The importance of the gut microbiota for regulation of whole body metabolism, energy homeostasis, development of the immune system and even complex behavioural traits is well documented. The acquisition of comprehensive gene catalogues of the human gut metagenome using “next generation sequencing” has immensely advanced our insight into the complex metagenome-host genome interaction and the connection between common human diseases and the gut microbiota. Causal links are difficult to establish in humans, and therefore, mice still serve as important models for functional studies. We used HiSeq2000-based whole metagenome sequencing to establish a catalogue of 2.6 million non-redundant microbial genes from faecal samples of 184 mice representing different strains, fed different diets, obtained from different providers, and kept in different housing laboratories to secure high diversity and representation. Similar to the human gut microbiome, more than 99% of the genes in the catalogue were bacterial, suggesting that the mouse microbiota overall comprises between 800 and 900 bacterial species. A core mouse gut microbiome was defined at the genus level comprising 60 genera, 25 of which were shared with the core genera in the human gut microbiome. Although the mouse gut microbiome was functionally similar to its human counterpart, sharing 79.9% of its KEGG orthologous groups, only 4.0% of the mouse gut microbial genes were shared with those identified in human gut microbiome, emphasising the need for a specific mouse catalogue. We observed marked differences regarding provider, housing laboratory, strains, gender and feed, emphasizing the need for carefully controlled experimental conditions and caution comparing data from different laboratories. As we have accounted for these factors in creating the catalogue, it provides a useful reference for future studies, including studies using short reads for comprehensive analyses of the mouse gut microbiome.