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The human metagenome set included all oral and stool metagenomes available in cMD as of May 2022, totaling 19,833 samples from 87 cohorts.
“We included all human metagenomes from oral and stool sources available as of May 2022, which resulted in a total of 19,833 samples from 87 cohorts.”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [27]
The ‘To the Editor’ section identifies curatedMetagenomicData as a source of human microbiome data from multiple body sites. It reports 5,716 samples in the version described, but does not establish which oral and stool samples were available in May 2022 or support the citing authors’ total of 19,833 samples from 87 cohorts. No page number is available in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measuredMetagenomic studies have been mainly conducted on single food types and on limited sample sizes, hindering inter-study integrative analyses currently available only for other environments such as the human gut.
“Nevertheless, metagenomic studies have been mainly conducted on single food types 18-24 and on limited sample sizes, 25,26 hindering inter-study integrative analyses currently available only for other environments such as the human gut. 27-31”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [27]
1,409 SGBs were detected at least once in both food and human environments.
“found 1,409 SGBs detected at least once in both food and human environments (Figure 5A; Table S5).”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [27]
The cited paper’s “To the Editor” section describes a curated human microbiome dataset and analyses of its samples, but does not report SGBs shared between food and human environments. Searches for “1,409 SGBs” and for species-level genome bins shared across those environments found no supporting passage in our copy. (LLM, conf=0.78)
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- Authors
- Pasolli, E., Schiffer, L., Manghi, P., Renson, A., Obenchain, V., Truong, D. T., Beghini, F., Malik, F., Ramos, M., Dowd, J. B., Huttenhower, C., Morgan, M., Segata, N., & Waldron, L.
- Affiliations
- University of Trento (IT)
- City University of New York (US)
- Roswell Park Comprehensive Cancer Center (US)
- Broad Institute (US)
- Corresponding author
- Segata, Nicola
- Waldron, Levi
- ORCID
- Venue
- Nature Methods
- Published
- 2017-11
- Volume
- 14
- Issue
- 11
- Pages
- 1023-1024
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC5862039
- OpenAlex
- W2952200190
- Cited by
- 514
- References
- 32
- Citations by year
- 2026: 84 · 2025: 75 · 2024: 85 · 2023: 65 · 2022: 51 · 2021: 54 · 2020: 46 · 2019: 35 · 2018: 13 · 2017: 2 · 2016: 1
- FWCI
- 10.56
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- Research Portal (King's College London) (submittedVersion, cc-by-nc)
- Iris (University of Trento) (submittedVersion)
- Funders
- National Science Foundation (0958379, FP7/2007-2013, 1126113, 0855217)
- City University of New York (ACI-1126113, CNS-0958379, CNS‐0855217)
- European Commission (707345, 2007–2013, FP7 2007-2013, H2020, FP7/2007, 618833)
- Ministero dell’Istruzione, dell’Università e della Ricerca (2007–2013, H2020, RBFR13EWWI_001)
- Fondazione Cassa Di Risparmio Di Trento E Rovereto (2013.0239, Rif.Int.2013.0239)
- LEO Pharma
- National Institutes of Health (FP7/2007-2013, CNS-0855217, CNS-0958379, H2020, 5u41hg004059-15)
- Research Foundation of The City University of New York
- Horizon 2020 Framework Programme (FP7/2007-2013, 707345)
- National Human Genome Research Institute (U41-HG004059, P41HG004059)
- National Cancer Institute (U24CA180996, 1R03CA191447-01A1)
- National Institute of Allergy and Infectious Diseases (R21AI121784)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- metagenomics, data curation, data accessibility, microbiome data, antibiotic use, gut microbiota, MetaPhlAn, colorectal cancer classification, explainable AI
- MeSH terms
- Gastrointestinal Microbiome, Humans, Software, Species Specificity, Genome, Human, Genome, Bacterial, Genome, Fungal, Computational Biology, Genome, Archaeal, Metagenomics, 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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