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Updated: May 10, 2026
Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
House dust metagenome and pulmonary function in a US farming population
Mikyeong Lee1, Abhishek Kaul2, James M Ward3
1Immunity Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), Durham, NC, 27709, USA. mikyeong.lee@nih.gov.
Background:
Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.
Results:
Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.
Conclusions:
Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.
Insights
Indoor dust microbes impact respiratory health. Specific microbial genera, not overall diversity, were linked to lung function and airway inflammation in adults, suggesting targeted environmental factors influence respiratory conditions.
Area of Science:
- Environmental microbiology
- Human health
- Pulmonary medicine
Background:
- Chronic exposure to indoor microorganisms can affect respiratory health.
- Advanced sequencing methods are needed to study adult respiratory outcomes.
- House dust harbors diverse microbial communities influencing indoor environments.
Purpose of the Study:
- To identify metagenomic profiles in house dust associated with quantitative measures of pulmonary function and airway inflammation in adults.
- To explore the relationship between specific microbial genera and continuous respiratory health traits.
- To apply novel high-dimensional inference methods for microbiome data analysis.
Main Methods:
- Whole metagenome shotgun sequencing of 1264 species from 389 genera in bedroom dust from 779 US homes.
- Analysis of overall microbial diversity using richness and Shannon index.
- Application of Lasso estimator with high-dimensional inference to identify differentially abundant genera related to pulmonary function and fractional exhaled nitric oxide (FeNO).
Main Results:
- Overall dust microbial diversity (richness, Shannon index) was not associated with pulmonary function measures (FEV1, FVC, FEV1/FVC) or FeNO.
- Numerous individual microbial genera showed differential abundance related to FEV1, FVC, FEV1/FVC, and FeNO (p < 0.05).
- Specific genera like Limosilactobacillus, Moraxella, and Stenotrophomonas were associated with pulmonary function and/or airway inflammation markers.
Conclusions:
- State-of-the-art metagenomic sequencing identified specific indoor microorganisms linked to pulmonary function and airway inflammation.
- Findings suggest novel environmental microbial components contribute to respiratory outcomes.
- The analytical methods are adaptable for studying microbiome associations with other continuous health outcomes.
