Abstract
Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge. As part of the Estonian Biobank, we established the Estonian Microbiome Cohort which includes stool, oral and plasma samples from 2509 participants and is supplemented with multi-omic measurements, questionnaires, and regular linkages to national electronic health records. Here we analyze stool data from deep metagenomic sequencing together with rich phenotyping, including 71 diseases, 136 medications, 21 dietary questions, 5 medical procedures, and 19 other factors. We identify numerous relationships (n = 3262) with different microbiome features. In this study, we extend the understanding of microbiome-host interactions using electronic health data and show that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases.
Highlights
Microbiome research is starting to move beyond the exploratory phase towards interventional trials and well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge
We analyzed the gut microbiome composition in more than 2500 adults from the Estonian Biobank (EstBB) who participated in the Estonian Microbiome Project (EstMB), which included stool sample collection and comprehensive phenotyping
Supported by the Estonian Human Genes Research Act, continuously updated personal health data from various electronic health records (EHRs) and re-examinations as well as a wide array of biological samples are used to promote the development of personalized medicine and to improve public health[9]
Summary
Microbiome research is starting to move beyond the exploratory phase towards interventional trials and well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge. We extend the understanding of microbiome-host interactions using electronic health data and show that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases. A recent extended study of 8208 individuals in the Dutch population shows that the 241 studied phenotypes from a broad set of categories explained approximately 15% of the variation in the microbiome composition and function between individuals, indicating that our current understanding of the factors that shape the microbiome is still limited[7]. We analyzed the gut microbiome composition in more than 2500 adults from the EstBB who participated in the Estonian Microbiome Project (EstMB), which included stool sample collection and comprehensive phenotyping. The project was established in order to study the role of the microbiome in health and disease as well as to evaluate its potential as a means to advance personalized medicine
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