| Title: | Human and bacterial genetic variation shape oral microbiomes and health |
| Journal: | Nature |
| Published: | 28 Jan 2026 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/41606319/ |
| DOI: | https://doi.org/10.1038/s41586-025-10037-7 |
Publication 18443
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Abstract
Human genetic variation influences all aspects of our biology, including the oral cavity1, 2-3, through which nutrients and microbes enter the body. Yet it is largely unknown which human genetic variants shape a person's oral microbiome and potentially promote its dysbiosis3, 4-5. We characterized the oral microbiomes of 12,519 people by re-analysing whole-genome sequencing reads from previously sequenced saliva-derived DNA. Human genetic variation at 11 loci (10 new) associated with variation in oral microbiome composition. Several of these related to carbohydrate availability; the strongest association (P = 3.0 × 10−188) involved the common FUT2 W154X loss-of-function variant, which associated with the abundances of 58 bacterial species. Human host genetics also seemed to powerfully shape genetic variation in oral bacterial species: these 11 host genetic variants also associated with variation of gene dosages in 68 regions of bacterial genomes. Common, multi-allelic copy number variation of AMY1, which encodes salivary amylase, associated with oral microbiome composition (P = 1.5 × 10−53) and with dentures use in UK Biobank (P = 5.9 × 10−35, n = 418,039) but not with body mass index (P = 0.85), suggesting that salivary amylase abundance impacts health by influencing the oral microbiome. Two other microbiome composition-associated loci, FUT2 and PITX1, also significantly associated with dentures risk, collectively nominating numerous host-microbial interactions that contribute to tooth decay.</p>
7 Authors
- Nolan Kamitaki
- Robert E. Handsaker
- Margaux L. A. Hujoel
- Ronen E. Mukamel
- Christina L. Usher
- Steven A. McCarroll
- Po-Ru Loh
1 Application
| Application ID | Title |
|---|---|
| 40709 | Exploring the effects of genome structural variation on human health and disease |
Enabling scientific discoveries that improve human health