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. 2021 Dec 31;7(1):132–144. doi: 10.1038/s41564-021-01023-6

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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. 6 — a, Abundances over time of the most relevant bacterial clusters depicted in Figs. 3 and 5 as important separate species/genera. Each bacterial group is normalized by its highest abundance at any time point. The highest abundance of each group (100% on the y axis) is depicted at the top as a percentage. Bifidobacterium and Bacteroides decrease over time, whereas the other groups increase over time but at different rates. b,c, Scatterplots of P. copri and the F. prausnitzii cluster (b) or the P. stercorea cluster (c). Because of the extremely high abundance of P. copri a numerically induced (weak) negative association is to be expected even between other clusters where no antagonistic interaction occurs, like with the P. stercorea cluster. The F. prausnitzii cluster, however, has a weak positive correlation with P. copri. d–f, Bacterial clusters and main species represent the main principal components within this dataset. d, PC1 is nearly fully described by the abundance of P. copri, the most abundant species at every point in time in this study. e, PC2 represents the antagonistic interaction between the Prevotella genus and the Bacteroides genus, where Prevotella is represented by the combined abundance of P. copri and the P. stercorea cluster. f, PC3 represents a shift away from a gut dominated by Bifidobacterium, as seen in young infants, towards the development of complex trophic networks as represented here by the combined abundance of the F. prausnitzii cluster, the P. stercorea cluster and the auxiliary cluster. PC3 is most strongly correlated with age. Percentages indicate the per cent variation explained by each principal component in the combined dataset.