Dataset Information

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

ABSTRACT: The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.

SUBMITTER: Asnicar F

PROVIDER: S-EPMC8353542 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

Asnicar Francesco F Berry Sarah E SE Valdes Ana M AM Nguyen Long H LH Piccinno Gianmarco G Drew David A DA Leeming Emily E Gibson Rachel R Le Roy Caroline C Khatib Haya Al HA Francis Lucy L Mazidi Mohsen M Mompeo Olatz O Valles-Colomer Mireia M Tett Adrian A Beghini Francesco F Dubois Léonard L Bazzani Davide D Thomas Andrew Maltez AM Mirzayi Chloe C Khleborodova Asya A Oh Sehyun S Hine Rachel R Bonnett Christopher C Capdevila Joan J Danzanvilliers Serge S Giordano Francesca F Geistlinger Ludwig L Waldron Levi L Davies Richard R Hadjigeorgiou George G Wolf Jonathan J Ordovás José M JM Gardner Christopher C Franks Paul W PW Chan Andrew T AT Huttenhower Curtis C Spector Tim D TD Segata Nicola N

Nature medicine 20210111 2

The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant ...[more]

PMID: 33432175

Similar Datasets

Project description:BackgroundDNA copy number variants (CNVs) are found in 15% of subjects with ID but their association with phenotypic abnormalities has been predominantly studied in smaller cohorts of subjects with detailed yet non-systematically categorized phenotypes, or larger cohorts (thousands of cases) with smaller number of generalized phenotypes.MethodsWe evaluated the association of de novo, familial and common CNVs detected in 78 ID subjects with phenotypic abnormalities classified using the Winter-Baraitser Dysmorphology Database (WBDD) (formerly the London Dysmorphology Database). Terminology for 34 primary (coarse) and 169 secondary (fine) phenotype features were used to categorize the abnormal phenotypes and determine the prevalence of each phenotype in patients grouped by the type of CNV they had.ResultsIn our cohort more than 50% of cases had abnormalities in primary categories related to head (cranium, forehead, ears, eye globes, eye associated structures, nose) as well as hands and feet. The median number of primary and secondary abnormalities was 12 and 18 per subject, respectively, indicating that the cohort consisted of subjects with a high number of phenotypic abnormalities (median De Vries score for the cohort was 5). The prevalence of each phenotypic abnormality was comparable in patients with de novo or familial CNVs in comparison to those with only common CNVs, although a trend for increased frequency of cranial and forehead abnormalities was noted in subjects with rare de novo and familial CNVs. Two clusters of subjects were identified based on the prevalence of each fine phenotypic feature, with an average of 28.3 and 13.5 abnormal phenotypes/subject in the two clusters respectively (P?<?0.05).ConclusionsOur study is a rare example of using standardized, deep morphologic phenotype clustering with phenotype/CNV correlation in a cohort of subjects with ID. The composition of the cohort inevitably influences the phenotype/genotype association, and our studies show that the influence of the de novo CNVs on the phenotype is less obvious in cohorts consisting of subjects with a high number of phenotypic abnormalities. The outcome of phenotype/genotype analysis also depends on the choice of phenotypes assessed and standardized phenotyping is required to minimize variability.

Dataset Information

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

Publications

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets