Processing Matters in Nutrient-Matched Laboratory Diets for Mice—Microbiome

SIMPLE SUMMARY: Feed for laboratory mice is available in different physical forms. However, there is insufficient standardization in nutrient composition and physical forms. Results pertaining to energy and nutrient digestibility show that differentially processed feed (pelleted vs. extruded) and even batches from the same provider (pelleted vs. pelleted) differ in starch gelatinization. Here we show that feed processing impacts the mice’s gastrointestinal microbiome. Reproducibility and comparability between experiments with differently processed feeds in laboratory mice should not be taken for granted. Therefore, details on dietary ingredients and feed processing should be specified in studies that include animal experiments. ABSTRACT: The composition of the microbiome is subject to the host’s diet. In commercial laboratory mouse diets, different physical forms of the same diets are available, containing—according to their labels—identical ingredients and nutrient compositions. However, variations in nutrient composition and starch gelatinization due to production processes and their impact on digestibility have been described. In this study, a total of 48 C57BL/J6 mice were assigned to two equal groups and were fed diets (produced with different processes—extruded vs. pelleted) for eight weeks in two biological replicates. At the end of the experiment, samples were collected from five different gastrointestinal regions, including the stomach, small intestine, cecum, large intestine, and an extracorporeal region (feces), and the microbiome was analyzed with 16S rRNA gene amplicon sequencing. The replicates in both experiments differed significantly in their relative abundances of Muribaculaceae species. Furthermore, the gastrointestinal content of pellet-fed mice contained larger numbers of Lactobacillus species. These results indicate that starch gelatinization and ingredient composition significantly influence microbial makeup. In conclusion, different feed processing methods may affect fundamental digestive and metabolic processes, impacting animal experiments and biasing microbiome data.