Fig. 2. Colonization of germ-free mice with bacterial communities.

A Relative abundance of bacteria in the inoculum and the caecal contents of mice colonized with base community or base community + C. scindens assessed by shotgun metagenomic sequencing. B Microbial genome copies per nanogram bacterial DNA in the caecal content of mice colonized with base community + C. scindens assessed by digital droplet PCR. The base community members were quantified using primer-probe sets for the gene tilS, and C. scindens was quantified using primer-probe sets for the baiCD gene (see Supplementary Table 1). C, D Bile acid levels in vena cava (C) and caecum (D) of mice colonized with base community or base community + C. scindens measured by UPLC-MS/MS. E–H Physiological parameters of the mice including body weight (E), adiposity (F), relative liver weight (G) and relative caecum weight (H) measured 2 weeks after colonization. I Insulin tolerance test performed by intraperitoneal injection of insulin. Glucose was measured at 0, 30, 60, 90, 120 min after injection and data is presented as percentage of glucose compared to the 0 min time point. J, K Fasting blood glucose (J) and insulin (K) were measured at the 0 min time point. n = 5 samples for the base community group (indicated by white color in B–K) and n = 4 samples for the base community + C. scindens group (indicated by orange color in B–K); P-values indicate differences between mice colonized with base community and base community + C. scindens analyzed with two-tailed Mann–Whitney (E–H and J, K) or 2-way ANOVA with Šidák multiple comparisons test (I). Error bars indicate standard error of the mean (C, D and I). CA cholic acid, DCA deoxycholic acid, βMCA beta-muricholic acid, TCA tauro-cholic acid, TDCA tauro-deoxycholic acid, TαMCA tauro-alpha-muricholic acid, TβMCA tauro-beta-muricholic acid, 7-oxoCA 7-oxocholic acid.