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. 2020 Sep 16;10:15183. doi: 10.1038/s41598-020-72197-y

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© The Author(s) 2020

Open AccessThis 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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Differential abundance analysis reveals key taxa changes. (A) Stacked barplot of DESeq2 log2 fold change values for pairwise comparisons across experimental group. Each bar represents an individual pairwise comparison between two experimental groups made at a specific time point. Tree represents approximate taxonomy of the bacterial families and was determined by manual supplementation of NCBI taxonomy. (B) Schematic illustrating the process of creating ternary patterns and performing taxonomic over-representation analysis on each ternary pattern and taxa pairing. Differential abundance analysis was performed at specified taxonomic levels allowing for the identification of ASVs with different patterns from their parental taxa. Fisher’s exact test for enrichment of ternary patterns among the ASVs of a given taxon was applied. Results were compared to the ternary pattern derived from the entire taxon as well, yielding new insight. This testing framework was applied independently for each ternary pattern. (C) Normalized abundances for four bacterial families of interest that were identified from differential abundance analysis results or taxonomic over-representation analysis results. Dots represent normalized count abundances of individual samples and are plotted against time. (D) Heatmap of taxonomic over-representation analysis results. Color is scaled from 0 to 0.05 and represents the BH-adjusted P-value derived from Fisher’s exact test for enrichment of ternary pattern among a taxon.