ArticleNature communications2022
Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The urinary microbiome in association with diabetes and diabetic kidney disease: A systematic review.PloS one · 2025Pooled it
- Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.Nature reviews. Clinical oncology · 2023Pooled it
- Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.NPJ biofilms and microbiomes · 2025Trial
- Drug-microbiome-host interactions: antimicrobial effects of non-antibiotic compounds.Nature reviews. Gastroenterology & hepatology · 2026Review
- Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.Microbiology spectrum · 2026Article
- Article
- Mapping the canine gut microbiome: insights from the Dog Aging Project.Nature communications · 2026Article
- Insights from adult gut microbiota using the Estonian cohort as a uniform model.Scientific reports · 2026Article
- Article
- Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.Nature medicine · 2026Article
- Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.Journal of hypertension · 2026Article
- Human gut archaea collection from Estonian population.Scientific data · 2026Article
- A novel framework for assessing causal effect of microbiome on health: long-term antibiotic usage as an instrument.Gut microbes · 2025Article
- Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.Microbiome · 2025Article
- Article
- A hidden confounder for microbiome studies: medications used years before sample collection.mSystems · 2025Article
- Deep phenotyping of health-disease continuum in the Human Phenotype Project.Nature medicine · 2025Article
- The gut microbiome connects nutrition and human health.Nature reviews. Gastroenterology & hepatology · 2025Review
- Article
- Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.Nutrition reviews · 2025Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.