Wild House Mice Sampling Protocol

Two hundred and seventeen wild house mice were caught around the southwestern French town of Espelette, during a five-week field work in September 2013 (first described in^{26 (link)}). Animals were live-trapped in 34 randomly chosen farms and brought back to a common location where they were euthanized with CO₂ and dissected on site. The presence of farm animals and use of poison was recorded for each farm (Suppl. Table 1). The pairwise distance between farms was calculated from their GPS coordinates with the “haversine” formula (Suppl. Table 3). Families were defined as groups of farms within which all farms are at most 2 km apart from each other, as suggested in;^{27 (link)} “super families” were defined as groups of farms within which all farms are at most 3.5 km apart from each other (Suppl. Tables 1 & 3, Figure 1a). For each mouse, body and tail length, weight and gender were recorded. The body mass index (BMI) was calculated as BMI = W/L,^{2 (link)} where W is the weight in kilograms, and L is the body length in meters (Suppl. Table 2). For the purposes of microbial analysis and histology, we chose the cecum, as it is the location in the gastrointestinal tract that harbors the most bacteria in mice, and because we had prior knowledge that B4galnt2 genotype can influence both microbiota and susceptibility to Enterobacteriaceae such as Salmonella Typhimurium^{22 (link)} or Citrobacter rodentium^{50 (link)} at this location. Further, little to no ileal inflammation is observed for either of the two above mentioned pathogens. The cecum was accordingly sampled in four pieces transversally (Suppl. Figure 8) and used for microbial analysis and histology. The tip of the cecum, thereafter referred as Cecum4 was stored in AllProtect (Qiagen) at +4°C; Cecum3 was stored in 10% formalin at +4°C; Cecum2 was stored in pre-reduced brain-heart infusion (BHI) with 20% glycerol at −80°C; Cecum1 was store in RNAlater at +4°C for 24 h, before removing the stabilizing solution and long-term storage at −20°C. A piece of the right ear was stored at −20°C and used for genotyping.