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. 2020 Jul 20;39(1):105–114. doi: 10.1038/s41587-020-0603-3

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© The Author(s) 2020

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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Extended Data Fig. 3 — a, Number of species found across the three metagenome-assembled genome sets, ordered by their level of overlap. Only those genomes recovered from the 1,554 metagenomic samples used by all three studies were considered in this analysis. b, Distribution of the proportion of species recovered per sample (n = 1,554) in each study set out of all species recovered across all three studies in the same samples. Box lengths represent the IQR of the data, and the whiskers the lowest and highest values within 1.5 times the IQR from the first and third quartiles, respectively. c, Estimated aligned fractions and average nucleotide identities (ANI) between conspecific genomes obtained in the same sample but in different MAG studies. Results for medium-quality genomes are illustrated in the top panel, whereas those for near complete (≥90% completeness) genomes are represented in the lower panel. Vertical dashed lines denote the median values. d, Number of species identified in three culture-based studies and their degree of overlap. The NCBI study set consists mainly of genomes from the Human Microbiome Project (HMP).