This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer
npj Biofilms and Microbiomes Open Access 30 March 2024
-
Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity
Scientific Reports Open Access 25 March 2024
-
Multi-omic integration of microbiome data for identifying disease-associated modules
Nature Communications Open Access 23 March 2024
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Huber, W. et al. Nat. Methods 12, 115–121 (2015).
Truong, D.T. et al. Nat. Methods 12, 902–903 (2015).
Abubucker, S. et al. PLoS Comput. Biol. 8, e1002358 (2012).
Human Microbiome Project Consortium Nature 486, 207–214 (2012).
Koren, O. et al. PLoS Comput. Biol. 9, e1002863 (2013).
Arumugam, M. et al. Nature 473, 174–180 (2011).
Acknowledgements
This work was made possible by the CUNY High Performance Computing Center, College of Staten Island, funded in part by the City and State of New York, CUNY Research Foundation, and National Science Foundation Grants CNS-0958379, CNS-0855217 and ACI 1126113. Support was provided by the European Union H2020 Marie-curie grant (707345) to E.P., the European Research Council (ERC-STG project MetaPG), MIUR “Futuro in Ricerca” RBFR13EWWI_001, the People Programme (Marie Curie Actions) of the European Union Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. PCIG13-GA-2013-618833, the LEO Pharma Foundation, and by Fondazione CARITRO fellowship Rif.Int.2013.0239 to N.S., the National Institute of Allergy and Infectious Diseases (1R21AI121784-01 to J.B.D. and L.W.) and the US National Cancer Institute (U24CA180996 to M.M. and L.W.).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 Clustering scores for enterotypes in gut WGS samples.
Consistent with Koren et al.5, these plots indicate weak support for any discrete clustering in the data and confirm that the three enterotypes hypothesis is likely an oversimplification that does not hold when considering large set of biogeographycally diverse populations. Thresholds for significance of clustering are presented as dashed lines, and are the same thresholds used by Koren et al.5. Each plot line represents an analysis that can be accomplished with one line of code using the R packages 'fpc' (prediction strength and Calinski-Harabasz) and 'cluster' (silhouette index), provided in the curatedMetagenomicData package examples.
Supplementary Figure 2 Health status classification from species abundance.
Six different classification problems of health status were attempted using a random forest algorithm and cross-validation to estimate prediction accuracy. Plots show ROC curves by using species abundance as microbiome features, one of the five data types considered in the Example 1 of Figure 1. Results are consistent with the meta-analysis conducted in32.
Supplementary Figure 3 Principal Coordinates Analysis (PCoA) plot of species abundance for gut samples on selected diseases.
Specimens are annotated by disease state (shape), study name (color), and abundance of Prevotella copri (size).
Supplementary Figure 4 Top correlations between metabolic pathways and genera.
Pearson correlation was calculated between each individual pathway (HUMAnN2 pathways from the full UniRef90 database) and each of the top 20 most abundant microbial genera, in a combined dataset obtained from merging 20 studies of gut specimens. The top correlations are 1) Ornithine de novo biosynthesis: Bacteroides (r = 0.86), activity that has been confirmed in cultures of this organism33, and 2) superpathway of allantoin degradation in yeast: Escherichia (r = 0.95). Although this superpathway has been associated with yeast, it includes subpathways (such as allantoin degradation to glyoxylate I and allantoin degradation to ureidoglycolate I) that are common in Escherichia, which is known to be an allantoin utilizier under anaerobic conditions34. Of note, the top 100 correlations have adjusted p < 0.001.
Supplementary Figure 5 Alpha diversity of taxa from 22 studies of the gut microbiome.
Shannon Alpha Diversity was calculated for each individual sample within each human gut microbiome study. The median diversity varies by a maximum factor of 1.5 between studies, however the variability within studies as measured by interquartile range varies by more than 3-fold.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–5, Supplementary Methods and Supplementary Tables 1–2
Life Sciences Reporting Summary
Life Sciences Reporting Summary
Supplementary Software
Snapshot of curatedMetagenomicData including pipelines, github.io website, and software. This is GitHub commit 7ec5083.
Rights and permissions
About this article
Cite this article
Pasolli, E., Schiffer, L., Manghi, P. et al. Accessible, curated metagenomic data through ExperimentHub. Nat Methods 14, 1023–1024 (2017). https://doi.org/10.1038/nmeth.4468
Published:
Issue Date:
DOI: https://doi.org/10.1038/nmeth.4468
This article is cited by
-
Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity
Scientific Reports (2024)
-
Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
Scientific Reports (2024)
-
Multi-omic integration of microbiome data for identifying disease-associated modules
Nature Communications (2024)
-
Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults
Scientific Data (2024)
-
Machine learning for microbiologists
Nature Reviews Microbiology (2024)