Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort

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.

Evaluating the clinical relevance of the enterotypes in the Estonian microbiome cohort

“…The volunteer-based Estonian microbiome cohort (EstMB) was established in 2017 with the aim of enriching the data of the Estonian Biobank (EstBB) with microbiome data ( Leitsalu et al, 2015 ; Aasmets et al, 2022 ). Stool, oral, and blood samples were collected from 2,509 EstBB participants (1,764 females and 745 males), aged 23–89 years.…”

“…Stool, oral, and blood samples were collected from 2,509 EstBB participants (1,764 females and 745 males), aged 23-89 years. The detailed information about the sample collection and available data are described in Aasmets et al, 2022. All participants included in the EstMB provided informed consent for the data and samples to be used for scientific purposes. This study was approved by the Research Ethics Committee of the University of Tartu (approval No.…”

“…Large-scale human microbiome studies have shown how the gut microbiome reflects our lifestyle and health ( Zhernakova et al, 2016 ; Jackson et al, 2018 ; Gacesa et al, 2020 ; Aasmets et al, 2022 ). The implications on health and disease have particularly fed the growing interest in the microbiome field with the possibility of using the microbiome profile as a novel tool for disease diagnostics and microbiome-informed personalized therapeutics in mind ( di Pierro, 2021 ; Zeevi et al, 2015 ).…”

“…Here, we provide a thorough phenotypic characterization of the subjects according to their fecal enterotype using the Estonian microbiome cohort dataset including shotgun metagenomic sequencing data from 2,509 individuals. The Estonian microbiome cohort takes advantage of electronic health records (EHR), which allows the characterization of the health and drug usage of the individual in great detail ( Aasmets et al, 2022 ). We evaluate the possibility of using enterotypes for disease diagnostics, detecting disease subtypes, and evaluating disease risk using the available follow-up health data from EHRs.…”

Antibiotics and mental health: The good, the bad and the ugly

“…Overall, the main determinant of gut microbiota architecture in adulthood is diet and, to a lesser extent, exercise but medications, especially antibiotics, play an important role [ 27 ].…”