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. 2023 Jun 5;11:127. doi: 10.1186/s40168-023-01563-5

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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 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Bacterial density and diversity measured during the first 30 months of life. A Bacterial density (16S rRNA gene copies/μl) compared across timepoints. B Within-specimen bacterial diversity (Shannon diversity) compared across timepoints. One-way analysis of variance (ANOVA) was used to compare alpha diversity indices between timepoints. Tukey’s Honest Significant Difference test was implemented to compare each pair of timepoints simultaneously pairwise. Median values are presented by horizontal lines within each of the boxplots while upper and lower ranges of the boxplots represent the 75% and 25% quartiles, respectively. Maximum and minimum values, excluding outliers, are presented by whiskers. C Principal coordinate analysis of between-specimen bacterial diversity (Aitchison distance). Alpha bags (90%) are used to enclose observations from each of the timepoints, excluding the 10% of the observations at the extremes of each cluster. Specimen collection age (in months) and the number of specimens included at each timepoint are shown at the bottom of each panel