Current understanding of the human microbiome
Open accessAbstract
Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities that are associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes and by mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this review, we focus on studies in humans to describe these challenges and propose strategies that leverage existing knowledge to move rapidly from correlation to causation and ultimately to translation into therapies.
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The gastrointestinal microbiome plays a central role in human health and disease.
“The gastrointestinal microbiome is now appreciated to play a central role in human health and disease [114,115].”
From Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment (2022) · cites this paper as [114]
This is the first meta-analysis that systematically reviewed published data and examined microbiota alterations in patients with ASD.
“Although several reviews suggested a microbiota alteration in patients with ASD (28, 30, 55–60), this is the first meta-analysis that systematically reviewed published data and examined microbiota alterations in patients with ASD.”
From Association Between Gut Microbiota and Autism Spectrum Disorder: A Systematic Review and Meta-Analysis (2019) · cites this paper as [57]
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- Authors
- Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R.
- Affiliations
- Argonne National Laboratory (US)
- NYU Langone Health (US)
- Northern Arizona University (US)
- Pacific Northwest National Laboratory (US)
- University of California, San Francisco (US)
- University of California San Diego (US)
- Corresponding author
- Knight, Rob
- Venue
- Nature Medicine
- Published
- 2018-04-01
- Volume
- 24
- Issue
- 4
- Pages
- 392-400
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- PMC
- PMC7043356
- OpenAlex
- W2797413896
- Semantic Scholar
- 3f6d8556dd69cea76a75e113aeb66699fa093dc2
- Cited by
- 2,609
- References
- 109
- Citations by year
- 2026: 263 · 2025: 343 · 2024: 440 · 2023: 367 · 2022: 375 · 2021: 323 · 2020: 263 · 2019: 174 · 2018: 57 · 2017: 1
- FWCI
- 20.00
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Medicine (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Cancer Institute (U54CA143925)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human microbiome, microbiome-disease association, obesity, inflammatory bowel disease, arthritis, autism spectrum disorder, microbial community genomics, multi-omics, correlation versus causation, microbiota-based therapy
- MeSH terms
- Disease, Humans, Life Style, Biomarkers, Translational Research, Biomedical, Precision Medicine, Microbiota
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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