Abstract
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host single nucleotide polymorphisms (SNPs) that are correlated with microbial taxa abundances. Using simulated data, we show that HOMINID has accuracy in identifying associated SNPs and performs better compared with existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs. Lastly, by using HOMINID on real data of human genetic variation and microbiome composition, we identified 13 human SNPs in which genetic variation is correlated with microbiome taxonomic composition across body sites. In conclusion, HOMINID is a powerful method to detect host genetic variants linked to microbiome composition and can facilitate discovery of mechanisms controlling host-microbiome interactions.
Highlights
The microbial communities found in and on the human body are influenced by multiple factors [1]
We present Host-Microbiome Interaction Identification (HOMINID), a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host single nucleotide polymorphisms (SNPs) that are correlated with microbial taxa abundances
We show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs
Summary
The microbial communities found in and on the human body are influenced by multiple factors [1]. Several candidate gene studies have found correlation between human genetic variation and the structure of the microbiome [4,5,6]. Genome-wide approaches can be useful to identify human genetic impact on the microbiome [7,8,9,10]. Researchers have utilized quantitative trait locus (QTL)–mapping approaches in the laboratory mouse and have identified multiple loci associated with the structure of gut microbial communities, some of which overlap with genes involved in immune response [11, 12]. Studies have used joint human genetic variation and Received: 7 November 2016; Revised: 19 July 2017; Accepted: 31 October 2017
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