2017
DOI: 10.1186/s40168-016-0227-5
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Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

Abstract: BackgroundThe degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder population of European decent.ResultsWe estimated the relative abundances (RAs) of genus level bacteria from 16S rRNA gene sequences and examined associations with 148,653 genetic variants (linkage … Show more

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Cited by 64 publications
(60 citation statements)
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References 89 publications
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“…Alpha-diversity and microbial or functional pathway abundances can simply be treated as individual quantitative traits where standard GWAS methods can be applied to each trait (7). The microbiome GWAS to date have used standard additive genetic modeling approaches (4, 10, 18, 30, 68), rank based correlations (5), or combination models, where common taxa are modeled as quantitative traits and rare taxa are modeled as binary traits (65). …”
Section: Identifying Microbiome-host Genotype Associationsmentioning
confidence: 99%
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“…Alpha-diversity and microbial or functional pathway abundances can simply be treated as individual quantitative traits where standard GWAS methods can be applied to each trait (7). The microbiome GWAS to date have used standard additive genetic modeling approaches (4, 10, 18, 30, 68), rank based correlations (5), or combination models, where common taxa are modeled as quantitative traits and rare taxa are modeled as binary traits (65). …”
Section: Identifying Microbiome-host Genotype Associationsmentioning
confidence: 99%
“…Genes associated with the microbiome of nasal, oral, and skin body sites drove most of the enrichment in these pathways. In a study of the nasal microbiota in a Hutterite population, Igartua et al used the Ingenuity Pathway Analysis Knowledge Base to identify protein-protein interaction (PPI) networks from genes near nasal microbiome associated loci (30). Both of the significant PPI networks identified contain highly connected proteins (hubs in the PPI network) that play important roles in modulating mucosal immunity (including IgA, IgG, IL12/IL12RA, TCR and STAT5A/B).…”
Section: Gwas Reveal Tissues Pathways and Genes Consistently Associmentioning
confidence: 99%
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“…21,22 More recent studies have used a genome-wide approach to calculate the heritability of microbial taxa and identify variants and genes in the human genome that correlate with variation in the microbiome across body sites. 17,18,[23][24][25][26] In addition, several studies have used similar analysis techniques to assess host genetic effects on the microbiome in the context of various human diseases and conditions. [26][27][28][29] Although results across cohorts have not had a high degree of overlap, several loci have been found to be associated across multiple studies, 19,30,31 indicating that in some cases, host genes can affect microbiome composition across different contexts.…”
Section: Human Genetic Control Of the Microbiomementioning
confidence: 99%
“…The lung microbiome largely overlaps with the oral microbiome, and is the result of microbial immigration, elimination and relative reproduction rates [10,11]. Microbiome communities are complex and dynamic and vary throughout life under the influence of the season, geography, local environment, body site and host characteristics like genotype, ethnicity, age, sex, body mass index, diet, drugs and health status [9][10][11][12]. This wide variety of influences makes it difficult to develop studies that account for all these factors.…”
mentioning
confidence: 99%