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. 2023 Feb 20;41(10):1424–1433. doi: 10.1038/s41587-023-01674-2

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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. 5 — a, Number of genome-wide SNPs between isolates from the same or different individuals for 14 isolates-rich species. The numbers after the species name represent the number of inter-individual (red) and intra-individual (blue) pairs. Definition of box-plot elements: center line: median; box limits: upper and lower 25th quartiles; whiskers: 1.5× interquartile range. b, Correlation between number of genome-wide SNPs and relative abundance in original fecal sample for isolates-rich species in individual H1. The size of dot represents number of isolates used in this analysis and the color represents proportion of SNPs present in only one genotype. c, Network of 2 kb + HGT frequency based on 409 isolates from H1. Nodes represent bacterial species and are colored by family. Node sizes are proportional to the number of isolates in the H1 collection and edges opacity are proportional to the HGT frequency between the two connected species. Edge color represents different types of HGT, that is, interphyla, intraphyla and interfamily, or intrafamily HGT and node outline color represent Gram staining of the species.