The browsable / downloadable table contains 1,389,120 association rows spanning
cohort-level (DMP) and meta-analysis results, with allele frequencies, effect sizes,
p-values, gene products, UniRef/Pfam annotations, SNV consequence classes and significance flags.
Overview KPIs describe the full study scale; charts on the Overview page summarise the
released association catalog that Explore queries.
What is a row?
Each row is one SNV–phenotype association within a study stratum (e.g. Meta-analysis or DMP):
the microbial SNV (species + genomic position + alleles), the host trait, sample size,
effect estimate, and annotation of the gene (if coding) that contains the SNV.
- StudyWideSig=TRUE — passes the study-wide significance cutoff for that analysis.
- Meta-analysis — combined evidence across cohorts; default Explore view.
- Missense / Synonymous / Non-coding — predicted SNV consequence.
How associations were derived
- Genotype common core-genome SNVs in gut microbial species from host metagenomes (UHGG references).
- Test associations with host phenotypes and exposures within cohorts; meta-analyse shared traits.
- Apply species-wide and study-wide significance thresholds; annotate variant consequences and gene products.
- Release the association catalog with interactive Explore and bulk downloads.
Using this website
- Overview — interactive statistics; click phenotype or species bars to open Explore with filters applied.
- Explore — unified search, filters, phenotype/species info cards, column selector and CSV export.
- Download — complete TSV plus genomes, GFF3, UniProt and CDS resources.
How to cite
If you use SNV-MWAS data, please cite:
Daoming Wang, et al. Microbiome-wide PheWAS links gut microbial SNVs to human health and exposures,
25 September 2024, PREPRINT (Version 1) available at
Research Square
[https://doi.org/10.21203/rs.3.rs-5063726/v1]
Fu Lab ·
Groningen Microbiome Hub ·
University Medical Center Groningen