It is well known that the microbiota of high fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity.
Using HiSeq-based whole genome sequencing we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin.
Here we present the sequence assemblies and annotations for those 54 samples, together with the gene catalogue and relevative abundance levels of both genes and OTUs. It is hoped these data can be used for comparison in future studies of a similar design.

To increase the value of mice models studies, we have used HiSeq2000-based whole genome sequencing to establish a catalogue of 2.6 million non-redundant microbial genes derived from 1,130 gigabases of microbial sequences from faecal samples of 184 mice of different strains and from different providers and housing laboratories. More than 99% of the genes are bacterial indicating that the mouse gut microbiota comprises at least 800-900 prevalent bacterial species.This reference gene catalog was annotated to Non-redundant protein sequences (NR) and Kyoto Encyclopedia of Genes and Genomes (KEGG) and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) databases.