Fig. 2

Quantification of microbial loads in lumenal contents and mucosa of the gastrointestinal tracts (GIT) of mice in the four experimental conditions: functional tail cups (TC-F), mock tail cups (TC-M), housing on wire floors (WF), and controls housed in standard conditions (CTRL). a Total 16S rRNA gene DNA copy loads, a proxy for total microbial loads, were measured along the GIT of mice of all groups (STM = stomach; SI1 = upper third of the small intestine (SI), SI2 = middle third of the SI, SI3 = lower third of the SI roughly corresponding to the duodenum, jejunum, and ileum respectively; CEC = cecum; COL = colon). Multiple comparisons were performed using a Kruskal–Wallis test, followed by pairwise comparisons using the Wilcoxon–Mann–Whitney test with false-discovery rate (FDR) correction. Individual data points are overlaid onto box-and-whisker plots; whiskers extend from the quartiles (Q2 and Q3) to the last data point within 1.5 × interquartile range (IQR). b Correlation between the microbial loads in the lumenal contents (per gram total contents) and in the mucosa (per 100 ng of mucosal DNA) of the mid-SI. N = 6 mice per experimental group