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. 2019 Mar 13;568(7753):505–510. doi: 10.1038/s41586-019-1058-x

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© The Author(s) 2019

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. 7 — a, The trees indicate the phylogenetic distribution of species-level OTUs from the human gut for Cyanobacteria, and a subclade within Clostridia. All OTUs within the Cyanobacteria phylum were assigned to the Melainabacteria class. Each tip indicates one species-level OTU. Circles indicates whether a medium- (open circle) or high-quality genome (closed circle) was recovered for MAGs from the HGM dataset (green), MAGs from PATRIC + IMG datasets (blue) or isolate genomes from PATRIC + IMG datasets (red). Diversity within these clades would have been missed without the inclusion of medium-quality MAGs. b, The tree indicates the phylogenetic distribution of bacterial genus-level OTUs from the human gut (n = 1,321 OTUs). The outer rings indicate whether an OTU contains a MAG from the HGM dataset (green), a MAG from PATRIC + IMG dataset (blue) or an isolate genome from PATRIC + IMG dataset (red). Labels indicate phyla. Large monophyletic clades that are depleted in isolate genomes are highlighted with green branches.