Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

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Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome. / Liu, Xiaomin; Tong, Xin; Zhu, Jie; Tian, Liu; Jie, Zhuye; Zou, Yuanqiang; Lin, Xiaoqian; Liang, Hewei; Li, Wenxi; Ju, Yanmei; Qin, Youwen; Zou, Leying; Lu, Haorong; Zhu, Shida; Jin, Xin; Xu, Xun; Yang, Huanming; Wang, Jian; Zong, Yang; Liu, Weibin; Hou, Yong; Jia, Huijue; Zhang, Tao.

In: Cell Discovery, Vol. 7, 117, 2021.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Liu, X, Tong, X, Zhu, J, Tian, L, Jie, Z, Zou, Y, Lin, X, Liang, H, Li, W, Ju, Y, Qin, Y, Zou, L, Lu, H, Zhu, S, Jin, X, Xu, X, Yang, H, Wang, J, Zong, Y, Liu, W, Hou, Y, Jia, H & Zhang, T 2021, 'Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome', Cell Discovery, vol. 7, 117. https://doi.org/10.1038/s41421-021-00356-0

APA

Liu, X., Tong, X., Zhu, J., Tian, L., Jie, Z., Zou, Y., Lin, X., Liang, H., Li, W., Ju, Y., Qin, Y., Zou, L., Lu, H., Zhu, S., Jin, X., Xu, X., Yang, H., Wang, J., Zong, Y., ... Zhang, T. (2021). Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome. Cell Discovery, 7, [117]. https://doi.org/10.1038/s41421-021-00356-0

Vancouver

Liu X, Tong X, Zhu J, Tian L, Jie Z, Zou Y et al. Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome. Cell Discovery. 2021;7. 117. https://doi.org/10.1038/s41421-021-00356-0

Author

Liu, Xiaomin ; Tong, Xin ; Zhu, Jie ; Tian, Liu ; Jie, Zhuye ; Zou, Yuanqiang ; Lin, Xiaoqian ; Liang, Hewei ; Li, Wenxi ; Ju, Yanmei ; Qin, Youwen ; Zou, Leying ; Lu, Haorong ; Zhu, Shida ; Jin, Xin ; Xu, Xun ; Yang, Huanming ; Wang, Jian ; Zong, Yang ; Liu, Weibin ; Hou, Yong ; Jia, Huijue ; Zhang, Tao. / Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome. In: Cell Discovery. 2021 ; Vol. 7.

Bibtex

@article{e38ef1bea3754271b9ad3f5f7921b052,
title = "Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome",
abstract = "The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for both the tongue dorsum (n = 2017) and saliva (n = 1915). We identified five genetic loci associated with oral microbiota at study-wide significance (p < 3.16 x 10(-11)). Four of the five associations were well replicated in an independent cohort of 1439 individuals: rs1196764 at APPL2 with Prevotella jejuni, Oribacterium uSGB 3339 and Solobacterium uSGB 315; rs3775944 at the serum uric acid transporter SLC2A9 with Oribacterium uSGB 1215, Oribacterium uSGB 489 and Lachnoanaerobaculum umeaense; rs4911713 near OR11H1 with species F0422 uSGB 392; and rs36186689 at LOC105371703 with Eggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of host genome-microbiome associations including six genome-wide significant associations mutually validated between the two niches. As many of the oral microbiome-associated genetic variants lie near miRNA genes, we tentatively validated the potential of host miRNAs to modulate the growth of specific oral bacteria. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk scores dominated over oral microbiome in predicting risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.",
keywords = "HUMAN GUT MICROBIOME, READ ALIGNMENT, HOST GENETICS, SERVICE, AGE",
author = "Xiaomin Liu and Xin Tong and Jie Zhu and Liu Tian and Zhuye Jie and Yuanqiang Zou and Xiaoqian Lin and Hewei Liang and Wenxi Li and Yanmei Ju and Youwen Qin and Leying Zou and Haorong Lu and Shida Zhu and Xin Jin and Xun Xu and Huanming Yang and Jian Wang and Yang Zong and Weibin Liu and Yong Hou and Huijue Jia and Tao Zhang",
year = "2021",
doi = "10.1038/s41421-021-00356-0",
language = "English",
volume = "7",
journal = "Cell Discovery",
issn = "2056-5968",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

AU - Liu, Xiaomin

AU - Tong, Xin

AU - Zhu, Jie

AU - Tian, Liu

AU - Jie, Zhuye

AU - Zou, Yuanqiang

AU - Lin, Xiaoqian

AU - Liang, Hewei

AU - Li, Wenxi

AU - Ju, Yanmei

AU - Qin, Youwen

AU - Zou, Leying

AU - Lu, Haorong

AU - Zhu, Shida

AU - Jin, Xin

AU - Xu, Xun

AU - Yang, Huanming

AU - Wang, Jian

AU - Zong, Yang

AU - Liu, Weibin

AU - Hou, Yong

AU - Jia, Huijue

AU - Zhang, Tao

PY - 2021

Y1 - 2021

N2 - The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for both the tongue dorsum (n = 2017) and saliva (n = 1915). We identified five genetic loci associated with oral microbiota at study-wide significance (p < 3.16 x 10(-11)). Four of the five associations were well replicated in an independent cohort of 1439 individuals: rs1196764 at APPL2 with Prevotella jejuni, Oribacterium uSGB 3339 and Solobacterium uSGB 315; rs3775944 at the serum uric acid transporter SLC2A9 with Oribacterium uSGB 1215, Oribacterium uSGB 489 and Lachnoanaerobaculum umeaense; rs4911713 near OR11H1 with species F0422 uSGB 392; and rs36186689 at LOC105371703 with Eggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of host genome-microbiome associations including six genome-wide significant associations mutually validated between the two niches. As many of the oral microbiome-associated genetic variants lie near miRNA genes, we tentatively validated the potential of host miRNAs to modulate the growth of specific oral bacteria. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk scores dominated over oral microbiome in predicting risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.

AB - The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for both the tongue dorsum (n = 2017) and saliva (n = 1915). We identified five genetic loci associated with oral microbiota at study-wide significance (p < 3.16 x 10(-11)). Four of the five associations were well replicated in an independent cohort of 1439 individuals: rs1196764 at APPL2 with Prevotella jejuni, Oribacterium uSGB 3339 and Solobacterium uSGB 315; rs3775944 at the serum uric acid transporter SLC2A9 with Oribacterium uSGB 1215, Oribacterium uSGB 489 and Lachnoanaerobaculum umeaense; rs4911713 near OR11H1 with species F0422 uSGB 392; and rs36186689 at LOC105371703 with Eggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of host genome-microbiome associations including six genome-wide significant associations mutually validated between the two niches. As many of the oral microbiome-associated genetic variants lie near miRNA genes, we tentatively validated the potential of host miRNAs to modulate the growth of specific oral bacteria. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk scores dominated over oral microbiome in predicting risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.

KW - HUMAN GUT MICROBIOME

KW - READ ALIGNMENT

KW - HOST GENETICS

KW - SERVICE

KW - AGE

U2 - 10.1038/s41421-021-00356-0

DO - 10.1038/s41421-021-00356-0

M3 - Journal article

C2 - 34873157

VL - 7

JO - Cell Discovery

JF - Cell Discovery

SN - 2056-5968

M1 - 117

ER -

ID: 287070951