“…The microbiota can profoundly impact diverse aspects of epithelial physiology, including autophagy, mucus production and antimicrobial defence mechanisms (Benjamin, Sumpter, Levine, & Hooper, ; Chen et al, ; Jakobsson et al, ). Certain microbiota members even influence intestinal epithelial stem cell numbers and their proliferative capacity in vivo (Lee et al, ; Pan et al, ; Reedy, Luo, Neish, & Jones, ; Savage, Siegel, Snellen, & Whitt, ; Sommer & Bäckhed, ; Stecher et al, ). As a result, the non‐equal microbiota composition between separately kept mouse lines represents a major confounding factor in studies of how host genetics affect gut physiology and disease (Hausmann & Hardt, ; Mamantopoulos et al, ; Mamantopoulos, Ronchi, McCoy, & Wullaert, ; Robertson et al, ; Stappenbeck & Virgin, ).…”