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. 2023 Jul 20;14:4369. doi: 10.1038/s41467-023-39982-5

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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. 4 — a Relative abundances of the 10 most abundant genera and species from all samples. X-axis is ordered by patient sample number. b Differential correlation analysis of species in A. fumigatus + (after colonization) relative to A. fumigatus - (before colonization) showing changes in the lung microbiome interactome after A. fumigatus colonization. Edge colors and class information indicate the direction of correlation for A. fumigatus -/A. fumigatus + . Associated count indicates the number of species pairs in the network exhibiting this pattern of change. Only species pairs with significant differential correlations were included (permutation test, p ≤ 0.05). An orange node background indicates significant differential abundance for species when comparing A. fumigatus - vs. A. fumigatus + samples (metagenomeSeq, zero-inflated Gaussian mixture model, p ≤ 0.05, Supplementary Data S6). Abbreviations: biosyn: biosynthesis; cys: cysteine; degr: degradation; Isoleu: isoleucine; met: methionine; mb: metabolism; Leu: leucine; Phe: phenylalanine; PAH: Polycyclic Aromatic Hydrocarbon; Try: tryptophan; Val: valine. Source data for Fig. 4 are provided in the Source Data file.