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. 2022 Sep 15;28(9):1902–1912. doi: 10.1038/s41591-022-01913-0

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© The Author(s) 2022

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, We analyzed a dataset of 316 FMT time series across ten disease indications and 22 cohorts, totaling 1,492 fecal metagenomes. Species pangenomes were built from reference genomes and newly generated MAGs and profiled across samples for taxonomic, functional and strain population composition, based on microbial SNVs and differential gene content. b, Each allogenic FMT was represented as a triad of donor pre-FMT (blue hues), recipient pre-FMT (yellow) and post-FMT (purple) samples; each sample’s strain population is indicated as an overlapping circle. c, FMT strain-level outcomes for each species were scored using patterns of determinant SNVs and gene content (Supplementary Table 5). d, Ternary diagram of the strain population space for conspecific recipient strain persistence, donor strain colonization, donor–recipient coexistence and influx of novel strains.