Fig. 3
Compositional and quantitative 16S rRNA gene amplicon sequencing analysis of the gut microbiota. a Principal component analysis (PCA) of the log10-transformed and standardized (mean = 0, SD = 1) absolute microbial abundance profiles in the stomach, mid-small intestine, and cecum. Loadings of the top contributing taxa are shown for each principal component. b Mean relative and absolute abundance profiles of microbiota in the mid-SI (order level) for all experimental conditions. Functional tail cups (TC-F), mock tail cups (TC-M), housing on wire floors (WF), and controls housed in standard conditions (CTRL). N = 6 mice per experimental group, 4 of which were used for sequencing. c Absolute abundances of microbial taxa (order level) compared between coprophagic and non-coprophagic mice along the mouse GIT. *Chloroplast and *Richettsiales (mitochondria) represent 16S rRNA gene DNA amplicons from food components of plant origin. Multiple comparisons were performed using the Kruskal–Wallis test