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. 2023 Feb 23;41(11):1633–1644. doi: 10.1038/s41587-023-01688-w

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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. 1 — a, From a collection of 1.01 M bacterial and archeal reference genomes and metagenomic-assembled genomes (MAGs) spanning 70,927 species-level genome bins (SGBs), our pipeline defined 5.1 M unique SGB-specific marker genes that are used by MetaPhlAn 4 (avg., 189 ± 34 per SGB). b, The expanded marker database allows MetaPhlAn 4 to detect the presence and estimate the relative abundance of 26,970 SGBs, 4,992 of which are candidate species without reference sequences (uSGBs) defined by at least five MAGs. The profiling is performed firstly by (1) aligning the reads of input metagenomes against the markers database, then (2) discarding low-quality alignments and (3) calculating the robust average coverage of the markers in each SGB that (4) are normalized across SGBs to report the SGB relative abundances (see Methods). All data are presented as mean ± s.d.