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. 2024 Oct 17;15:8979. doi: 10.1038/s41467-024-53454-4

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — LOTUS vOTUs that were classified as a virus (n = 25941) were included in the analysis. A Margalef’s (species) richness in patients at baseline (Baseline, n = 31) and patients following antibiotic treatment (Post Abx, n = 32). Differences were tested using a two-sided Mann–Whitney test (p < 0.0001) following assessment of normal distribution with Shapiro-Wilk test (Baseline: p = 0.0102, Batches: p < 0.0001). Errors are ± SEM. B Principal coordinate analysis (PCO) on Aitchinson distances between patients at baseline (Baseline, green) and patients following antibiotic treatment (Post Abx, purple). Differences between groups were tested using PERMANOVA and PERMDISP. C Volcano plot of differential abundance analysis of vOTUs between patients at baseline (Baseline) and patients following antibiotic treatment using ZicoSeq. 408 vOTUs were identified to be significantly differentially abundant between groups. D Classification of vOTUs that were significantly differentially abundant. Legend is % prevalence. Source data are provided as a Source Data file.