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. 2020 Oct 30;6:47. doi: 10.1038/s41522-020-00155-7

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© The Author(s) 2020

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 Multidimensional scaling (MDS) ordination plot of healthy and peri-implantitis sites based on the Bray–Curtis distance between microbiome samples highlights a strong condition-specific clustering. p values were obtained by PERMANOVA. b Ordination plot (MDS) of healthy and peri-implantitis metagenomic samples based on the abundance of microbial UniProt90 gene families. p values were obtained by PERMANOVA. c Alpha-diversity distributions computed after rarefaction to the same sequencing depth and estimated as the richness of species and d as richness of UniProt90 gene families show a trend of decreased diversity in peri-implantitis sites. p values were obtained by the two-tailed Wilcoxon signed-rank test. e Distribution of PiRC index values (the total abundance species in the peri-implantitis-related complex) in healthy and peri-implantitis samples. p value was obtained by the two-tailed Wilcoxon signed-rank test. f Intra-condition beta-diversity (Bray–Curtis dissimilarity) for microbial species and g gene families points at a converging microbiome structure in diseased peri-implantitis sites. p values were obtained by two-tailed Wilcoxon signed-rank test. h Relative abundances (log scale) and effect sizes (LDA score from LEfSe) of the 10 microbial species and i gene families most strongly associated with either the healthy sites or the sites with peri-implantitis (top 10 species/gene families effect sizes per class). All the comparisons in this figure are performed using the sample from the main site in each subject without considering the contralateral samples.