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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. 5 — a–c, OTUs were identified for 296 genomes from the Bacteroides genus on the basis of average-linkage clustering of whole-genome ANI, using the ANIcalculator (v.1.0). The ANI cut-offs used for forming OTUs are indicated in the panel titles (94–97% ANI). The alignment fraction cut-offs, defined as the required percentage of genome length aligned between genome pairs (20–60%), is indicated by line colour. In each panel, the vertical axis indicates the number of OTUs identified from genomes on the basis of the ANI cut-off, alignment fraction cut-off and the degree of incompleteness and/or amount of contamination present in the 296 genomes. a, OTUs were identified for the 296 Bacteroides genomes with up to 80% of genes randomly removed. The number of OTUs is inflated when genomes are incomplete and the alignment fraction is >20%. b, OTUs were identified for the 296 Bacteroides genomes with up to 20% of genes from a different one of the 296 genomes. The number of OTUs is not affected by contamination when genomes are complete. c, OTUs were identified for the 296 Bacteroides genomes with 50% of genes randomly removed and up to 20% of genes from a different one of the 296 genomes, representing a worst-case scenario. The number of OTUs is inflated by contamination when genomes are 50% complete. Using a lower ANI threshold (for example, 94 or 95% versus 96 or 97%) reduces the negative effect of contamination. On the basis of these experiments, we chose an alignment fraction cut-off of 20% and an ANI cut-off of 95% for identifying OTUs from MAGs and reference genomes in the current study.