The gastrointestinal tracts of mammals, including mice, are colonised with a diverse microecosystem. The caeca of normal conventional mice have been estimated to contain from 100 to 1000 individual species, and the number of bacteria can reach levels of up to 10¹¹ bacteria/g of faeces.^1,2 These microorganisms provide essential nutrients for their host and also colonise mucosal niches, which may partly influence the host response against microbial pathogens.^2–7 By far, the greatest concentration and different types of bacteria comprising the gastrointestinal microflora of mice and humans reside in the caecum and colon.^8,9,10 The fusiform-shaped bacteria, spirochetes and spiral-shaped bacteria were shown by histology to be almost exclusively located in the mucinous secretion overlaying the epithelium of the large bowel, and apparently in intimate association with the epithelial barrier.¹⁰ In the 1960s, Schaedler et al¹¹ colonised germ-free mice with selected bacteria isolated from “normal” mice. He then supplied animal breeders with this series of microorganisms^12,13 for use in colonising their mouse colonies. The one known as the Schaedler flora (SF) was the most popular. It contained eight anaerobic bacteria. In 1978, National Cancer Institute revised the SF of eight anaerobic bacteria to standardise the microbiota to be used in colonising axenic (germ-free) rodents. The newly defined microbiota, now known as altered Schaedler flora (ASF), consisted of two lactobacilli, a Bacteroides sp, a spiral-shaped bacterium and four fusiform-shaped, extremely oxygen-sensitive bacteria.¹⁴

In the past, monitoring of the gnotobiotic animals relied on examining the morphology of the microorganisms with a limited evaluation of the organisms, biochemical traits and growth characteristics. Most published mouse studies evaluating the pathogenesis of inflammatory bowel disease (IBD) therefore simply refer to gut flora as …