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Interplay between the human gut microbiome and host metabolism
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Abstract
The human gut is inhabited by a complex and metabolically active microbial ecosystem. While many studies focused on the effect of individual microbial taxa on human health, their overall metabolic potential has been under-explored. Using whole-metagenome shotgun sequencing data in 1,004 twins, we first observed that unrelated subjects share, on average, almost double the number of metabolic pathways (82%) than species (43%). Then, using 673 blood and 713 faecal metabolites, we found metabolic pathways to be associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species showed less than 3,000 associations. Finally, we estimated that the microbiome was involved in a dialogue between 71% of faecal, and 15% of blood, metabolites. This study underlines the importance of studying the microbial metabolic potential rather than focusing purely on taxonomy to find therapeutic and diagnostic targets, and provides a unique resource describing the interplay between the microbiome and the systemic and faecal metabolic environments.
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The human gut microbiome is a major determinant of plasma metabolome, potentially playing a more dominant role than genetics.
“The rationale is further supported by several studies that demonstrated that the human gut microbiome is a major determinant of plasma metabolome, potentially playing a more dominant role than genetics.26–28”
From Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases (2024) · cites this paper as [27]
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Metadata
- Authors
- Visconti, A., Le Roy, C. I., Rosa, F., Rossi, N., Martin, T. C., Mohney, R. P., Li, W., de Rinaldis, E., Bell, J. T., Venter, J. C., Nelson, K. E., Spector, T. D., & Falchi, M.
- Affiliations
- King's College London (GB)
- University of Lisbon (PT)
- Metabolon (United States) (US)
- J. Craig Venter Institute (US)
- Corresponding author
- Spector, Tim D.
- Falchi, Mario
- ORCID
- Venue
- Nature Communications
- Published
- 2019-10-03
- Volume
- 10
- Issue
- 1
- Pages
- 4505-4505
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6776654
- OpenAlex
- W2977433364
- Cited by
- 782
- References
- 65
- Citations by year
- 2026: 98 · 2025: 109 · 2024: 114 · 2023: 132 · 2022: 137 · 2021: 113 · 2020: 68 · 2019: 6
- FWCI
- 26.81
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Wellcome Trust
- Joint Programming Initiative A healthy diet for a healthy life
- National Institute for Health and Care Research
- King's College London
- European Commission
- Medical Research Council (MR/N030125/1, MR/N01183X/1)
- Menzies Centre for Australian Studies, King's College London, University of London
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, host metabolism, microbial metabolic potential, metabolic pathways, fecal metabolites, blood metabolites, microbial species, twins, microbiome-host interactions, metabolite associations
- MeSH terms
- Gastrointestinal Microbiome, Whole Genome Sequencing, Host Microbial Interactions, Age Factors, Aged, Aged, 80 and over, Bacteria, Feces, Female, Humans, Male, Middle Aged, Biomarkers, Age Distribution, Metabolic Networks and Pathways, Metagenome, Metabolomics, Metabolome, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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