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. 2023 Jan 19;41(9):1320–1331. doi: 10.1038/s41587-022-01628-0

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a–d, Clustering through t-SNE⁵² of reaction presence across all pathways per reconstruction. Coordinates were statistically different across taxonomic units (Kruskal–Wallis test, P = 0.0001 in all cases). a, Members of the largest classes. b, Members of the largest families. c, Members of the Bacilli class by genus. d, Members of the Gammaproteobacteria class by genus. e–h, Features of all AGORA2 reconstructions across phyla: e, Number of reactions. f, Number of metabolites. g, Number of genes. h, growth rate in h⁻¹ on aerobic Western diet.