Fig 1.
Water decontamination technique and bedding material surveys.
Results of surveys on different water decontamination techniques performed on December 2015 (A), and survey on different bedding materials performed on March 2016 (B). Surveys were performed through Compmed listserv. Darkened bars represent water and bedding used in this study.
Table 1.
Main effects of bedding and water treatment on the fecal and cecal microbiota.
Table 2.
Pairwise PERMANOVA of Bray-Curtis similarity indices between cecal samples.
Fig 2.
Principal coordinate analysis (PCoA) of pairwise comparisons of selected groups.
PCoAs of comparisons between groups housed in corn cob bedding offered either reverse osmosis or autoclaved treated water (A), corn cob or paperchip bedding offered reverse osmosis water (B), and corn cob or paperchip bedding offered autoclaved or reverse osmosis treated water respectively (C). Significant differences (p<0.05) in cecal microbiota composition between these group comparisons were detected via pairwise PERMANOVA (Table 2).
Fig 3.
Richness and diversity of fecal and cecal microbiota at endpoint.
Tukey’s box plot of endpoint fecal and cecal Richness (number of distinct OTUs) (A and B), Shannon Diversity Index (C and D), and Simpson diversity index (E and F). Bottom axis represents combination of bedding and water decontamination method: autoclaving with reverse osmosis (RO), autoclaving with hydrochloric acid (HCl), autoclaving with sulfuric acid (H2SO4), and autoclaving alone (Autoclaved). Asterisks represent significant main effect of bedding in two-way ANOVA (S3 Table). Like lower case letters indicate significantly different (p<0.05) comparisons between groups as determined via two-way ANOVA followed by Tukey’s post hoc test. For example, the Corn cob/HCl and Paperchip/HCl groups are labeled with an “a” indicating that a significant difference was found between these two groups.
Fig 4.
Random forest analysis selection of operational taxonomic units (OTUs).
Random forest analysis of the selected most important OTUs to classify groups. Scale on left represents abundance of OTUs in each group. Asterisks represent OTUs that were significant in two-way ANOVA (S3 Table).